Structural analysis of 2ece

STRUCTURAL ANALYSIS

SBP 1 Amino Acid FASTA FORMAT Sequence

>2ECE:A|PDBID|CHAIN|SEQUENCE

MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP

Figure 2.1Gene 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

Figure 2.2 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

Figure 2.3 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 2.4 SABLE server results.

Figure 2.5 Shows structural helices(red) and beta sheets (yellow) of SBP designed from pymol

Figure 2.6 PDBsum of structural representation of SELENBP1 showing disulphide bonds networks (yellow), loops, helices (labelled blue) and beta sheets ( labelled Red)

Figure 2.7 PDBsum shows the beta and a- helices of SELENBP1

STRUCTURAL COMPARISONS

Figure 2.8 Surface Structure of SBP: Note the few clefts compared to the DNA isomerase shown below.

Figure 2.9 pdb (1yua)-Topo-Zn DNA isomerase surface structure[1]

Figure 2.10 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.([ref 3])

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 2.11below.

1RI6 DOMAINS

full structure

Domain 1

Domain 2

Domain 3

2ECE DOMAINS

Domain 3

Domain 2

Domain 1

full structure

Figure 2.12Complex Of Bovine Odorant Binding Protein (Obp) With A Selenium Containing Odorant)"Image:Ligand of bovine.png" [[2]]

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