Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
PULS Group, Institute for Theoretical Physics FAU Erlangen-Nürnberg, Staudtstraße 7, Erlangen, Germany.
Chemistry. 2021 May 20;27(29):7930-7941. doi: 10.1002/chem.202100416. Epub 2021 Apr 22.
Diol dehydratase, dependent on coenzyme B (B -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B -independent glycerol dehydratase (B -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B -dDDH and that of resistance of B -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.
二醇脱水酶依赖辅酶 B（B-DDDH），具有一个奇特的特点，即其天然底物甘油（GOL）会使其失活。令人惊讶的是，同功酶 B 独立甘油脱水酶（B-iGDH）不会被 GOL 引发自杀失活。在此，我们提出了一系列QM/MM 和 MD 计算，旨在理解 B-DDDH 中底物诱导自杀失活的机制，以及 B-iGDH 对失活的抵抗机制。我们表明，GOL 酶促转化的第一步，即氢提取，可以从底物的两端（GOL 的 C1 或 C3）发生。尽管在两种酶中 C1 提取都会导致产物形成，但在 B-DDDH 中 C3 提取会导致形成低能量自由基中间体，该中间体有效地被困在势能表面的深阱中。这种自由基中间体的长寿命可能使其发生副反应，从而导致失活。相比之下，在 B-iGDH 中，C3 提取是一个吸热步骤；因此，所得的自由基中间体不是低能量的，并且反应物的反向形成是可能的。
