Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12

J Am Chem Soc. 2018 Jul 11;140(27):8487-8496. doi: 10.1021/jacs.8b03109. Epub 2018 Jun 29.

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-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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biocatalysis
  • Clostridium butyricum / chemistry
  • Clostridium butyricum / enzymology*
  • Clostridium butyricum / metabolism
  • Glyceraldehyde / analogs & derivatives*
  • Glyceraldehyde / chemistry
  • Glyceraldehyde / metabolism
  • Glycerol / chemistry
  • Glycerol / metabolism*
  • Hydro-Lyases / metabolism*
  • Klebsiella pneumoniae / chemistry
  • Klebsiella pneumoniae / enzymology*
  • Klebsiella pneumoniae / metabolism
  • Models, Molecular
  • Propane / chemistry
  • Propane / metabolism*
  • Vitamin B 12 / chemistry
  • Vitamin B 12 / metabolism*

Substances

  • 3-hydroxypropionaldehyde
  • Glyceraldehyde
  • Hydro-Lyases
  • glycerol dehydratase
  • Vitamin B 12
  • Glycerol
  • Propane