title: QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics.
abstract: The conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA catalyzed by 4-chlorobenzoyl-CoA dehalogenase is investigated using combined QM/MM approaches. The calculated potential of mean force at the PM3/CHARMM level supports the proposed nucleophilic aromatic substitution mechanism. In particular, a Meisenheimer intermediate was found, stabilized by hydrogen bonds between the benzoyl carbonyl of the ligand and two backbone amide NHs at positions 64 and 114. Mutation of Gly113 to Ala significantly increases the barrier by disrupting the hydrogen bond with the Gly114 backbone. The formation of the Meisenheimer complex is accompanied by significant charge redistribution and structural changes in the substrate benzoyl moiety, consistent with experimental observations. Theoretical results suggest that the reaction rate is limited by the formation of the Meisenheimer complex, rather than by its decomposition. A kinetic model based on the calculated free energy profile is found to be consistent with the experimental time course data.
authors.affiliation: Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA.
authors.forename: Dingguo
authors.initials: D
authors.lastname: Xu
authors.forename: Yanseng
authors.initials: Y
authors.lastname: Wei
authors.forename: Jingbo
authors.initials: J
authors.lastname: Wu
authors.forename: Debra
authors.initials: D
authors.lastname: Dunaway-Mariano
authors.forename: Hua
authors.initials: H
authors.lastname: Guo
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
authors.forename: Jiali
authors.initials: J
authors.lastname: Gao
mesh_terms: D000214:Acyl Coenzyme A / Q000737:chemistry* / Q000378:metabolism*; D002384:Catalysis; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D006867:Hydrolases / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D000214:Acyl Coenzyme A; C084334:4-chlorobenzoyl coenzyme A; D006867:Hydrolases; C084333:4-chlorobenzoyl coenzyme A dehalogenase