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

Adenosylcobalamin (AdoCbl) (coenzyme B-12) 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 (beta/alpha)(8) barrel seems to be a common molecular apparatus for coenzyme B-12-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 coenzyme's 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. (C) 2000 Elsevier Science B.V. All rights reserved.