A Structural Analysis of the Mode of Action of ORF1 in Pseudaminobacter salicylatoxidans: Prediction of its Role in the Global Sulfur Oxidation Operon (sox)

Abstract

The sulfur compound metabolizing sox operon of microbes consists of two transcriptional units. Recently a new orf, which code for protein named ORF1, was identified in Pseudaminobacter salicylatoxidans which is one of the most prominent sulfur oxidizers. Sequence analyses reveal ORF1 has the signature sequence of the dsr family of sulfate ion binding proteins. It is present in an analogoues position as the ORF1 of Starkeya novella. There are no studies regarding the structural biology ORF1 of Pseudaminobacter salicylatoxidans. In order to elucidate the structural aspects of the mechanistic details of of the protein, homology modeling technique has been employed to construct the three-dimensional structure of ORF1. ORF1 from Starkeya novella is known to interact with the transcriptional activator SigE which is known to bind to its adjacent promoter DNA sequence and thereby regulate the sox gene cluster in Starkeya novella. Pseudaminobacter salicylatoxidans does not contain the SigE protein but instead possesses another transcriptional activator SoxR which performs similar function as SigE. In order to verify whether ORF1 of Pseudaminobacter salicylatoxidans serves the similar function as that of Starkeya novella by molecular docking analyses have been performed using the models of ORF1 and SoxR to predict the favourable binding interactions of the proteins. The putative sulfate ion binding residues of ORF1 has also been identified by docking sulfate ion on to it. This study provides a rational framework for understanding of the structural as well as the molecular basis of the mechanism of the regulation of sulfur oxidation reactions ORF1 proteins via the sox operon.