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Computational biology and chemistry

Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox).


PMID 16720104

Abstract

Microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. These reactions are mediated by phylogenetically diverse prokaryotes containing the sulfur oxidizing gene cluster (sox). The sox gene cluster of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units. Recently two new orfs, which code for proteins named, SigE and ORF1, were identified in Starkeya novella. Sequence analyses reveal that SigE protein has the signature sequence of ECF-type sigma factors and a helix-turn-helix (HTH) DNA binding motif whereas ORF1 is possibly an anti ECF-sigma factor, which also has the signature sequence of the dsr family of sulfate ion binding proteins. We employed homology modeling to construct the three-dimensional structures of these proteins. The model of SigE was docked on to its promoter DNA to investigate the favourable binding modes of the protein. Interactions of SigE with its anti-sigma factor ORF1 were also reported after docking these proteins. We also identified the putative sulfate ion binding residues of ORF1 by docking sulfate ion on to it. Our study provides a rational framework for understanding of the structural as well as the molecular basis of the mechanism of the regulation of sulfur oxidation reactions by SigE and ORF1 proteins via the sox operon.

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