Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
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里氏木霉纤维素酶 Cel7A 催化的糖苷键水解机制：通过执行 MD、QM 和 QM/MM 计算进行的综合理论研究
DOI：
10.1021/jp1064177
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发表时间：
2010-11-25
影响因子：
3.3
通讯作者：
Wang, Lushan
中科院分区：
文献类型：
--
作者：
Li, Jinghua;Du, Likai;Wang, Lushan
里氏木霉纤维素酶Cel 7A是目前世界上最丰富、最有效的纤维素酶之一。结构研究已经确定Cel 7A是一种保留糖苷酶，并且它可以从纤维素链的还原端开始水解纤维二糖单元。为了阐明纤维素酶Cel 7A的酶催化机理，本文采用分子动力学（MD）、量子力学（QM）和量子力学（QM/MM）方法对纤维素酶Cel 7A进行了多尺度的理论研究。在精确的理论水平上，我们展示了催化循环的机制细节，其中涉及两次异头中心的构型反转：第一次导致糖苷键断裂并形成共价糖基-酶中间体，第二次将异头碳恢复到其原始构型。计算结果提供了这两个过程的详细结构和能量信息，这两个过程都是通过松散的过渡态结构按照S（N）2型机制进行的。它清楚地表明，糖苷键水解涉及共价糖基-酶中间体的形成，这已被确定为势能面上的最小值。在催化活性区，氢键相互作用贯穿于催化循环的整个过程，这对于稳定糖基-酶中间体具有特别重要的意义。目前的结果提供了一个明确的范例一般糖苷酶的机制，水解的糖苷键与净保留的异头构型。
Cellulase Cel7A from Trichoderma reesei is one of the most abundant and effective cellulases. Structural studies have established that Cel7A is a retaining glycosidase and it can processively hydrolyze cellobiose units from the reducing end of a cellulose chain. Here, to elucidate the mechanism of enzymatic catalysis of cellulase Cel7A, we carried out a multisized level theoretical study by performing MD, QM, and QM/MM calculations. At the accurate level of theory, we showed the mechanism details of the catalytic cycle, which involves the configuration inversion of the anomeric center twice: the first results in the glycosidic bond cleavage and the formation of covalent glycosyl-enzyme intermediate, and the second restores the anomeric carbon to its original configuration. Calculated results have provided detailed structural and energetic information about these two processes, both of which proceed according to a S(N)2-type-like mechanism via loose transition state structures. It is clearly indicated that the glycosidic bond hydrolysis involves the formation of a covalent glycosyl-enzyme intermediate, which has been identified as the minimum on the potential energy surface. At the catalytic active region, hydrogen bond interactions exist throughout the whole process of the catalytic cycle, which are of special importance for stabilizing the glycosyl-enzyme intermediate. The present results provide a clear paradigm of the mechanisms of general glycosidases, which hydrolyze the glycosidic bonds with net retention of the anomeric configuration.