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首页> 外文期刊>RSC Advances >QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme
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QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme

机译：对II型异戊烯基二磷酸-二甲基烯丙基二磷酸异构酶的QM / MM研究表明黄素辅酶具有新作用

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摘要

The type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the reversible isomerization of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Although a growing body of experiments have suggested that the flavin coenzyme of IDI-2 serves a novel function as an acid–base catalyst, the detailed reaction mechanism of IDI-2 is still unknown. In this paper, a combined quantum-mechanical/molecular-mechanical (QM/MM) approach has been applied to investigate the detailed reaction mechanism of IDI-2. The one-base mechanism in which the N-5 nitrogen of the zwitterionic form of reduced FMN acts as the acid–base catalyst has been supported by our computational results, and a IPP-FMN adduct is also proposed for the first time. The mechanistic details including the fundamental reaction pathways, the complete energy profiles of the whole catalytic cycle, and the specific role of the coenzyme and key residues are all obtained. It is proved that IDI-2 employs novel flavin chemistry with the coenzyme acting as a general acid–base catalyst.
机译：II型异戊烯基二磷酸：二甲基烯丙基二磷酸异构酶（IDI-2）催化异戊烯基焦磷酸（IPP）和二甲基烯丙基焦磷酸（DMAPP）的可逆异构化。尽管越来越多的实验表明IDI-2的黄素辅酶起酸碱催化剂的新作用，但IDI-2的详细反应机理仍然未知。本文采用量子力学/分子力学（QM / MM）相结合的方法研究了IDI-2的详细反应机理。我们的计算结果支持了一种单碱机理，其中两性离子形式的还原FMN的N-5氮充当酸碱催化剂，并且也首次提出了IPP-FMN加合物。包括基本反应途径，整个催化循环的完整能量分布以及辅酶和关键残基的特定作用在内的机理细节均已获得。事实证明，IDI-2采用新颖的黄素化学，辅酶可作为一般的酸碱催化剂。

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