In silico studies on structural, functional, and evolutionary analysis of bacterial chromate reductase family responsible for high chromate bioremediation efficiency

Abstract

Abstract: In the present study, sequence and structural aspects of five bacterial chromate reductase-related enzymes from Escherichia coli, Pseudomonas putida, Shigella flexneri, and Synechocystis sp. have been investigated. Comparative sequence analyses of different chromate reductase family enzymes showed that Ser13 in E. coli quinone reductase remains conserved among most of the homologous proteins and plays an important role in Flavin mononucleotide (FMN) binding. Comparative protein–ligand binding energy calculation from the docking of all the five modeled complexes of bacterial chromate reductase-related enzymes depicted that quinone reductase from S. flexneri has the highest binding affinity (−7.97 kcal/mol) with FMN. Molecular interactions study suggested that the quinone reductase from P. putida has the highest number of bonded interactions with FMN. In silico mutation design (Y85N) in E. coli ChrR confirmed the significant role of Tyr85 residue in maintaining the network established at the tetramer interface of this enzyme during substrate interaction. Analyses from molecular simulation trajectories also suggested that the mutant E. coli ChrR is much stable than the wild-type form during the interaction with substrate FMN. The present study revealed the interrelationship between the structure and function of bacterial chromate reductase-related enzymes which will help to understand their importance in chromium bioremediation. Graphic abstract: [Figure not available: see fulltext.]