Homology modeling and molecular dynamics study of the interactions of SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions in Pseudaminobacter salicylatoxidans

Abstract

Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, some of which are involved in the extraction of metal ions from their sulfur containing ores. The sulfur oxidizing gene cluster (sox) of α- Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxY is known to be a sulfur covalently binding protein, which binds sulfur anions to form the first covalently bound sulfur adduct in the novel global sulfur anion oxidation cycle. SoxZ, a sulfur compound chelating protein, binds to SoxY forming a complex to which SoxB, a sulfate thiol-esterase binds and ultimately cleaves the sulfur adduct. We employed homology modeling to construct the three-dimensional structures of the SoxY and SoxZ proteins from Psedaminobacter salicylatoxidans. With the help of docking and molecular dynamics studies we have identified the residues of SoxY and SoxZ involved in the interaction. The probable mechanistic details of the interactions of the SoxYZ complex in the binding of sulfur anions are also established. Present study provides a rational basis to illustrate the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.