Glycerol as a Substrate and Inactivator of Coenzyme B12‐Dependent Diol Dehydratase. Issue 29 (22nd April 2021)

• Record Type: Journal Article
• Authors: Bilić, Luka; Barić, Danijela; Sandala, Gregory M.; Smith, David Mathew; Kovačević, Borislav
• Is Part Of: Chemistry. Volume 27:Issue 29(2021)
• Page Start: 7930
• Page End: 7941
• Publication Date: 2021-04-22
• Subjects: B12-dependent diol Dehydratase -- B12-independent glycerol dehydratase -- density functional calculations -- enzyme catalysis -- inactivation mechanism; Chemistry -- Periodicals; 540
• DOI: 10.1002/chem.202100416
• Languages: English
• ISSNs: 0947-6539

Abstract

Abstract: Diol dehydratase, dependent on coenzyme B12 (B12 ‐dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B12 ‐ independent glycerol dehydratase (B12 ‐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 B12 ‐dDDH and that of resistance of B12 ‐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 B12 ‐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 B12 ‐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. Abstract : Two distinct enzymes, coenzyme B12 ‐dependent diol dehydratase (B12 ‐dDDH) and coenzyme B12 ‐independent glycerol dehydratase (B12 ‐iGDH), are capable of catalyzing the selective transformation of glycerol to 3‐hydroxypropionaldehyde. Only the former enzyme is subject to substrate‐induced inactivation, however. Utilizing molecular dynamics (MD), quantum mechanical (QM), and hybrid QM/MM techniques, we found that inactivation in B12 ‐dDDH occurs if hydrogen abstraction takes place from the 'wrong' side (C3) of glycerol.