Structural insight into the functionality of the transcriptional regulator SoxR from Paracoccus pantotrophus in sulfur oxidation operon

Abstract

The redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle mediated by prokaryotes of different phylogenetic groups. The Sulfur oxidizing gene cluster (Sox) of α-Proteobacteria comprises of at least 15 genes, which form two transcriptional units, viz., SoxSRT and SoxVWXYZABCDEFGH. Biochemical studies reveal 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 as observed in case of other well studied ArsR family proteins, but there are a number of well conserved residues present throughout the sequence that are previously identified in other known ArsR family proteins collectively called atypical ArsR proteins. In the present study homology modeling is employed to construct the three-dimensional structure of the SoxR from α-Proteobacteria Paracoccus pantotrophus. The predicted homology model of SoxR shows an overall structural similarity with winged helix-turn-helix family of DNA binding proteins. Since SoxR is a DNA binding protein we docked the modeled SoxR on to its promoter DNA sequence to predict the probable mode of interaction between them. Present studies are expected to contribute in designing experiments for future genetic and biochemical experiments to elucidate the role of different residues in classification of SoxR as an atypical ArsR family of proteins as well as DNA binding that would help to understand the regulation of sox gene expression in sulfur lithotrophs of α-Proteobacteria family