(436d) Mechanism of a Hotdog Fold Thioesterase-Catalyzed Reaction Proposed by QM/MM Metadynamics Simulation

Members of a number of thioesterase and hydroxyacyl dehydratase families have HotDog structural folds, while members of other families have other folds. These enzymes are mainly involved in fatty acid synthesis, but they catalyze other reactions as well. We have tabulated the primary and tertiary structures of all these enzymes as part of the ThYme database of enzymes involved in fatty acid synthesis and related reactions. To date many putative mechanisms have been proposed, none conclusively, for HotDog fold thioesterases based on existing crystal structures. We employ QM/MM metadynamics molecular simulation techniques to explore putative mechanisms of this type of thioesterase. An acid-base two-step mechanism is found where an aspartate residue orients and activates a water nucleophile that attacks the thioester carbon atom. A serine residue donates a proton to break the thioester bond, and it receives a proton from a histidine residue. The transition states and energy barriers are elucidated.