http://compbio.biosci.uq.edu.au/mediawiki/api.php?action=feedcontributions&user=NatashaFerber&feedformat=atomMDWiki - User contributions [en]2024-03-28T12:40:02ZUser contributionsMediaWiki 1.39.6http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=106243bsqA Results2008-06-10T01:06:04Z<p>NatashaFerber: /* Multiple sequence alignment */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' Arylsulfatase K as a heterodimer; 3b5q chain A and B]]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4''' ASK interactions with other proteins. Gene neighbourhood evidence indicated by green lines, cooccurance evidence by dark blue lines and homology by light blue.'']]<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. Results are shown below.<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
'Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
STS was chosen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
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<br />
[[Image:alignmentN.png|centre|'''Figure: 5''' Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2]]<br />
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<br />
[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.]]<br />
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[[Image:STSsite2.png|centre|framed|'''Figure 6:''' Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
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<br />
<br />
[[Image:ASKsite4.png|centre|framed|'''figure 7:''' Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity]] <br />
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[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage. This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate-entry path]]<br />
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[[Image:STSwhole.png|center|framed|'''Figure 9:''' Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
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[[Image:ASAgreen.png|centre|framed|'''Figure 10:''' Catalytic site of ASA. Substrate entry path is wider and shorter compaired to that of STS and much similar to the catalytic site of ASK.]]<br />
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<br />
<br />
== Possible function and likely substrates of ASK ==<br />
<br />
ASA is a water soluble enzyme found in lysosomes, where the catalytic site is closer to the surface and substrate-entry path is narrower and wider in contrast to that of STS. Structural comparison shows ASK catalsytic site architecture is much similar to that of ASA, eventhough subcellular localization is very different. ASA binds to membrane lipid sulphatides and show a number of hydrophibic patches near the catalytic site. However an exact substrate binding site is not defined. ASK structure also show number of hydrophobic residues on the surface (Figure 11) indication the hydrophobic nature of the substrate it binds. <br />
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[[Image:ASKhydro.png.jpg|centre|framed|'''figure 11:''' Surfece of ASK show number of hydrophobic residues, which might me involved in the substrate binding]] <br />
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<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 12'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
==Phylogeny Tree==<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. Significant conservation among all the different species are seen suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 13'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=106073bsqA References2008-06-10T01:02:22Z<p>NatashaFerber: </p>
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<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
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*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
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*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
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*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
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*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
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*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990) Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
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*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
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*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=106043bsqA Methods & Materials2008-06-10T01:01:46Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignments' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
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<br />
'''BLAST''' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using '''ClustalX''', which was used to align the gaps among all the species sequences. '''TreeView''' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in '''MEGA4''', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Introduction&diff=105973bsqA Introduction2008-06-10T00:59:35Z<p>NatashaFerber: </p>
<hr />
<div>Sulfatases are enzymes that hydrolyze sulfate ester bonds. Seventeen unique genes encoding sulfatases have been identified in humans. These are categorized as EC '''3.1.6.''' in enzyme classifications. They all participate in metabolic processes [1]. Most of the family members contain a highly conserved cystine (C) residue and a bivalent metal binding site [4]. The majority of sulfatases are located in lysosymes with acidic pH optima (typically between 5 and 5.5). Most of the sulfatases, including Arylsulfatase A (ASA), Arylsulfatase B (ASB) and N-acetylgalactosamine-6-sulfatase (G6S), are water soluble [1].<br />
<br />
An examination of sulfatases with defined functions is helpful in appreciation of the diversity of this enzyme family. ASA is a lysosomal enzyme which hydrolyzes cerebroside sulphate. ASB is also a lysosomal enzyme which hydrolyzes the sulphate ester group from N-acetylgalactosamine 4-sulphate group of dermatine sulphate. Arylsulfatase C (ASC) is a microsomal membrane-bound enzyme that hydrolyses 3β-hydroxysteroid sulfates and is hence also known as steroid sulfatase (STS) [ProFinc]. Substrates hydrolysed by sulfatases include cerebroside sulfate, dermatan sulfate, heparin and keratan sulfate, and steroid sulfates [3]. Previous investigations have revealed that arylsulfatases D, E, F, G, H, J and K are localized in ER and golgi compartments of the cell [2,3].<br />
<br />
The sulfatase studied in this experiment is arylsulfatase K (ASK) from ''Bacteroides thetaiotaomicron''. A crystal structure has been obtained for this enzyme, but the function and substrates are unknown. Sequence conservation, structural similarity, other proteins that ASK is known to interact with, and the level of conservation of some key residues that may be involved in its catalytic activity, were all examined in this experiment to determine the possible function of ASK.<br />
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[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Results Results]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5qA_Conclusion&diff=105283b5qA Conclusion2008-06-10T00:30:57Z<p>NatashaFerber: </p>
<hr />
<div>Among the different species, high sequence conservation has been seen and suggests an evolutionary conserved gene family sharing a common ancestor. Serine has been identified in bacteria instead of cysteine with modifying factor AstB. Although cysteine has identified first through evolution with modifying factor SUMF1, it has later been established that serine evolved with AstB, which has been transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=105213bsqA Results2008-06-10T00:27:46Z<p>NatashaFerber: /* Phylogeny Tree */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' Arylsulfatase K as a heterodimer; 3b5q chain A and B]]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4''' ASK interactions with other proteins. Gene neighbourhood evidence indicated by green lines, cooccurance evidence by dark blue lines and homology by light blue.'']]<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. Results are shown below.<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
'Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
STS was chosen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
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[[Image:alignmentN.png|centre|'''Figure: 5''' Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2]]<br />
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[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.]]<br />
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[[Image:STSsite2.png|centre|framed|'''Figure 6:''' Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
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[[Image:ASKsite4.png|centre|framed|'''figure 7:''' Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity]] <br />
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[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage. This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate-entry path]]<br />
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[[Image:STSwhole.png|center|framed|'''Figure 9:''' Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
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== Multiple sequence alignment ==<br />
