|
|
| (20 intermediate revisions by one other user not shown) |
| Line 1: |
Line 1: |
| == STRUCTURAL ANALYSIS ==
| | Methods employed to obtain the analytical data was devided into three categories |
|
| |
|
| '''SBP 1 Amino Acid FASTA FORMAT Sequence'''
| | [[Methods for evolutionary analysis]] |
|
| |
|
| >2ECE:A|PDBID|CHAIN|SEQUENCE
| | [[Methods for structural analysis]] |
|
| |
|
| MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA
| | [[Methods for functional analysis]] |
| CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG
| |
| EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR
| |
| IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP
| |
| PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS
| |
| LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP
| |
|
| |
|
| [[Image:PBB_GE_SELENBP1_214433_s_at_fs.png|alt text|thumb|border|center|abc]]
| | Back to [[Selenium binding protein]] |
| | |
| | |
| [[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]]
| |
| | |
| | |
| | |
| | |
| '''Query name''': SBP 1 ( 2ECE )
| |
| Structure prediction by SABLE
| |
| | |
| | |
| '''Data source''': Derived from the SABLE server prediction
| |
| | |
| | |
| [[Image:SABLE.gif|frame|border|left|'''Figure 2''' SBP amino acid structure prediction 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]]
| |
| | |
| '''Figure 4''' Shows structural helices(red) and beta sheets (yellow) of SBP designed from pymol
| |
| | |
| | |
| [[Image:secondary structure.gif]]
| |
| | |
| '''Figure 5'''
| |
| | |
| | |
| [[Image:pdb_cartoon_2ece.png]]
| |
| | |
| '''Figure 6'''
| |
| | |
| STRUCTURAL COMPARISONS
| |
| | |
| [[Image:surface of 2ece.png]]
| |
| | |
| Surface Structure of SBP: Note the few clefts compared to the DNA isomerase shown below.
| |
| | |
| | |
| [[Image:1YUA SURFACE STRUCTURE.JPG]]]]]
| |
| | |
| [http://www.ncbi.nlm.nih.gov/entrez/query/static/gifs/entrez_struc.gif]
| |
| | |
| [[Image:Rat fatty acid binding protein 2IFB.jpg]] | |
| | |
| 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 below.
| |
| | |
| | |
| '''1RI6 DOMAINS'''
| |
| | |
| | |
| [[Image:1RI6 A 0.png]]
| |
|
| |
| | |
| [[Image:1RI6 A 1.png]]
| |
| | |
|
| |
| [[Image:1RI6 A 2.png]]
| |
| | |
| | |
| [[Image:1RI6 A 3.png]]
| |
| | |
| | |
|
| |
| '''2ECE DOMAINS'''
| |
| | |
| | |
| [[Image:2ece A 3.png]]
| |
| | |
| | |
| | |
| [[Image:2ece A 2.png]]
| |
| | |
| | |
| [[Image:2ece A 1.png]]
| |
| | |
| | |
| [[Image:2ece A 0.png]]
| |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
|
| |
| | |
| | |
| | |
| [[Image:Ligand of bovine.png]]
| |
| | |
| | |
| (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]]
| |
| | |
| == SEQUENCE ANALYSIS ==
| |
| Selenium binding protein 1 (SELENBP1)
| |
| SELECTED PROTEIN SIMILARITIES
| |
| Comparison of sequences in UniGene with selected protein reference sequences. The alignments can suggest function of a gene.
| |
| [http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=632460]
| |
