Inactivation Mechanism of Glycerol Dehydration by Diol Dehydratase from Combined Quantum Mechanical/Molecular Mechanical Calculations

Abstract

Inactivation of diol dehydratase during the glycerol dehydration reaction is studied on the basis of quantum mechanical/molecular mechanical calculations. Glycerol is not a chiral compound but contains a prochiral carbon atom. Once it is bound to the active site, the enzyme adopts two binding conformations. One is predominantly responsible for the product-forming reaction (GR conformation), and the other primarily contributes to inactivation (GS conformation). Reactant radical is converted into a product and byproduct in the product-forming reaction and inactivation, respectively. The OH group migrates from C2 to C1 in the product-forming reaction, whereas the transfer of a hydrogen from the 3-OH group of glycerol to C1 takes place during the inactivation. The activation barrier of the hydrogen transfer does not depend on the substrate-binding conformation. On the other hand, the activation barrier of OH group migration is sensitive to conformation and is 4.5 kcal/mol lower in the GR conformation than in the GS conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the GS conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in GR-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the GS conformation, which shows that the inactivation is favored in the GS conformation