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* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 10'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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==Phylogeny Tree==<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. Significant conservation among all the different species are seen suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 11'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=105143bsqA Discussion2008-06-10T00:25:18Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
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<div>=== Structure and possible function of arylsulfatase K ===<br />
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Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3]. N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function [3]. However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [3,4]. <br />
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Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi, which is neutrl. [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine out of ten key catalytic residues in STS are conserved with ASA and ASB [3]. These residues of STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290 (''Figure 6'') [3]. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG) [2,3].<br />
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MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in purple on 'figure: 7' under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
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As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
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Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a 0.2Å difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4Å crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae'',which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process. See 'evolution of sulfatases' for details. <br />
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The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. Conservation within C-terminus doesn't seem to corelate with types of substrate these enzymes bind with.<br />
The crystal structures of STS (figure 9) showes the catalytic site buried deep within the molecule facing the membrane bound region, while that of ASA shows the active site more exposed to the exterior (figure 10). Therefore type of substrate which binds to ASK may be different in charge, size and conformation to that of STS. <br />
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=== Evolution of sulfatases===<br />
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The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
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Previous phylogeny studies have found decades ago the sulfatase family underwent a posttranslational modification which is vital for their enzymatic activity. Modifications involved highly conserved cysteine located in the active site of sulfatase, which is modified into formylglycine (FG). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
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In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FG, however another modifying factor named AtsB is used rather than SUMF1, which are found not be related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which in turn transferred to other bacteria through horizontal transfer.<br />
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Multiple sequence alignment has shown species containing ASB, ASA, ASC and glucosamine-6-sulfatase show similarity extending over entire sequences, especially observed in the N- terminal, which composes one third of the protein. More specifically, conserved amino acid regions containing arginine and histidine residues. Peters (1990) determined histidine and arginine are essential for the catalytic activity in ASA suggesting that the conserved amino acid regions are involved in the assembly of the active sites of all four arylsulfatases.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Structure_and_Function&diff=104663b5q Structure and Function2008-06-09T23:56:02Z<p>NatashaFerber: /* Finding the functional site and mechamism of action */</p>
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<div>== Arylsulfatase K structure==<br />
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[[Image:ASK.png|centre|framed|'''Figure 1:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
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'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
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[[Image:reactionASK.png]]<br />
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Sulfatases are enzymes,which hydrolyse sulfate ester bonds of substrates. These are categorised as '''EC 3.1.6.''' in enzyme classifications. Most of the family members has shown to contain a highly conserved cystine residue and a bivalent metal binding site.<br />
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Arylsulphatase A (ASA) is a lysosomal enzyme which hydrolyzes cerebroside sulphate. Arylsulphatase B (ASB),also a lysosomal enzyme, which hydrolyzes the sulphate ester group from N-acetylgalactosamine 4-sulphate group of dermatan sulphate.<br />
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==Sequence conservation==<br />
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MSA data revealed several highly conserved residues in the N-terminal region of all sequences aligned. These residues are shown below as an alignment of Arylsulfatase K with the sequence of human stroid sulfatase.<br />
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[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
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'''Figure 2:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
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[[Image:alignmentN.png]]<br />
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== Structural alignment ==<br />
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*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
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No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
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'''''Figure 3:''' Structurally related proteins. (No 1 and 2 are two chains of arylsulfatase K)''.<br />
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*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
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:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
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== Arylsulfatase K (BT1596) Interactions with other proteins ==<br />
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[[Image:net.png|centre|framed|'''Figure 4:''' ''IProtein-protein interactions of ASK'']]<br />
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'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
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'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
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All these enzymes has generaly the same function, but acts on different substrate.<br />
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==Finding the functional site and mechanism of action==<br />
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Published data on catalytic activity of STS and ASA was found in literature search.<br />
Both STS and ASA shows a divalent metal binding site in the catalytic site, but th crystal structure of ASK doesn't show this. However, three out of four residues which provide oxygen ligans to hold the cation are conserved in ASK. They are shown highlighted in purple in STS-ASK alignment. <br />
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[[Image:alignmentN.png]]<br />
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The Aspartic acid (D) in 35th position of STS is immidiatly followed by a second aspartic acid. This is substituted by a histidine in ASK. But when the side chain of two residues are examined, it is a possibility for one Nitrogen in five-member-ring to donate a lone pair to form a coordinate bond with a divalent cation. Therefore ASK active site may hold a divalent cation. <br />
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Three out of five catalytic resideus were also conserved between ASK and STS (shown highlighted in red). The characteristic cystine residue of sulfatases is conserved in STS, but replaced by serine in ASK. Biologycally acive STS has cystine post translationally modified in to a Formylglycine (FG). The crystal structure doesn't show a FG in ASK structure, however this may be a result of inadequite resolution. The crystal structure has obtained at 2.4 A resolution while bond lenghts of C=O and C-O are 1.2 A and 1.4 A respectively. Further evidence from literature suggests that a subset of ASK found in bacteria including ''Bacteroides thetaiotamicron'' and ''Klebsiella pneumoneae'' use a S, post translationally modified to a FG, for the same cataltic action[[http://www.jbc.org/cgi/reprint/273/9/4835]].Finally H290 of STS in not conserven in either ASK or ASA, but the 3D structure shows a different H in the colse proximity and this H in ASA is conserved in most ASA from different species.<br />
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[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' ''Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.'']]<br />
