Protein modeling and active site binding mode interactions of myrosinase–sinigrin in Brassica juncea—An in silico approach

Myrosinase, the only known S-glycosidase, occurs particularly in Cruciferae family. It is responsible for the hydrolysis of glucosinolates and serves as a vital element of plant defense system. The biological and chemical properties of myrosinase catalyzed products of glucosinolates are well characterized. The myrosinase-protein-sequence of Brassica juncea was retrieved from NCBI database and its 3-D model was generated on the basis of crystal structure of 1MYR-A, 1E4M-M and 1DWA-M chains of myrosinase from Sinapis alba by employing Modeller9v7 program. Homolog templates from S. alba exhibited 72% identity with target sequence. The model was optimized by using molecular dynamics (MD) approach together with simulated annealing (SA) methods in the same Modeller program, and eventually verified and validated on SAVES (Structure Analysis and Verification Server) and PROCHECK programs, respectively. Ramachandran plot obtained through PROCHECK program depicted that 99.8% of total residues were confined to the allowed region while only one residue (Thr92) was restrained to the disallowed region. Additionally, B. juncea myrosinase contains three disulphide bridges which were found to be conserved in S. alba homologs as well. Further, overlapping of B. juncea myrosinase with that of template protein 1MYR-A from S. alba stipulates the amino acid residues Arg115, Gln207, Thr210, Asn350, Tyr352 and Glu429 that constitute active site of the enzyme. Active site analysis also speculates the presence of a hydrophobic pocket in addition to seven N-glycosylation sites. Docking studies of enzyme and substrate illuminate the interactions of various active site residues with diverse groups of sinigrin. Therefore, the present study furnishes the first significant, in silico insight into the 3-D structure, active site machinery, and enzyme–substrate interactions of B. juncea myrosinase.

Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (122 K)Download as PowerPoint slideResearch highlights▶ 3-D structural model of B. juncea myrosinase contains three disulphide bridges. ▶ Active site analysis showed that amino acid residues Arg 115, Gln 207, Thr 210, Asn 350, Tyr 352 and Glu 429 constitute the active site of enzyme alongwith the presence of a hydrophobic pocket. ▶ Docking studies showed that sinigrin molecule with a twisted boat conformation for the glucose ring fitted the active site of enzyme in a perfect manner. ▶ Results furnishes the first significant, in silico insight into 3-D structure, active site machinery, and enzyme-substrate interactions of B. juncea myrosinase.