Results 2ece: Difference between revisions
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[[ | == STRUCTURAL ANALYSIS == | ||
'''SBP 1 Amino Acid FASTA FORMAT Sequence''' | |||
>2ECE:A|PDBID|CHAIN|SEQUENCE | |||
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA | |||
CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG | |||
EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR | |||
IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP | |||
PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS | |||
LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP | |||
[[Image:PBB_GE_SELENBP1_214433_s_at_fs.png|frame|border|center|Gene expression of the SELENBP1 gene based on gene atlas of the mouse and human protein -encoding transcriptomes-proc. Natl. Ac. Sci. 101 (16) 6062-7]] | |||
[[Image:2ece_bio_r_500structure.jpg|frame|border|left|'''Figure 1''' X-ray structure of hypothetical selenium-binding protein from ''Sulfolobus tokodaii'', ST0059 ( http://www.proteopedia.org/wiki/index.php/2ece ) and the JenaLib Jmol viewer showing SBP 1 secondary structure spinning [http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2ece&MODE=asymmetric]] | |||
[[Image:SABLE.gif|frame|border|left|'''Figure 2''' SBP amino acid structure prediction derived from the SABLE server prediction- '''Query name''': SBP 1 ( 2ECE ) | |||
Structure prediction by SABLE | |||
'''Data source''': Derived from the SABLE server prediction | |||
]] | |||
'''WARNING!''' Given sequence appeared to be a soluble protein, no TM domains found! | |||
Output format is the following: | |||
'''1st line''' -> residue numeration | |||
'''2nd line''' -> query amino acid sequence | |||
'''3rd line''' -> trans-membrane domain prediction (T-TM region, '''N'''-soluble part) | |||
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKI | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
VHKVELPYINDELHHFGWNACSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREP | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
KIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEGEGPGGILMLDHYSFEPLGKW | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
EIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEI | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
PAEPLEGNLPEILKPFKAVPPLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTG | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
KVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNSLYSTWDNQFYPEGLKGWMVK | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
LNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP | |||
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |||
'''Figure 3''' SABLE server results. | |||
[[Image:movie0001.png|frame|border|left|'''Figure 4''' Shows structural helices(red) and beta sheets (yellow) of SBP designed from pymol | |||
]] | |||
[[Image:secondary structure.gif|frame|border|left|'''Figure 5''' PDBsum of structural representation of SELENBP1 showing disulphide bonds networks (yellow), loops, helices (labelled blue) and beta sheets ( labelled Red)]] | |||
[[Image:pdb_cartoon_2ece.png|frame|border|left|'''Figure 6''' PDBsum shows the beta and a- helices of SELENBP1 ]] | |||
STRUCTURAL COMPARISONS | |||
[[Image:surface of 2ece.png|frame|border|left|'''Figure 7''' Surface Structure of SBP: Note the few clefts compared to the DNA isomerase shown below.]] | |||
[[Image:1YUA SURFACE STRUCTURE.JPG|frame|border|left|'''Figure 8''' pdb (1yua)-Topo-Zn DNA isomerase surface structure[http://www.ncbi.nlm.nih.gov/entrez/query/static/gifs/entrez_struc.gif] ]] | |||
[[Image:Rat fatty acid binding protein 2IFB.jpg|frame|border|left|'''Figure 9''' Rat fatty acid binding protein 2IFB, a was found to have 92.5% homology to 14 KDa Selenium binding protein purified from rat liver using column chromatography and SDS-Gel techniques.([[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/References_2ece ref 3]])]] | |||
Explore SBP features and structural summary here [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61601].The domains of SBP are shown here [http://www.ncbi.nlm.nih.gov/sites/entrez?db=domains&cmd=search&term=2ece] | |||
Notice how the domains are similar to the putative Isomerase domains of E.coli on '''Figure 10'''below. | |||
'''1RI6 DOMAINS''' | |||
[[Image:1RI6 A 0.png|frame|800x800px|left|full structure]] | |||
[[Image:1RI6 A 1.png|frame|left|Domain 1]] | |||
[[Image:1RI6 A 2.png|frame|left|Domain 2]] | |||
[[Image:1RI6 A 3.png|frame|left|Domain 3]] | |||
'''2ECE DOMAINS''' | |||
[[Image:2ece A 3.png|frame|left|Domain 3]] | |||
[[Image:2ece A 2.png|frame|left|Domain 2]] | |||
[[Image:2ece A 1.png|frame|left|Domain 1]] | |||
[[Image:2ece A 0.png|frame|left|full structure]] | |||
[[Image:Ligand of bovine.png|frame|left|'''Figure 11'''Complex Of Bovine Odorant Binding Protein (Obp) With A Selenium Containing Odorant)"Image:Ligand of bovine.png" [[http://compbio.chemistry.uq.edu.au/mediawiki/upload/2/23/Ligand_of_bovine.png]]]] | |||
[[FUNCTIONAL analysis of 2ece]] | |||
[[Image:SBP with Sele atom.png]] | [[Image:SBP with Sele atom.png]] | ||
The red coloured region is the region carring Se, and it is evident that the Se is incorporated in an amino acid of the helix chain.(Pymol Image) | The red coloured region is the region carring Se, and it is evident that the Se is incorporated in an amino acid of the helix chain.(Pymol Image) |
Revision as of 11:00, 9 June 2008
STRUCTURAL ANALYSIS
SBP 1 Amino Acid FASTA FORMAT Sequence
>2ECE:A|PDBID|CHAIN|SEQUENCE
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP
![](/mediawiki/upload/9/9e/2ece_bio_r_500structure.jpg)
WARNING! Given sequence appeared to be a soluble protein, no TM domains found!
Output format is the following:
1st line -> residue numeration
2nd line -> query amino acid sequence
3rd line -> trans-membrane domain prediction (T-TM region, N-soluble part)
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKI NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN VHKVELPYINDELHHFGWNACSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREP NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN KIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEGEGPGGILMLDHYSFEPLGKW NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN EIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEI NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PAEPLEGNLPEILKPFKAVPPLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTG NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN KVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNSLYSTWDNQFYPEGLKGWMVK NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN LNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Figure 3 SABLE server results.
STRUCTURAL COMPARISONS
![](/mediawiki/upload/e/ed/Rat_fatty_acid_binding_protein_2IFB.jpg)
Explore SBP features and structural summary here [3].The domains of SBP are shown here [4]
Notice how the domains are similar to the putative Isomerase domains of E.coli on Figure 10below.
1RI6 DOMAINS
2ECE DOMAINS
![](/mediawiki/upload/2/23/Ligand_of_bovine.png)
The red coloured region is the region carring Se, and it is evident that the Se is incorporated in an amino acid of the helix chain.(Pymol Image)