title: A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon.
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, which also take part in the extraction of metal ions from their sulfur containing ores. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 16 genes, forming two transcriptional units, viz., soxSRT and soxVWXYZABCDEFGH. SoxY is known to be a sulfur covalently binding protein, which binds sulfur anions (such as sulfate) to form SoxY-thiocysteine-S-sulfate, 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, SoxZ, and SoxB from Paracoccus pantotrophus. With the help of docking and molecular dynamics studies we have identified the residues of SoxY, SoxZ, and SoxB involved in the interaction. The probable mechanisms of the binding of SoxY with sulfate as well as the removal of sulfate from the SoxYZ complex are also established. Our study provides a rational basis to illustrate the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these industrially 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 / Q000235:genetics; D000838:Anions; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D001703:Biophysics / Q000379:methods*; D002244:Carbon / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D007477:Ions; D008958:Models, Molecular; D005810:Multigene Family; D009154:Mutation; D009876:Operon; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000378:metabolism*; D050862:Oxidoreductases Acting on Sulfur Group Donors; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D042084:Paracoccus pantotrophus / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013431:Sulfates / Q000737:chemistry; D013455:Sulfur / Q000737:chemistry; D013869:Thiolester Hydrolases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000838:Anions; D001426:Bacterial Proteins; D002352:Carrier Proteins; D007477:Ions; D013431:Sulfates; D013455:Sulfur; D002244:Carbon; D010088:Oxidoreductases; D050862:Oxidoreductases Acting on Sulfur Group Donors; C413329:SoxZ protein, Paracoccus pantotrophus; D013869:Thiolester Hydrolases; D010100:Oxygen