Theoretical study on the mechanism of catalysis of coenzyme B ₁₂-dependent diol dehydratase

The energy profile of the diol dehydratase reaction is discussed from theoretical calculations at the B3LYP/6311G* level of density functional theory. The differences between the energy diagrams of models with and without K ⁺ ion are rather small except for the substrate binding and the OH group migration. The most important role of K ⁺ ion in the diol dehydratase catalysis is to fix substrates and intermediates in proper positions in order to ensure the hydrogen abstraction and recombination between them and the adenosyl group. In the course of the reaction, substrates and reaction intermediates would always be kept bound to K ⁺ ion until the release of product aldehyde from the active site. Given the neutral radical state of the substrate, the OH group migration proceeds in a concerted mechanism. In this process, K ⁺ ion can work as an inhibitor of intramolecular hydrogen bond, which decreases the activation energy by 4.0 kcal/mol, due to the destabilization of reactant 1,2-dihydroxypropyl radical. The lowering of the activation energy by K ⁺ ion, however, is rather small, and thus the contributions of active-site amino acid residues to the OH group migration must be taken into consideration to explain that the hydrogen abstraction is the rate-determining step for the overall reaction.