Department of Physical Chemistry , Ruđer Bošković Institute , 10000 Zagreb , Croatia.
Department of Chemistry and Biochemistry , Mount Allison University , Sackville , New Brunswick E4L 1G8 , Canada.
J Am Chem Soc. 2018 Jul 11;140(27):8487-8496. doi: 10.1021/jacs.8b03109. Epub 2018 Jun 29.
We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B-dependent enzyme and the other which is a coenzyme-B-independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B-dependent enzyme proceeds via a 1,2-OH shift, which benefits from a significant catalytic reduction in the barrier. In contrast, the same reaction in the presence of the coenzyme-B-independent enzyme is unlikely to involve the 1,2-OH shift; instead, a strong preference for direct loss of water from a radical intermediate is indicated. We show that this preference, and ultimately the evolution of such enzymes, is strongly linked with the reactivities of the species responsible for abstracting a hydrogen atom from the substrate. It appears that the hydrogen-reabstraction step involving the product-related radical is fundamental to the mechanistic preference. The unconventional 1,2-OH shift seems to be required to generate a product-related radical of sufficient reactivity to cleave the relatively inactive C-H bond arising from the B cofactor. In the absence of B, it is the relatively weak S-H bond of a cysteine residue that must be homolyzed. Such a transformation is much less demanding, and its inclusion apparently enables a simpler overall dehydration mechanism.
我们提出了一系列的QM/MM 计算，旨在理解甘油的生物脱水机制。引人注目且不寻常的是，这个过程由两种不同的自由基酶催化，其中一种是辅酶 B 依赖性酶，另一种是非辅酶 B 依赖性酶。我们表明，在辅酶 B 依赖性酶存在的情况下，甘油脱水通过 1,2-OH 迁移进行，这得益于显著降低了反应的能垒。相比之下，在非辅酶 B 依赖性酶存在的情况下，同样的反应不太可能涉及 1,2-OH 迁移；相反，强烈倾向于从自由基中间体直接失去水分子。我们表明，这种偏好，以及最终这些酶的进化，与负责从底物中提取氢原子的物种的反应性密切相关。似乎涉及产物相关自由基的氢原子再结合步骤对于确定反应机制的偏好至关重要。这种非传统的 1,2-OH 迁移似乎是产生足够反应性的产物相关自由基所必需的，以裂解来自 B 辅因子的相对不活跃的 C-H 键。没有 B 时，必须是半胱氨酸残基的相对较弱的 S-H 键发生均裂。这种转化的要求低得多，其包含显然使更简单的整体脱水机制成为可能。
