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Chemistry (Weinheim an der Bergstrasse, Germany)

On the reaction of glycerol dehydratase with but-3-ene-1,2-diol.


PMID 19326378

Abstract

High-level conventional ab initio and density functional theory (DFT) calculations have been performed to examine the fate of the native substrate glycerol (1) and its analogue but-3-ene-1,2-diol (7) in the coenzyme B(12)-dependent enzyme glycerol dehydratase (GDH). Experimental studies find that 7 irreversibly inactivates GDH, though the mechanism for the inactivation remains unknown. Interestingly, the EPR data suggest that the spin density for an observed radical is located in the vicinity of the C1 atom, which has been interpreted to indicate termination of the pathway at the substrate-derived radical 8. Our calculations show that if analogue 7 were to follow a similar mechanistic pathway to that followed by 1, then the reaction would be unlikely to stop at 8 but would rather proceed to the highly stabilized product-related radical 9. However, the EPR characteristics of 9 would not be consistent with the observed EPR data. Calculations involving an initial H-atom abstraction from the C2 position of 7 identify alternative radicals that might account for the EPR data, though they are of relatively high energy. A proposal that could explain the experimental observations is that the enzyme binds 7 in such a manner as to prevent the efficient transformation of 8. Recent work with the related enzyme diol dehydratase suggests that a common, but as yet unexplained, inactivation mechanism may be operative for both enzymes. Finally, we note the good overall performance of the MPWB1K, BMK, M05-2X, and B2-PLYP DFT procedures for these reactions, with the BMK method producing the best results.

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