Methods 2ece: Difference between revisions

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== 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


 
Back to [[Selenium binding protein]]
[[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 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]]
 
 
(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]

Latest revision as of 15:01, 9 June 2008

Methods employed to obtain the analytical data was devided into three categories

Methods for evolutionary analysis

Methods for structural analysis

Methods for functional analysis

Back to Selenium binding protein

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