title: Investigation of the rescue mechanism catalyzed by a nucleophile mutant of rice BGlu1.
abstract: In the present study, the quantum mechanical/molecular mechanical (QM/MM) method was used to investigate the rescue mechanism of an E386G mutant as well as the glycosylation mechanism of the wild rice β-D-glucosidase. E386G mutant experiences an asynchronous collaborative process to glycosylate the anionic formate with an energy barrier of 22.6 kcal/mol, while the energy barrier is 25.9 kcal/mol for the wild complex. The low energy barrier of the mutated complex suggests that anionic formate might be a good nucleophile to attack the anomeric carbon atom. Both energy barriers can be lowered when the leaving departure releases from the active site, suggesting that the product release, rather than chemistry, contributes to the rate limiting in BGlu1 mutants. Structure analyses also indicate that the external nucleophile has little steric hindrance with pocket residues and adjusts freely to proceed the rescue mechanism of the mutated complex. Our calculations provide a guide for the selectivity of exogenous nucleophiles in the future study of β-glucosidase.
authors.affiliation: College of Chemistry Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China; School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, China.
authors.forename: Jinhu
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.affiliation: School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, China. Electronic address: rutaoliu@sdu.edu.cn.
authors.forename: Rutao
authors.initials: R
authors.lastname: Liu
authors.affiliation: School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Liu
mesh_terms: D008958:Models, Molecular; D009154:Mutation; D012275:Oryza / Q000235:genetics*; D001617:beta-Glucosidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D001617:beta-Glucosidase
keywords: Anionic formate; Anomeric carbon; E386G mutant; Quantum mechanical/molecular mechanical (QM/MM); Rescue mechanism; β-Glucosidase