Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B<sub>12</sub>.
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Abstract | :
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. |
Year of Publication | :
2018
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Journal | :
Journal of the American Chemical Society
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Volume | :
140
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Issue | :
27
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Number of Pages | :
8487-8496
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Date Published | :
2018
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ISSN Number | :
0002-7863
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URL | :
https://dx.doi.org/10.1021/jacs.8b03109
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DOI | :
10.1021/jacs.8b03109
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Short Title | :
J Am Chem Soc
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