QM/MM studies on the glycosylation mechanism of rice BGlu1 β-glucosidase

The quantum-mechanical/molecular-mechanical (QM/MM) method was used to study the glycosylation mechanism of rice BGlu1 β-glucosidase in complex with laminaribiose. The calculation results reveal that the glycosylation step experiences a concerted process from the reactant to the glycosyl-enzyme complex with an activation barrier of 15.7 kcal/mol, in which an oxocarbenium cation-like transition state (TS) is formed. At the TS, the terminal saccharide residue planarizes toward the half-chair conformation, and the glycosidic bond cleavage is promoted by the attacks of proton donor (E176) on glycosidic oxygen and nucleophilic residue (E386) on the anomeric carbon of laminaribiose. Both the nucleophilic glutamate (E386) and acid/base catalyst (E176) establish shorter hydrogen bridges with the C2-hydroxyl groups of sugar ring, which play an important role in the catalytic reaction of rice BGlu1 β-glucosidase.

Graphical abstractThe quantum mechanical/molecular mechanical (QM/MM) method was used to study the general glycosylation mechanism of rice BGlu1 β-glucosidase. The reaction experiences an oxocarbenium cation-like transition state with a barrier of 15.7 kcal/mol. Both the nucleophilic glutamate (E386) and acid/base catalyst (E176) have hydrogen bonding interactions with the substrate, which is useful in stabilizing the transition state and lowering the barrier.Figure optionsDownload full-size imageDownload high-quality image (20 K)Download as PowerPoint slideHighlights► The glycosylation mechanism of rice β-glucosidases was studied by using QM/MM method. ► The catalytic reaction experiences an oxocarbenium cation-like transition state. ► The attacks of E176 on glycosidic oxygen and E386 on anomeric carbon are concerted. ► The energy barrier derived from QM/MM method is much lower than those from simplified models.