title: Molecular mechanism of a hotdog-fold acyl-CoA thioesterase.
abstract: Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and metabolism, as well as polyketide biosynthesis. The reaction molecular mechanism of most hotdog-fold acyl-CoA thioesterases remains unknown, but several hypotheses have been put forward in structural and biochemical investigations. The reaction of a human thioesterase (hTHEM2), representing a thioesterase family with a hotdog fold where a coenzyme A moiety is cleaved, was simulated by quantum mechanics/molecular mechanics metadynamics techniques to elucidate atomic and electronic details of its mechanism, its transition-state conformation, and the free energy landscape of the process. A single-displacement acid-base-like mechanism, in which a nucleophilic water molecule is activated by an aspartate residue acting as a base, was found, confirming previous experimental proposals. The results provide unambiguous evidence of the formation of a tetrahedral-like transition state. They also explain the roles of other conserved active-site residues during the reaction, especially that of a nearby histidine/serine pair that protonates the thioester sulfur atom, the participation of which could not be elucidated from mutation analyses alone.
authors.affiliation: Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230 (USA).
authors.forename: David C
authors.initials: DC
authors.lastname: Cantu
authors.forename: Albert
authors.initials: A
authors.lastname: Ardèvol
authors.forename: Carme
authors.initials: C
authors.lastname: Rovira
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Reilly
mesh_terms: D000214:Acyl Coenzyme A / Q000378:metabolism; D020134:Catalytic Domain; D006801:Humans; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011522:Protons; D013869:Thiolester Hydrolases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000214:Acyl Coenzyme A; D011522:Protons; C044181:hexanoyl-coenzyme A; C514740:ACOT13 protein, human; D013869:Thiolester Hydrolases
keywords: Car-Parrinello; metadynamics; molecular dynamics; nucleophilic attack; protonation