Structure analysis and molecular docking studies of laccase from “Bacillus licheniformis NS2324”

• DOI: 10.1016/j.scenv.2023.100004
• Publication Date: 2023-05-19T16:56:50Z
• Authors: Navleen Kaur Chopra; Divya Singhal; Ribhav Saini; Sonica Sondhi
• Keywords: 0301 basic medicine; Chemistry; 03 medical and health sciences; Structure prediction; Laccase; Bacillus licheniformis; Homology modeling; QD1-999; Environmental technology. Sanitary engineering; TD1-1066

Laccase in prokaryotes have enormous application as biocatalysts. Nevertheless, very few laccases have been characterized structurally till date. Recently, a prokaryotic laccase from“Bacillus licheniformis NS2324” have been was cloned and expresses in E. coli. The present research was focused on in silicostructure prediction and characterization of cloned laccase gene isolated from “B. licheniformisNS2324”.In this study various homology modeling servers were used to predict the protein structure of the cloned laccase. Total 17 models were predicted with servers like SWISS-MODEL, ModWeb, Geno3D,I-TASSER,HHPRED using different template structures. All of these models were further validated through PROTSAV, PROCHECK and SAVES server.The best scoring model predicted by SWISS MODEL was selected and submitted in PMDB database. Selected and submitted protein structure was used further for in silico protein structure characterization and docking studies on leather dyes. It was found that all the 33 tested acid leather dyes were docked perfectly to laccase structure with good binding affinity. Acid orange 56 was having highest affinity of − 9.6 kcal mol−1for binding site. A binding affinity of − 9.3 kcal mol−1 and − 9.2 kcal mol−1 was achieved by docking acid red 97 and acid yellow 110 with laccase respectively. The docking studies were further validated by wet laboratory dye decolorization studies which showed a maximum of 96.26 ± 2.51% of (acid orange 56) and a minimum of 61.87 ± 1.30% (acid red 18) This is, to the best of our knowledge, the first study that reports model building from extracellular B. licheniformis laccase and docking with acid leather dyes.