The structure and the mechanism of action of coenzyme B12-dependent diol dehydratases

Adenosylcobalamin (AdoCbl) (coenzyme B12) serves as a cofactor for enzymatic radical reactions. The recently solved X-ray structure of diol dehydratase in complex with cyanocobalamin (CN-Cbl) revealed the base-on mode of cobalamin binding. The active-site cavity inside the (β/α)8 barrel seems to be a common molecular apparatus for coenzyme B12-dependent enzymes to spatially isolate highly reactive radical intermediates. Based on the direct ion–dipolar interactions between two hydroxyl groups of substrate and potassium ion in the active site and theoretical calculations, a new mechanism for diol dehydratase is proposed here in which a potassium ion participates directly in the catalysis. The mechanism of activation of the coenzymeʹs cobalt–carbon bond by which a catalytic radical is generated in the active site of diol dehydratase is also discussed on the basis of the conformation of the enzyme-bound cobalamin. It was highly suggested that the reactivity of the cobalt atom is controlled by the length of the CoN bond. Therefore, the role of the 5,6-dimethylbenzimidazole (DBI) moiety of cobalamin coenzyme in the enzyme catalysis is most likely to prevent the enzyme from mechanism-based inactivation by keeping the CoN bond distance long through steric repulsion between the flattened corrin ring and the base.