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[[Image:STSsite2.png|centre|framed|'''Figure 6:''' ''Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
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[[Image:ASKsite4.png|centre|framed|'''figure 7:''' ''Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity'']] <br />
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[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage. This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path]]<br />
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[[Image:STSwhole.png|center|framed|'''Figure 9:''' Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
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[[Image:ASAgreen.png|centre|framed|'''Figure 10:''' Catalytic site of ASA. Substrate entry path is wider and shorter compaired to that of STS and much similar to the catalytic site of ASK.]]<br />
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== Conservation of the C-terminus ==<br />
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C-terminus of sulfatases are recognised to contain a substrate binding site, hence weakly conserved throughout the family due to the variation of types of substrates used. However, when the C-terminal regions in two sequence alignment of ASK and STN was looked at, the level of conservation was very high. Based on this evidence it is predicted, that STS and ASK shair substrates.<br />
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[[Image:alignmentC.png]]<br />
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== Possible function and likely substrates of ASK ==<br />
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STS is a membrane bound enzyme, mostly found in human placenta and skin fibroblasts. It converts sex-stroid precursors to ative estrogen and androgen, thereofre give a local suppley of these hormones (Ghosh, D., 2007). ASK is a water soluble enzyme localysed in ER. No tissue localization is specified to the data. Based on all the above evidence, the possible function of ASK may be binding and activating stroids in the ER lumen.<br />
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Click here to go [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Arylsulfatase_K ''Back'']</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=104563bsqA Discussion2008-06-09T23:47:59Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
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<div>=== Structure and possible function of arylsulfatase K ===<br />
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Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3]. N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function [3]. However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [3,4]. <br />
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Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi, which is neutrl. [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine out of ten key catalytic residues in STS are conserved with ASA and ASB [3]. These residues of STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290 (''Figure 6'') [3]. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG) [2,3].<br />
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MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in purple on 'figure: 7' under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
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As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
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Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a 0.2Å difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4Å crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae'',which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process. See 'evolution of sulfatases' for details. <br />
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The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. Conservation within C-terminus doesn't seem to corelate with types of substrate these enzymes bind with.<br />
The crystal structures of STS (figure 9) showes the catalytic site buried deep within the molecule facing the membrane bound region, while that of ASA shows the active site more exposed to the exterior (figure 10). Therefore type of substrate which binds to ASK may be different in charge, size and conformation to that of STS. <br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found decades ago the sulfatase family underwent a posttranslational modification which is vital for their enzymatic activity. Modifications involved highly conserved cysteine located in the active site of sulfatase, which is modified into formylglycine (FG). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FG, however another modifying factor named AtsB is used rather than SUMF1, which are found not be related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which in turn transferred to other bacteria through horizontal transfer.<br />
<br />
<br />
Multiple sequence alignment has shown species containing ASB, ASA, ASC and glucosamine-6-sulfatase show similarity extending over entire sequences, especially observed in the N- terminal, which composes one third of the protein. More specifically, conserved amino acid regions containing arginine and histidine residues. Peters (1990) determined histidine and arginine are essential for the catalytic activity in ASA suggesting that the conserved amino acids regions are involved in the assembly of the active sites of all four arylsulfatases.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=104353bsqA Discussion2008-06-09T23:42:20Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
<hr />
<div>=== Structure and possible function of arylsulfatase K ===<br />
<br />
<br />
Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3]. N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function [3]. However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [3,4]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi, which is neutrl. [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine out of ten key catalytic residues in STS are conserved with ASA and ASB [3]. These residues of STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290 (''Figure 6'') [3]. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG) [2,3].<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in purple on 'figure: 7' under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a 0.2Å difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4Å crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae'',which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process. See 'evolution of sulfatases' for details. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. Conservation within C-terminus doesn't seem to corelate with types of substrate these enzymes bind with.<br />
The crystal structures of STS (figure 9) showes the catalytic site buried deep within the molecule facing the membrane bound region, while that of ASA shows the active site more exposed to the exterior (figure 10). Therefore type of substrate which binds to ASK may be different in charge, size and conformation to that of STS. <br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found decades ago the sulfatase family underwent a posttranslational modification which is vital for their enzymatic activity. Modifications involved highly conserved cysteine located in the active site of sulfatase, which is modified into formylglycine (FG). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FG, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.<br />
<br />
<br />
Multiple sequence alignment has shown species containing ASB, ASA, ASC and glucosamine-6-sulfatase show similarity extending over entire sequences, especially observed in the N- terminal, which composes one third of the protein. More specifically, conserved amino acid regions containing arginine and histidine residues. Peters (1990) determined histidine and arginine are essential for the catalytic activity in ASA suggesting that the conserved amino acids regions are involved in the assembly of the active sites of all four arylsulfatases.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Report&diff=104243b5q Report2008-06-09T23:38:25Z<p>NatashaFerber: </p>
<hr />
<div>== Structure, Function and Evolution of the Protein Arylsulfatase K; 3b5qA ==<br />
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Darshani Rupasinghe and Natasha Ferber<br />
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[[3bsqA Title]]<br />
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[[3bsqA Abstract]]<br />
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[[3bsqA Introduction]]<br />
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[[3bsqA Results]]<br />
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[[3bsqA Discussion]]<br />
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[[3b5qA Conclusion]]<br />
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[[3bsqA Methods & Materials]]<br />
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[[3bsqA References]]<br />
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return to [[3bsqA]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Evolution&diff=104033b5q Evolution2008-06-09T23:28:02Z<p>NatashaFerber: /* Evolutionary Tree */</p>
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<div>== Sequence Homology==<br />
Multiple sequence alignment (MSA)<br />
