Computational investigation of the enzymatic mechanisms of phosphothreonine lyase

SpvC, a virulence effector injected through type III secretion system by some Salmonella serovars, belongs to the newly discovered enzyme family, phosphothreonine lyase. Previous experimental studies have demonstrated that SpvC irreversibly inactivates mitogen-activated protein kinases by removing the phosphate group from phosphothreonine-containing substrate through a β-elimination mechanism, and results in a β-methyldehydroalanine product. Interestingly, further biochemical investigations also indicated a secondary reaction occurring other than elimination, where a covalently bound complex is formed. Here, we employed molecular dynamics simulations and quantum mechanics calculations to gain insights on the microscopic details of such novel reaction mechanisms. Our theoretical results are consistent with the experimental observations, in which the critical stages of SpvC catalyzed reaction are revealed and the roles of several important binding site residues are reconciled. The deprotonation and precise position of the catalytic base K136 are facilitated by the formation of the fully desolvated active site upon substrate binding. The abstraction of the alpha hydrogen by K136 and the elimination of the phosphate group occur nearly simultaneously, promoted by the proton donation from the catalytic acid H106, and thus strongly supports an E2-like mechanism. K104, which is not directly involved in the enzymatic reaction, stabilizes the transition state and facilitates the reaction to occur. Remarkably, the subsequent deprotonation of K136 happens to be a natural sequel of the primary elimination reaction, restores its nucleophile capacity to attack the double bond containing elimination product, and leads to a covalently bound complex via a Michael-addition mechanism. The reaction mechanism used by phosphothreonine lyases might serve as a method of programmed regulation to fine tune their enzymatic activity.