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Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12
Borislav Kovačević1, Danijela Barić1, Darko Babić1
1Department of Physical Chemistry , Ruđer Bošković Institute , 10000 Zagreb , Croatia.
Journal of the American Chemical Society
|June 13, 2018
Summary
This study reveals how two radical enzymes catalyze glycerol dehydration differently. One uses a coenzyme-B12-dependent 1,2-OH shift, while the other, independent enzyme favors direct water loss for glycerol dehydration.
Area of Science:
- Biochemistry
- Enzymology
- Computational Chemistry
Background:
- Glycerol dehydration is a crucial biological process.
- This reaction is catalyzed by two distinct radical enzymes.
- One enzyme is dependent on coenzyme B12, while the other is not.
Purpose of the Study:
- To elucidate the distinct mechanisms of glycerol dehydration catalyzed by coenzyme B12-dependent and independent radical enzymes.
- To understand the role of radical intermediates and cofactor involvement in these enzymatic reactions.
Main Methods:
- Quantum Mechanics/Molecular Mechanics (QM/MM) calculations were employed.
- The study analyzed reaction pathways and energy barriers.
- Investigated the role of specific chemical bonds and radical species.
Main Results:
- The coenzyme B12-dependent enzyme utilizes a 1,2-OH shift, significantly lowering the reaction barrier.
- The coenzyme B12-independent enzyme favors direct water loss from a radical intermediate.
- Enzyme evolution is linked to the reactivity of hydrogen-abstracting species.
Conclusions:
- The unconventional 1,2-OH shift is necessary for the B12-dependent enzyme to activate the C-H bond of the cofactor.
- The B12-independent enzyme utilizes a weaker S-H bond from cysteine, enabling a simpler dehydration mechanism.
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