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[[BLASTP results| Proteins, Organism names & Sequences]]<br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 1.1'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx2.jpg|800px|thumb|'''Figure 1.2'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx3a.jpg|800px|thumb|'''Figure 1.3'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx4a.jpg|800px|thumb|'''Figure 1.4'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx5a.jpg|800px|thumb|'''Figure 1.5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx6a.jpg|800px|thumb|'''Figure 1.6'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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== Evolutionary Tree==<br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K using Treeview, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[Image:bootstrap tree_final.jpg|right|thumb|800px|'''Figure 3'''<Br>Phylogeny rooted tree showing bootstrap values using MEGA4]]<Br><br />
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[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract Sequence homology of arylsulfatases]<br />
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Click here to go [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Arylsulfatase_K ''Back'']</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=103983bsqA Discussion2008-06-09T23:25:15Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
<hr />
<div>=== Structure and possible function of arylsulfatase K ===<br />
<br />
<br />
Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3]. N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function [3]. However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [3,4]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi, which is neutrl. [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine out of ten key catalytic residues in STS are conserved with ASA and ASB [3]. These residues of STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290 (''Figure 6'') [3]. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG) [2,3].<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in purple on 'figure: 7' under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a 0.2Å difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4Å crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae'',which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process. See 'evolution of sulfatases' for details. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. Conservation within C-terminus doesn't seem to corelate with types of substrate these enzymes bind with.<br />
The crystal structures of STS (figure 9) showes the catalytic site buried deep within the molecule facing the membrane bound region, while that of ASA shows the active site more exposed to the exterior (figure 10). Therefore type of substrate which binds to ASK may be different in charge, size and conformation to that of STS. <br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found decades ago the sulfatase family underwent a posttranslational modification which is vital for their enzymatic activity. Modifications involved highly conserved cysteine located in the active site of sulfatase, which is modified into formylglycine (FG). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FG, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.<br />
<br />
<br />
Multiple sequence alignment has shown species containing ASB, ASA, ASC and glucosamine-6-sulfatase show similiarity extending over entire sequences, especially observed in the N- terminal, which composes one third of the protein. More specifically, conserved amino acid regions containing arginine and histidine residues. Peters (1990) determined histidine and arginine are essential for the catalytic activity in ASA suggesting that the conserved amino acids regions are involved in the assembly of the active sites of all four arylsulfatases.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Conclusion&diff=101303bsqA Conclusion2008-06-09T13:56:06Z<p>NatashaFerber: </p>
<hr />
<div>STS is a membrane bound enzyme, mostly found in human placenta and skin fibroblasts. Itconverts sex-stroid precursors to ative estrogen and androgen, thereofre give a local suppley of these hormones (Ghosh, D., 2007). ASK is a water soluble enzyme localysed in ER of the cell. No tissue localization is specified to the data. However, based on all the above evidence, the possible function ASK may be binding and activation of post translationally modified steroids in the ER lumen.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Conclusion&diff=101283bsqA Conclusion2008-06-09T13:55:34Z<p>NatashaFerber: </p>
<hr />
<div>STS is a membrane bound enzyme, mostly found in human placenta and skin fibroblasts. Itconverts sex-stroid precursors to ative estrogen and androgen, thereofre give a local suppley of these hormones (Ghosh, D., 2007). ASK is a water soluble enzyme localysed in ER of the cell. No tissue localization is specified to the data. However, based on all the above evidence, the possible function ASK may be binding and activation of post translationally modified stroids in the ER lumen.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101273bsqA Discussion2008-06-09T13:51:09Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine out of ten key catalytic residues in STS are conserved with ASA and ASB [3]. These residues of STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290 (''Figure 6'')[3]. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG) [2,3].<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of '''(to be completed)'''<br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found decades ago the sulfatase family underwent a posttranslational modification which is vital for their enzymatic activity. Modifications involved highly conserved cysteine located in the active site of sulfatase, which is modified into formylglycine (FGly). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FGly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.<br />
<br />
<br />
Multiple sequence alignment has shown species containing ASB, ASA, ASC and glucosamine-6-sulfatase show similiarity extending over entire sequences, especially observed in the N- terminal, which composes one third of the protein. More specifically, conserved amino acid regions containing arginine and histidine residues. Peters (1990) determined histidine and arginine are essential for the catalytic activity in ASA suggesting that the conserved amino acids regions are involved in the assembly of the active sites of all four arylsulfatases.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101193bsqA Discussion2008-06-09T13:37:16Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of '''(to be completed)'''<br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found sulfatases go through posttranslational modification of the cysteine residue within the active site of the enzyme to formylglycine (FGly). The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into FGly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101153bsqA Discussion2008-06-09T13:35:34Z<p>NatashaFerber: /* Evolution of sulfatases */</p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of '''(to be completed)'''<br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found sulfatases go through posttranslational modification of the cysteine residue within the active site of the enzyme to Fgly. The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into Fgly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101133bsqA Discussion2008-06-09T13:35:09Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of '''(to be completed)'''<br />
<br />
<br />
=== Evolution of sulfatases===<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
Previous phylogeny studies have found sulfatases go through posttranslational modification of the cysteine residue within the active site of the enzyme to Fgly. The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into Fgly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101073bsqA Discussion2008-06-09T13:33:49Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of '''(to be completed)'''<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
Previous phylogeny studies have found sulfatases go through posttranslational modification of the cysteine residue within the active site of the enzyme to Fgly. The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into Fgly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=101063bsqA Discussion2008-06-09T13:33:06Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of<br />
<br />
The phylogeny tree shows evidence that sulfatases are found in species of Bacteria and Eukaryotes. Few of the lower Eukaryotes, Archaea and most plant species lack sulfatases. The significant sequence conservation among different species suggests that sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. Bacteria and lower eukaryotes have fewer sulfatase genes compared with the higher eukaryotes such as humans, suggesting that a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
Previous phylogeny studies have found sulfatases go through posttranslational modification of the cysteine residue within the active site of the enzyme to Fgly. The modification factor of cysteine is SUMF1. This gene is highly conserved across species including prokaryotes to eukaryotes ranging from bacteria, fruit flies to mammals. It has been determined that species containing SUMF1 will also contain sulfatases in their genome, this suggests that the sulfatases are targets for this posttranslational modification. SUMF1 and SUMF2 have been identified, however only in vertebrates. Analysis of the evolution of these two factors suggests that SUMF2 evolved independently of SUMF1. <br />
