Bioinformatics Section, CCSHAU, Hisar 125004, India.
J Mol Graph Model. 2011 Feb;29(5):740-6. doi: 10.1016/j.jmgm.2010.12.004. Epub 2010 Dec 17.
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.
黑芥子硫苷酶，唯一已知的 S-糖基酶，主要存在于十字花科植物中。它负责水解硫代葡萄糖苷，是植物防御系统的重要组成部分。黑芥子硫苷酶催化硫代葡萄糖苷产物的生物学和化学性质已得到充分表征。从 NCBI 数据库中检索到芥菜黑芥子硫苷酶的蛋白质序列，并基于白芥子黑芥子硫苷酶的 1MYR-A、1E4M-M 和 1DWA-M 链的晶体结构，运用 Modeller9v7 程序生成其 3-D 模型。来自白芥子的同源模板与目标序列具有 72%的同一性。该模型通过分子动力学（MD）方法和相同的 Modeller 程序中的模拟退火（SA）方法进行优化，最后分别在 SAVES（结构分析和验证服务器）和 PROCHECK 程序中进行验证和验证。通过 PROCHECK 程序获得的 Ramachandran 图显示，总残基的 99.8%被限制在允许区域内，而只有一个残基（Thr92）被限制在不允许区域内。此外，芥菜黑芥子硫苷酶含有三个二硫键，在白芥子的同源物中也被发现是保守的。此外，芥菜黑芥子硫苷酶与白芥子模板蛋白 1MYR-A 的重叠表明，构成酶活性位点的氨基酸残基为 Arg115、Gln207、Thr210、Asn350、Tyr352 和 Glu429。活性位点分析还推测存在一个除了七个 N-糖基化位点之外的疏水口袋。酶和底物的对接研究阐明了各种活性位点残基与黑芥子硫苷不同基团之间的相互作用。因此，本研究首次提供了芥菜黑芥子硫苷酶的 3-D 结构、活性位点机制和酶-底物相互作用的重要计算见解。
