Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 Å Resolution

Human methionine adenosyltransferase MAT2A provides S-adenosyl-l-methionine (AdoMet) for methyl-transfer reactions. Epigenetic methylations influence expression patterns in development and in cancer. Transition-state analysis and kinetic studies have described the mechanism of AdoMet and triphosphate formation at the catalytic site. Hydrolysis of triphosphate to pyrophosphate and phosphate by MAT2A is required for product release and proceeds through a second chemical transition state. Crystal structures of MAT2A with analogues of AdoMet and pyrophosphate were obtained in the presence of Mg²⁺, Al³⁺, and F^-. MgF₃^- is trapped as a PO₃^- mimic in a structure with malonate filling the pyrophosphate site. NMR demonstrates that MgF₃^- and AlF₃⁰ are bound by MAT2A as mimics of the departing phosphoryl group. Crystallographic analysis reveals a planar MgF₃^- acting to mimic a phosphoryl (PO₃^-) leaving group. The modeled transition state with PO₃^- has the phosphorus atom sandwiched symmetrically and equidistant (approximately 2 Å) between a pyrophosphate oxygen and the water nucleophile. A catalytic site arginine directs the nucleophilic water to the phosphoryl leaving group. The catalytic geometry of the transition-state reconstruction predicts a loose transition state with characteristics of symmetric nucleophilic displacement.