<br />
In addition, it has been found that some bacteria have been identified with serine in place of cysteine and this has been true for ASK. As well as cysteine, serine also undergoes modification into Fgly, however another modifying factor named AtsB is used rather than SUMF1, which are found not br related. Studies show most bacteria containing SUMF1 genes will side with cysteine-type sulfatase, whereas the AtsB gene will side with both cysteine and serine-type sulfatases, suggesting that AstB modifies both types of sulfatases. Evolutionary analysis proposes the first type of sulfatase was in fact cysteine, which also coevolved with SUMF1 modifier. Later serine evolved with the AstB modifier, which inturn transferred to other bacteria through horizontal transfer.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Evolution&diff=100973b5q Evolution2008-06-09T13:17:32Z<p>NatashaFerber: /* Evolutionary Tree */</p>
<hr />
<div>== Sequence Homology==<br />
Multiple sequence alignment (MSA)<br />
<br />
[[BLASTP results| Proteins, Organism names & Sequences]]<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 1.1'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
[[Image:clustalx2.jpg|800px|thumb|'''Figure 1.2'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
[[Image:clustalx3a.jpg|800px|thumb|'''Figure 1.3'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
[[Image:clustalx4a.jpg|800px|thumb|'''Figure 1.4'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx5a.jpg|800px|thumb|'''Figure 1.5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx6a.jpg|800px|thumb|'''Figure 1.6'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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== Evolutionary Tree==<br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K using Treeview, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[Image:bootstrap tree_final.jpg|right|thumb|800px|'''Figure 3'''<Br>Phylogeny rooted tree showing bootstrap values from MEGA4]]<Br><br />
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[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract Sequence homology of arylsulfatases]<br />
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Click here to go [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Arylsulfatase_K ''Back'']</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Evolution&diff=100963b5q Evolution2008-06-09T13:17:15Z<p>NatashaFerber: /* Evolutionary Tree */</p>
<hr />
<div>== Sequence Homology==<br />
Multiple sequence alignment (MSA)<br />
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[[BLASTP results| Proteins, Organism names & Sequences]]<br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 1.1'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx2.jpg|800px|thumb|'''Figure 1.2'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx3a.jpg|800px|thumb|'''Figure 1.3'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx4a.jpg|800px|thumb|'''Figure 1.4'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx5a.jpg|800px|thumb|'''Figure 1.5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx6a.jpg|800px|thumb|'''Figure 1.6'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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== Evolutionary Tree==<br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K using Treeview, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[Image:bootstrap tree_final.jpg|right|thumb|800px|'''Figure 3'''<Br>Phylogeny rooted tree showing bootstrap values from MEG4]]<Br><br />
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[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract Sequence homology of arylsulfatases]<br />
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Click here to go [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Arylsulfatase_K ''Back'']</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=100883bsqA Discussion2008-06-09T13:10:46Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alighment (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
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Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
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MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Discussion&diff=100873bsqA Discussion2008-06-09T13:10:26Z<p>NatashaFerber: </p>
<hr />
<div>'''Multiple sequence alighment''' (MSA) revealed several conserved residues throughout the whole sulfatase family, predominantly in the N-terminal region of the sequence. As mentioned in the introduction, ASA and ASB are lysosomal enzymes while ASC is a microsomal enzyme. Arylsulfatases D, E, F, G, H, J and K are localized in the ER and golgi compartments [3].<br />
N-Acetylgalascosamine-4-sulfatase, ASA and STS were shown to be most similar in structure to ASK in 'DALI' results and may be appropriate models for the mechanism of action of ASK. Only STS is fully functionally characterized. STS possesses a set of nine residues which are essential for function ([[http://www.ncbi.nlm.nih.gov/pubmed/17558559?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]] [1]). However, STS is a membrane bound protein which consists of a globular domain bearing the catalytic site and a transmembrane domain made up of two antiparallel hydrophobic alpha helices. The three dimensional structure of ASK is not indicative of a transmembrane domain, so it is probably a water soluble enzyme found in ER [1]. <br />
<br />
Evidence from previous experiments state that ASA binds membrane lipid sulfatids and is localised in lysosomes [2]. The pH within lysosomes (5 - 5.5) is much lower than that found within the ER and golgi (neutral, find out) [3]. The water-soluble domain of STS is therefore likely to be a better model for the catalytic site of ASK. Nine key catalytic residues in STS are D35, D36, D342, G343, C75, R79, K134, K368, H136 and H290. The first four residues provide oxygen ligands for the divalent cation binding while others participate in hydrolysis of the substrate. It should be noted that cysteine is post translationally modified to a formylglycine (FG).<br />
<br />
MSA revealed that these STS catalytic residues are conserved generally all through the enzyme family and especially in ASA. These residues were marked on the crystal structure of ASK using PyMol and they compose a very similar catalytic site to that of STS. Five out of nine STS key residues were found to be very similar to ASK, both in sequence alignment and in positioning within the active site. However D36 and C75 of STS seemed to have been replaced with histidine and serine respectively, while the role of STS-K368 appears to be replaced with K296 in ASK. When these residues were marked in the crystal structure, a histidine was found in the same position of catalytic site as in STS, but occurred at position 284 of ASK sequence. It is marked in ‘cyan’ on Figure 2 under 'results'. The STS-K368-like residue in ASK (K296) seemed to have been conserved throughout the MSA. <br />
<br />
As mentioned earlier, there are four residues which provide electronegative oxygen ligands to hold the divalent cation (for example, calcium or magnesium) in the catalytic site. Three of these residues (D24, D283 and G284) are conserved in ASK, but D36 in STS is replaced by a histidine. This is likely to be a conservative change as the histidine contains two nitrogen atoms whose lone pairs could form a coordinate bond with the divalent cation as can the oxygen atoms of aspartic acid.<br />
<br />
Finally, the C75 of STS has been replaced by a serine in the bacterial ASK. This serine could easily be converted to a formylglycine. <br />
The difference between the serine and formylglycine funtional groups, a O.2A difference in bond length and the absence of two hydrogen atoms in formylglycine, cannot be differentiated at 2.4A crystal structure resolution. An experiment performed on ''Klebsiella pneumoneae’’,which expresses a very similar ASK to that of ''Bacteroides thetaiotaomicrone'', revealed that the analogous serine residue is oxidised to formylglycine. A certain group of bacteria including two of above mentioned strains use a different post translational modification system in this process[[http://www.jbc.org/cgi/reprint/273/9/4835]]. <br />
<br />
The C-terminus of sulfatases contains a substrate binding site and is hence weakly conserved throughout the family due to the variation of types of substrates used. When the C-terminal regions of STS/ASK and ASA/ASK were aligned, both alignments showed 27.9% and 27.3% homology respectively. C-terminal regions of</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100843bsqA Methods & Materials2008-06-09T13:07:22Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignments' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
<br />
'''BLAST''' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using '''ClustalX''', which was used to align the gaps among all the species sequences. '''TreeView''' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in '''MEGA4''', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100823bsqA Methods & Materials2008-06-09T13:06:52Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
<br />
