Methods 2ece

STRUCTURAL ANALYSIS

SBP 1 Amino Acid FASTA FORMAT Sequence

>2ECE:A|PDBID|CHAIN|SEQUENCE

MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP

abc

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

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.

Figure 4 Shows structural helices(red) and beta sheets (yellow) of SBP designed from pymol

Figure 5

Figure 6

STRUCTURAL COMPARISONS

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

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[1]

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 [2].The domains of SBP are shown here [3] Notice how the domains are similar to the putative Isomerase domains of E.coli below.

1RI6 DOMAINS

2ECE DOMAINS

(Complex Of Bovine Odorant Binding Protein (Obp) With A Selenium Containing Odorant)"Image:Ligand of bovine.png" [[4]]

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. [5]