Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12 (CROSBI ID 253553)
Prilog u časopisu | izvorni znanstveni rad | međunarodna recenzija
Podaci o odgovornosti
Kovačević, Borislav ; Barić, Danijela ; Babić, Darko ; Bilić, Luka ; Hanževački, Marko ; Sandala, Gregory M. ; Radom, Leo ; Smith, David M.
engleski
Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12
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-B12-dependent enzyme and the other which is a coenzyme-B12-independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B12-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-B12-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 B12 cofactor. In the absence of B12, 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.
B12-dependent GDH ; B12-indipendent B12 ; QM/MM ; mechanism of catalysis
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Podaci o izdanju
140 (27)
2018.
8487-8496
objavljeno
0002-7863
1520-5126
10.1021/jacs.8b03109
Povezanost rada
Kemija