Methods 2ece: Difference between revisions

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STRUCTURAL COMPARISONS
STRUCTURAL COMPARISONS


[[Image:surface of 2ece.png]]
[[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.]]


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




[[Image:1YUA SURFACE STRUCTURE.JPG]]]]]
 
[[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]
[http://www.ncbi.nlm.nih.gov/entrez/query/static/gifs/entrez_struc.gif]

Revision as of 07:39, 9 June 2008

STRUCTURAL ANALYSIS

SBP 1 Amino Acid FASTA FORMAT Sequence

>2ECE:A|PDBID|CHAIN|SEQUENCE

MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP


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


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



Figure 6 PDBsum shows the beta and a- helices of SELENBP1




STRUCTURAL COMPARISONS

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]

[1]

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.([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


1RI6 A 0.png


1RI6 A 1.png


1RI6 A 2.png


1RI6 A 3.png


2ECE DOMAINS


2ece A 3.png


2ece A 2.png


2ece A 1.png


2ece A 0.png








Ligand of bovine.png


(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]