'''BLAST''' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using '''ClustalX''', which was used to align the gaps among all the species sequences. '''TreeView''' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in '''MEGA4''', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100813bsqA Methods & Materials2008-06-09T13:05:50Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
<br />
''''BLAST'''' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using 'ClustalX', which was used to align the gaps among all the species sequences. 'TreeView' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in 'MEGA4', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100803bsqA Methods & Materials2008-06-09T13:05:28Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
<br />
'BLAST' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using 'ClustalX', which was used to align the gaps among all the species sequences. 'TreeView' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in 'MEGA4', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100793bsqA Methods & Materials2008-06-09T13:04:38Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
<br />
'BLAST' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using 'ClustalX', which was used to align the gaps among all the species sequences. 'TreeView' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in 'MEGA4', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100773bsqA Methods & Materials2008-06-09T13:04:28Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
'BLAST' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using 'ClustalX', which was used to align the gaps among all the species sequences. 'TreeView' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in 'MEGA4', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Methods_%26_Materials&diff=100753bsqA Methods & Materials2008-06-09T13:04:15Z<p>NatashaFerber: </p>
<hr />
<div>Multiple sequence alugnment was made using '''clustalX''' from the DVD.<br />
The crystal structure of all proteins involved (ASA, ASK and STS) were viewed using the protein data bank text file, downloaded to the '''PyMol''' (Downloaded version in 'colaborative learning center' (CLC)).<br />
The structural alignment was done using the [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 DALI server] with PDB identifiers.<br />
Protein interaction of ASK were searched with the programme [http://string.embl.de/ 'STRING']which is available online.<br />
The protein name or PDB identifier was not detected by 'STRING', therefore the aminoacid sequence was used.<br />
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
'Two sequence alignment' of ASK and STS was done with the programme [http://www.expasy.ch/tools/sim-prot.html SIM]. The method used was 'BLOSUM62'. A 'gap penalty' of 5 and 'gap extension penalty' of 2 were used to optimise the alignment according to what was observed in 'clustalX'.The pylogenic tree was made using the 'clusalX' alignment and viewed with '''Treeview''' from the DVD.<br />
<br />
'BLAST' search performed using the crystal structure of a putative sulfatase found from to Bacteroides Thetaiotaomicron (gi|160286517) to determine all the related species. Multiple sequence alignment was found using 'ClustalX', which was used to align the gaps among all the species sequences. 'TreeView' constructed a phylogeny tree using taxonomy to name and group all the species and illustrate the divergence and nature of the common ancestors. Phylogenetic analyses were conducted in 'MEGA4', including determining the bootstrap values. The evolutionary history was inferred using the Neighbor-Joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. All positions containing alignment gaps and missing data were eliminated only in pair-wise sequence comparisons. There were a total of 1222 positions in the final dataset.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=100713bsqA Results2008-06-09T12:59:26Z<p>NatashaFerber: </p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']]<br />
<br />
<br />
[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' ''Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.'']]<br />
<br />
<br />
[[Image:STSsite2.png|centre|framed|'''Figure 6:''' ''Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
<br />
<br />
<br />
[[Image:ASKsite4.png|centre|framed|'''figure 7:''' ''Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity'']] <br />
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<br />
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[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' ''Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage.'' This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path'']]<br />
<br />
[[Image:STSwhole.png|center|framed|'''Figure 9:''' ''Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
<br />
<br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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==Phylogeny Tree==<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=100693bsqA Results2008-06-09T12:59:07Z<p>NatashaFerber: </p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']]<br />
<br />
<br />
[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' ''Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.'']]<br />
<br />
<br />
[[Image:STSsite2.png|centre|framed|'''Figure 6:''' ''Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
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[[Image:ASKsite4.png|centre|framed|'''figure 7:''' ''Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity'']] <br />
<br />
<br />
<br />
<br />
[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' ''Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage.'' This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path'']]<br />
<br />
[[Image:STSwhole.png|center|framed|'''Figure 9:''' ''Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
<br />
<br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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<br />
==Phylogeny Tree==<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=100663bsqA Results2008-06-09T12:58:38Z<p>NatashaFerber: /* Phylogeny Tree */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']]<br />
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[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' ''Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.'']]<br />
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[[Image:STSsite2.png|centre|framed|'''Figure 6:''' ''Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
<br />
<br />
<br />
[[Image:ASKsite4.png|centre|framed|'''figure 7:''' ''Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity'']] <br />
<br />
<br />
<br />
<br />
[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' ''Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage.'' This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path'']]<br />
<br />
[[Image:STSwhole.png|center|framed|'''Figure 9:''' ''Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
<br />
<br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Phylogeny Tree==<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=100633bsqA Results2008-06-09T12:58:13Z<p>NatashaFerber: </p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5q-A and B are two chains of ASK dimer and 2qzu-A is ASK of Bacterioides fragilis. N-acetylgalactosamine-4-sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most structurally similar proteins to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
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All these enzymes has generaly the same function, but acts on different substrate.<br />
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== Two sequence alignment of ASK and STS == <br />
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STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
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[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']]<br />
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[[Image:ASAsite1.png|centre|framed|'''Figure 5:''' ''Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound.'']]<br />
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[[Image:STSsite2.png|centre|framed|'''Figure 6:''' ''Catalytic site of STS with calsium ino bound (Blue). Cation binding residues are marked in 'cyan' and catalytic residues are marked in pink]]<br />
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[[Image:ASKsite4.png|centre|framed|'''figure 7:''' ''Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in '''grey''' are possible to be involved in divalent metal binding , while residues marked in '''magenta''' are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in '''cyan''' is not strictly consetved in '''MSA''', but the only available nucleophile in the close proximity'']] <br />
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[[Image:surfacegreen.png|centre|framed|'''Figure 8:''' ''Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage.'' This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path'']]<br />
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[[Image:STSwhole.png|center|framed|'''Figure 9:''' ''Surface of STS and catalytic site. Substrate moving path is much narrover and longer compared to that of ASK]]<br />
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All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
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No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
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'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
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The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
