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[[Functional analysis of 2ece]]
[[Functional analysis of 2ece]]


== STRUCTURAL ANALYSIS ==
Back to main page [[Selenium binding protein]]
 
'''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 SELENBP 1 (pdb 2ece) ==
 
 
[[Image:SBP with Sele atom.png|frame|border|left|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)
]]

Latest revision as of 14:40, 9 June 2008

The results were seperated into two categories.

Evolutionary analysis of 2ece

Structural analysis of 2ece

Functional analysis of 2ece

Back to main page Selenium binding protein

Retrieved from "http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Results_2ece&oldid=10182"