title: Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase.
abstract: A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.
authors.affiliation: Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kamachi
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Toraya
authors.forename: Kazunari
authors.initials: K
authors.lastname: Yoshizawa
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D003038:Cobamides / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D004252:DNA Mutational Analysis / Q000379:methods; D004789:Enzyme Activation; D006859:Hydrogen / Q000737:chemistry; D009154:Mutation; D011408:Propanediol Dehydratase / Q000737:chemistry* / Q000235:genetics*; D019946:Propylene Glycol / Q000737:chemistry; D011409:Propylene Glycols / Q000378:metabolism; D011487:Protein Conformation; D014805:Vitamin B 12 / Q000096:biosynthesis*
chemical_list: D003038:Cobamides; D011409:Propylene Glycols; D019946:Propylene Glycol; D006859:Hydrogen; D011408:Propanediol Dehydratase; C000913:cobamamide; D014805:Vitamin B 12