title: Structural insight into the interactions of SoxV, SoxW and SoxS 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 transfer chains. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxV is known to be a CcdA homolog involved in the transport of reductants from cytoplasm to periplasm. SoxW and SoxS are periplasmic thioredoxins, which (SoxW) interact with SoxV and thereby help in the redox reactions. We have employed homology modeling to construct the three-dimensional structures of the SoxV, SoxW and SoxS proteins from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics simulations we have identified the amino acid residues of these proteins involved in the interaction. The probable biochemical mechanism of the transport of reductants through the interactions of these proteins has also been investigated. Our study provides a rational basis to interpret the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.
authors.affiliation: Bioinformatics Center, Bose Institute, AJC Bose Centenary Building, P1/12 CIT Scheme VIIM, Kolkata 700 054, India. angshu@bic.boseinst.ernet.in
authors.forename: Angshuman
authors.initials: A
authors.lastname: Bagchi
authors.forename: Tapash Chandra
authors.initials: TC
authors.lastname: Ghosh
mesh_terms: D020561:Alphaproteobacteria; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D003593:Cytoplasm / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D010084:Oxidation-Reduction; D019897:Periplasm / Q000378:metabolism; D019163:Reducing Agents / Q000378:metabolism*; D041903:Rhodovulum; D016415:Sequence Alignment; D013455:Sulfur / Q000737:chemistry* / Q000378:metabolism; D013879:Thioredoxins / Q000378:metabolism; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D019163:Reducing Agents; D015534:Trans-Activators; D013879:Thioredoxins; D013455:Sulfur