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== Multiple sequence alignment ==<br />
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* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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===Phylogeny Tree===<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3b5q_Evolution&diff=100563b5q Evolution2008-06-09T12:53:37Z<p>NatashaFerber: </p>
<hr />
<div>== Sequence Homology==<br />
Multiple sequence alignment (MSA)<br />
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[[BLASTP results| Proteins, Organism names & Sequences]]<br />
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[[Image:clustalx1a.jpg|800px|thumb|'''Figure 1.1'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx2.jpg|800px|thumb|'''Figure 1.2'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx3a.jpg|800px|thumb|'''Figure 1.3'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx4a.jpg|800px|thumb|'''Figure 1.4'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx5a.jpg|800px|thumb|'''Figure 1.5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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[[Image:clustalx6a.jpg|800px|thumb|'''Figure 1.6'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
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== Evolutionary Tree==<br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[Image:bootstrap tree_final.jpg|right|thumb|800px|'''Figure 3'''<Br>Phylogeny rooted tree showing bootstrap values]]<Br><br />
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[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract Sequence homology of arylsulfatases]<br />
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Click here to go [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Arylsulfatase_K ''Back'']</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98183bsqA Results2008-06-09T08:39:36Z<p>NatashaFerber: /* Phylogeny Tree */</p>
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<div>==Multiple sequence alignment ==<br />
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Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
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[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
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'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
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== Arylsulfatase K structure==<br />
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[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
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'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
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[[Image:reactionASK.png]]<br />
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== Structural alignment ==<br />
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*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
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No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
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'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
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*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
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:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
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== Arylsulfatase K interactions with other proteins ==<br />
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[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
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'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
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'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
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Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
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'''ProFunc''' results for ASK interacting proteins.<br />
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*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
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:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
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*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
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All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
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[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
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All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
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No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
===Phylogeny Tree===<br />
*There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
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[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
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[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98173bsqA Results2008-06-09T08:39:16Z<p>NatashaFerber: /* Phylogeny Tree */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
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[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
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'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
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<br />
== Arylsulfatase K structure==<br />
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[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
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'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
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<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
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No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
===Phylogeny Tree===<br />
There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]], shown in the red is eukayotes and in the blue are all the bacterial species. There shows significant conservation among all the different species suggesting sulfatases are members of an evolutionary conserved gene family sharing a common ancestor. However, the bacteria and lower eukaryotes show fewer sulfatase genes compared with higher eukaryotes such as homo sapiens. This may suggest a common ancestor was more closely related to sulfatases present today in lower sulfatases. <br />
<br />
<br />
[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98123bsqA Results2008-06-09T08:32:32Z<p>NatashaFerber: /* Phylogeny Tree */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
===Phylogeny Tree===<br />
There are 2 main groups shown on the tree that has been constructed using results from [[BLASTP results]]<br />
<br />
<br />
[[Image:treeA.jpg|right|thumb|800px|'''Figure 2'''<Br>Evolutionary tree of proteins showing sequence homology with arylsulfatase K, red represents eukaryotes and blue represents bacteria]]<Br><br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98103bsqA Results2008-06-09T08:28:26Z<p>NatashaFerber: /* Multiple sequence alignment */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
===Phylogeny Tree===<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98093bsqA Results2008-06-09T08:26:48Z<p>NatashaFerber: /* Multiple sequence alignment */</p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
* The multiple sequence alignment constructed in clustalx shows similiarity extended across the entire sequences, especially observed in N-termainal. The N-terminal showed conserved regions of amino acids containing arginine and histidine residues, which have found to be involved in the assembly of active sites of most arylsulfatases. <br />
<br />
<br />
[[Image:clustalx1a.jpg|800px|thumb|'''Figure 5'''<Br> Multiple sequence alignment (MSA) of proteins showing sequence homology to arylsulfatse K obtained from ClustalX]]<Br><br />
<br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Results&diff=98063bsqA Results2008-06-09T08:17:13Z<p>NatashaFerber: </p>
<hr />
<div>==Multiple sequence alignment ==<br />
<br />
<br />
Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.<br />
<br />
[[Image:MSA1.png]]<br />
[[Image:MAS2.png]]<br />
[[Image:MAS3.png]]<br />
[[Image:MSA4.png]]<br />
[[Image:MSA5.png]]<br />
[[Image:MSA6.png]]<br />
[[Image:MSA7.png]]<br />
<br />
'''Figure 1:''' ''Multiple sequence alignment (MSA). Residues which are concerved across the entire sulfatase family are marked in red''<br />
<br />
<br />
== Arylsulfatase K structure==<br />
<br />
[[Image:ASK.png|centre|framed|'''Figure 2:''' ''Arylsulfatase K as a heterodimer; 3b5q chain A and B'']]<br />
<br />
<br />
<br />
'''Protein data bank''' profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.<br />
<br />
<br />
[[Image:reactionASK.png]]<br />
<br />
<br />
<br />
<br />
== Structural alignment ==<br />
<br />
*Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 3'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''figure 3:''' ''Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''.<br />
<br />
<br />
<br />
*The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc]<br />
<br />
<br />
:'''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.<br />
:'''Steryl-sulfatase''' is a sulfuric ester hydrolase found in endoplasmin reticulums.<br />
<br />
<br />
== Arylsulfatase K interactions with other proteins ==<br />
