In silico approach for bioremediation of arsenic by structure prediction and docking studies of arsenite oxidase from Pseudomonas stutzeri TS44

Abstract

Pseudomonas stutzeri TS44 is a moderately halotolerant, arsenite-oxidizing bacterium, containing genes for arsenite oxidation, arsenic resistance, and ectoine/hydroxyectoine biosynthesis. This paper reports in silico studies to understand bioremediation to eliminate toxic metal arsenic in water, air and soil by arsenite oxidase (AO), the bacterial enzyme from P. stutzeri TS44 that can be used for a low cost and eco-friendly removal of arsenite from the environment. To understand the activity of AO in elimination of arsenite, sequence analysis was carried out and homologs, orthologs, domains, family, and conserved residues were identified followed by model generation using various homology modeling tools. The generated models were validated for the best quality protein structure and the best model was used for further optimization using energy minimization approach. Molecular docking studies were performed to study the binding interaction of AO with arsenite. The study predicts and validates the 3D structure of P. stutzeri TS44 arsenite oxidase and reports four active site residues (His197, Glu205, Arg421, and His425) from a close structural homolog of AO from A. faecalis (PDB ID: 1G8K_A). The molecular docking studies suggested the formation of a stable complex and in silico site-directed mutagenesis revealed the importance of Arg421, which resulted in a decrease in stability of the complex when mutated. The study implicates P. stutzeri TS44 arsenite oxidase as a non virulent protein for low cost and eco-friendly bioremediation of arsenite.