title: Homology modeling of a transcriptional regulator SoxR of the Lithotrophic sulfur oxidation (Sox) operon in alpha-proteobacteria.
abstract: Microbial oxidation of reduced inorganic sulfur compounds in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units, viz soxSRT and soxVWXYZABCDEFGH. Sequence analysis reveals that SoxR belongs to the ArsR family of helix-turn-helix DNA binding proteins. Although SoxR proteins do not contain the conserved metal-binding box, ELCVCDL, but there are a number of well conserved residues present throughout the sequence that are previously identified in the known ArsR family proteins. We employed homology modeling to construct the three-dimensional structure of the SoxR from chemolithotrophic alpha-Proteobacteria Pseudaminobacter salicylatoxidans KCT001. The predicted homology model of SoxR shows an overall structural similarity with winged helix-turn-helix family proteins. Since dimerization is essential for DNA binding and repression by the ArsR family proteins we have generated the dimeric model of SoxR that enables us to predict the DNA binding residues of the protein as well as the interaction of SoxR with the predicted promoter region of sox gene cluster.
authors.affiliation: Bioinformatics Center, Bose Institute, AJC Bose Centenary Building, P1/12 CIT Scheme VIIM, Kolkata, West Bengal 700 054, India.
authors.forename: Angshuman
authors.initials: A
authors.lastname: Bagchi
authors.forename: Debjani
authors.initials: D
authors.lastname: Roy
authors.forename: Pradosh
authors.initials: P
authors.lastname: Roy
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics / Q000378:metabolism*; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D004247:DNA / Q000378:metabolism; D019281:Dimerization; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C070724:SoxR protein, Bacteria; D004247:DNA