Structural identification of a novel thioredoxin SoxS: Prediction of the function in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle

Abstract

Microbial redox reactions involving 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 also take part in the extraction of metal ions from their sulfur containing ores. These sulfur oxidizers oxidize inorganic sulfur compounds like sulfide, thiosulfate, etc. to produce reductants that are used for carbon dioxide fixation or in respiratory electron transport chains. The sulfur-oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxS is a periplasmic thioredoxin and an essential component of sox operon. It is required for optimal expression of the sox gene cluster. All thioredoxins are involved in interaction with DNA polymerase. We have employed homology modeling to construct the three-dimensional structure of the SoxS protein from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics studies we have identified the amino acid residues of the protein involved in the interaction with DNA polymerase to structurally classify SoxS as a thioredoxin. The probable biochemical mechanism of the involvement of the protein in sulfur oxidation has also been investigated. Our study provides a rational basis to interpret the structural classification of SoxS as a thioredoxin and thereby to predict the possible molecular mechanism of the regulation of sulfur anion oxidation reactions by these ecologically important organisms.