Catalytic Site Prediction of Azoreductase Enzyme of E. coli with Potentially Important Industrial Dyes Using Molecular Docking Tools

Abstract

Abstract:Azoreductase is an FMN-dependent and NADH-dependent enzyme of Escherichia coli. This enzyme is responsible for the degradation of azo dyes. In this study, we retrieved the crystal structure of the enzyme from PDB and 18 azo dyes from NCBI PubChem compound. These azo dyes were then docked with the FMN-dependent NADH-azoreductase enzyme to analyze the binding affinity of the azo dyes with the enzymes and predict the catalytic sites. In this approach, we identified the catalytic residues of FMN-dependent and NADH dependent enzyme of Escherichia coli which were then evaluated in terms of properties including function, conservation, hydrogen bonding, B-factor and flexibility. The results indicated that Phe-172, Glu-174, Lys-145, Asp-146 and Lys-169 played an important role as catalytic site residues in the enzyme. It is hoped that this information will provide a better understanding of enzyme mechanisms and also be used to improve the designing strategies for dyes detoxification. In this study, the approach emphasizes on a better understanding of the biodegradation of some of the commercially important azodyes mediated by azoreductase from E. coli. Furthermore, the catalytic site residues information is essential for understanding and altering the substrate specificity and for the design of a harmless azodye.

Degradation of sulphonated mono and di-azo dye as the sole carbon source inSerratia marcescens: Insights from combined wet and dry lab analysis

“…Six of these residues (Arg, Thr, Phe, Met, Gly, Asn) were common to interactions of AzoR-MO in Oedogonium subpalgiostomum AP1 [63]. None of our MO binding residues were similar to that of Pseudomonas putida [64]. CR formed one hydrogen bond and ten hydrophobic interactions (with residue Met 56, Gly58, Phe59, Thr60, Asn100, Lys106, Ala113, Arg114, Ala115, Leu152, Tyr156).…”

“…CR formed one hydrogen bond and ten hydrophobic interactions (with residue Met 56, Gly58, Phe59, Thr60, Asn100, Lys106, Ala113, Arg114, Ala115, Leu152, Tyr156). Two of these residues were common when compared to CR-AzoR interaction of Pseudomonas putida [64].…”

Omics-Based Approaches in Research on Textile Dye Microbial Decolorization

“…They proved that azoreductase AzrC showed a high affinity toward hydrophobic dyes such as Acid Red 88. Molecular docking was also applied to assess FMN-dependent NADH-azoreductase from the bacteria E. coli with 18 azo dyes [ 126 ]. The use of molecular modeling and docking allows for the screening of pollutant’s susceptibility to degradation by already characterized enzymes and enables the preliminary selection of dye–microorganism–enzyme systems employed further in textile dye decolorization and degradation studies.…”