Direct participation of potassium ion in the catalysis of Coenzyme B12-dependent diol dehydratase

The direct ion-dipolar interactions between potassium ion (K⁺) and the two hydroxyl groups of the substrate are the most striking feature of the crystal structure of coenzyme B₁₂-dependent diol dehydratase. We carried out density-functional-theory computations to determine whether K⁺ can assist the 1,2-shift of the hydroxyl group in the substrate-derived radical. Between a stepwise abstraction/recombination reaction proceeding via a direct hydroxide abstraction by K⁺ and a concerted hydroxyl group migration assisted by K⁺, only a transition state for the latter concerted mechanism was found from our computations. The barrier height for the transition state from the complexed radical decreases by only 2.3 kcal/mol upon coordination of the migrating hydroxyl group to K⁺, which corresponds to a 42-fold rate acceleration at 37°C. The net binding energy upon replacement of the K⁺-bound water for substrate was calculated to be 10.7 kcal/mol. It can be considered that such a large binding energy is at least partly used for the substrate-induced conformational changes in the enzyme that trigger the homolytic cleavage of the Co-C bond of the coenzyme and the subsequent catalysis by a radical mechanism. We propose here a new mechanism for diol dehydratase in which K⁺ plays a direct role in the catalysis.