title: Energetic feasibility of hydrogen abstraction and recombination in coenzyme B(12)-dependent diol dehydratase reaction.
abstract: Coenzyme B(12) serves as a cofactor for enzymatic radical reactions. The essential steps in all the coenzyme B(12)-dependent rearrangements are two hydrogen abstraction steps: hydrogen abstraction of the adenosyl radical from substrates, and hydrogen back-abstraction (recombination) of a product-derived radical from 5'-deoxyadenosine. The energetic feasibility of these hydrogen abstraction steps in the diol dehyratase reaction was examined by theoretical calculations with a protein-free, simplified model at the B3LYP/6-311G* level of density functional theory. Activation energies for the hydrogen abstraction and recombination with 1,2-propanediol as substrate are 9.0 and 15.1 kcal/mol, respectively, and essentially not affected by coordination of the substrate and the radical intermediate to K+. Since these energies can be considered to be supplied by the substrate-binding energy, the computational results with this simplified model indicate that the hydrogen abstraction and recombination in the coenzyme B(12)-dependent diol dehydratase reaction are energetically feasible.
authors.affiliation: Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan. toraya@biotech.okayama-u.ac.jp
authors.forename: T
authors.initials: T
authors.lastname: Toraya
authors.forename: M
authors.initials: M
authors.lastname: Eda
authors.forename: T
authors.initials: T
authors.lastname: Kamachi
authors.forename: K
authors.initials: K
authors.lastname: Yoshizawa
mesh_terms: D000447:Aldehydes / Q000378:metabolism*; D001692:Biological Transport / Q000502:physiology; D003038:Cobamides / Q000378:metabolism*; D019295:Computational Biology; D017665:Hydroxyl Radical / Q000378:metabolism*; D011408:Propanediol Dehydratase / Q000378:metabolism*; D011522:Protons; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D000447:Aldehydes; D003038:Cobamides; D011522:Protons; D017665:Hydroxyl Radical; D011408:Propanediol Dehydratase; C000913:cobamamide