<br />
[[Image:net.png|centre|framed|'''figure: 4'''ASK interactions with other proteins. Green lines indicate neighbourhood evidence; Dark blue lines, cooccurance and light blue lines homology'']]<br />
<br />
<br />
'''Input Protein''' <br />
*BT1596 Putative sulfatase yidJ (481 aa) of ''Bacteroides thetaiotaomicron''. <br />
<br />
'''Predicted Functional Partners''' <br />
*BT3796: Putative secreted sulfatase ydeN (518 aa). <br />
*BT1595 Transcription termination factor rho (722 aa). <br />
*BT1597 Two-component system sensor histidine kinase (539 aa). <br />
*'''BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).''' <br />
*BT1598 Putative two-component system sensor histidine (655 aa). <br />
*'''BT3101 N-sulphoglucosamine sulphohydrolase (455 aa)'''. <br />
*'''BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa)'''.<br />
<br />
Subcellular interactions of arylsulfatase K were searched usnig the programme '''STRING''', based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.<br />
<br />
<br />
<br />
<br />
<br />
'''ProFunc''' results for ASK interacting proteins.<br />
<br />
*'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate.<br />
*'''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.<br />
<br />
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''<br />
<br />
*'''N-acetylgalactosamine-4- sulfatase (Arylsulfatase B)''' hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)<br />
<br />
All these enzymes has generaly the same function, but acts on different substrate.<br />
<br />
<br />
== Two sequence alignment of ASK and STS == <br />
<br />
<br />
STS was chossen to be the most similar enzyme to ASK due to the shired subcellylar localization. Two sequence alignmnt between ASK and STS is shown is ''figure: 5''. <br />
<br />
<br />
[[Image:alignmentN.png|centre|framed|'''Figure: 5''' ''Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2'']] <br />
<br />
<br />
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.<br />
<br />
No: Chain Z rmsd lali nres %id Description<br />
1: 3b5q-A 73.6 0.0 464 464 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
2: 3b5q-B 70.2 0.3 464 467 100 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
3: 2qzu-A 35.1 2.5 375 465 25 MOLECULE: PUTATIVE SULFATASE YIDJ; <br />
4: 1fsu 28.7 2.8 344 474 22 MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE; <br />
5: 1n2l-A 28.4 3.0 343 483 25 MOLECULE: ARYLSULFATASE A; <br />
6: 1n2k-A 28.1 3.1 342 482 25 MOLECULE: ARYLSULFATASE A; <br />
7: 1e2s-P 28.1 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
8: 1e3c-P 28.0 3.1 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
9: 1e33-P 28.0 3.1 342 480 25 MOLECULE: ARYLSULFATASE A; <br />
10: 1e1z-P 27.9 3.0 341 481 26 MOLECULE: ARYLSULFATASE A; <br />
11: 1auk 27.8 3.1 340 481 26 MOLECULE: ARYLSULFATASE A; <br />
12: 1p49-A 27.7 2.9 338 548 24 MOLECULE: STERYL-SULFATASE; <br />
13: 1hdh-B 27.4 3.1 365 525 23 MOLECULE: ARYLSULFATASE; <br />
14: 1hdh-A 27.4 3.0 363 525 23 MOLECULE: ARYLSULFATASE; <br />
15: 2rh6-A 24.3 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
16: 2rh6-B 24.2 2.6 257 382 14 MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE; <br />
<br />
'''''figure 4:''' Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa''. <br />
<br />
<br />
The function of highly related proteins was searched using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].<br />
<br />
<br />
== Multiple sequence alignment ==<br />
<br />
<br />
<br />
<br />
[[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/3bsqA_Discussion Discussion]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_Abstract&diff=98053bsqA Abstract2008-06-09T08:12:30Z<p>NatashaFerber: </p>
<hr />
<div>Sulfatases are hydrolytic enzymes which cleave sulfate ester bonds of their substrates [1]. Sulfatases show highly conserved sequence features, especially at the N-terminal region where the catalytic site is located. Arylsulfatase K (ASK) is a water-soluble enzyme found in the endoplasmic retuculum (ER) [1]. Sequence alignment studies show that the catalytic site of STS shares many key residues within ASK in addition to the above mentioned universally conserved residues, suggesting that the function and substrates of STS may be similar to that of ASK. Based on evolutionary analysis a cysteine residue, which is present in all sulfatases are highly conserved across the evolution of the sulfatase family. With exceptions in some bacteria including ASK, which show a serine residue in place of cysteine.</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=98013bsqA References2008-06-09T07:56:52Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990) Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
<br />
*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
<br />
*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076<br />
<br />
----<br />
[[3b5q abstract | Abstract]] | [[3b5q intro| Introduction]] | [[3b5q results| Results]] | [[3b5q discussion| Discussion]] |<br />
[[3b5q conclusion| Conclusion]] | [[3b5q method| Method]] | [[3b5q references| References]]<br />
<br />
[[Arylsulfatase K| Back To Main Arylsulfatase K Page]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=97983bsqA References2008-06-09T07:54:59Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990) Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
<br />
*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
<br />
*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076<br />
<br />
----<br />
[[3b5q abstract | Abstract]] | [[3b5q intro| Introduction]] | [[3b5q results| Results]] | [[3b5q discussion| Discussion]] |<br />
[[3b5q conclusion| Conclusion]] | [[3b5q method| Method]] | [[3b5q references| References]]<br />
<br />
[[Bifunctional coenzyme A synthase (CoA synthase)| Back To Main CoA Synthase Page]]</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=97973bsqA References2008-06-09T07:49:23Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990) Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
<br />
*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
<br />
*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=97953bsqA References2008-06-09T07:49:01Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990) Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B.<br />
J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
<br />
*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
<br />
*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=97943bsqA References2008-06-09T07:48:40Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases. Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
*Peters, C., Schmidt, B., Rommerskirch, W., Rupp, K., Zühlsdorf, M., Vingron, M., Meyer, H. E., Pohlmann, R. and von Figura, K. (1990)<br />
Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B.<br />
J Biol. Chem. ''25''; 265(6), 3374-81[http://www.ncbi.nlm.nih.gov/pubmed/2303452?dopt=Abstract]<br />
<br />
*Sardello, M., Annunziata, I., Roma, G. and Ballabio, A. (2005) Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship. Human molecular genetics. 14: 3203-3217<br />
<br />
*Saitou, N. & Nei, M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4: 406-425.<br />
<br />
*Stein, C., Gieselmann, V., Kreysing, J., Schmidt, B., Pohlmann, R., Waheed, A., Meyer, H. E., O’Brien, J. S. and Figura, K. V. (1989) Cloning and expression of human arylsulfatase A. The Journal of Biological Chemistry. 15: 1252-1259<br />
<br />
*Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-1599.<br />
<br />
*Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K, Chiang, H. C., Hooper, L. V. and Gordon, J. I. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 28: 2074-2076</div>NatashaFerberhttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=3bsqA_References&diff=97933bsqA References2008-06-09T07:47:59Z<p>NatashaFerber: </p>
<hr />
<div>*Chang, P. L., Varey, P. A., Rosa, N. E., Ameen, M. and Davidson, R. G. (1986) Association of steroid sulfatase with one of the arylsulfatase C isozymes in human fibroblasts. J. Biol. Chem. ''261''(31), 14443-14447[http://www.jbc.org/cgi/content/abstract/261/31/14443].<br />
<br />
<br />
*Diez-Roux,G. and Ballabio, A. (2005) Sulfatases and human<br />
diseases. Annu. Rev. Genomics Hum. Genet. ''6'', 355-379 [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.6.080604.162334]<br />
<br />
*Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution. ''39'': 783-791.<br />
<br />
*Ghosh, D. (2007) Human sulfatases: A structural perspective to catalysis.Cell.Mol.Life Sci. ''64'', 2013-2022 [http://www.springerlink.com/content/an3576355142n7j3/]<br />
<br />
*Ghosh, D. (2005) Three-dimensional structures of sulfatases.<br />
Methods Enzymol. ''400'', 273–293 [http://www.ncbi.nlm.nih.gov/pubmed/16399355]<br />
<br />
*Kreysing, J., Figura, K. V. and Gieselmann, V. (1990) Structure of the arylsulfatase A gene. Biochemistry. 191: 627-631<br />
<br />
*Lee, G. D. and Van Etten, R. L. (1975) Evidence for an essential histidine residue in rabbit liver aryl sulfatase A. Arch. Biochem. Biophys. ''171'', 424-434 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WB5-4DW2GDD-10P&_user=331728&_coverDate=12%2F31%2F1975&_rdoc=7&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236701%231975%23998289997%23530640%23FLA%23display%23Volume)&_cdi=6701&_sort=d&_docanchor=&_ct=47&_acct=C000016898&_version=1&_urlVersion=0&_userid=331728&md5=df8338bf2f8217aaf132754546dffed5]<br />
<br />
<br />
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