7RXV

Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine, Malonate (MLA) and MgF3

Summary for 7RXV

• Entry DOI: 10.2210/pdb7rxv/pdb
• Related: 7L1A 7RXW 7RXX
• Descriptor: S-adenosylmethionine synthase isoform type-2, 5'-DEOXY-5'-METHYLTHIOADENOSINE, ALANINE, ... (10 entities in total)
• Functional Keywords: sam synthetase, enzyme mechanism, inhibitor, transition state, transferase-inhibitor complex, transferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 47052.62

Authors

Fedorov, E.,Niland, C.N.,Schramm, V.L.,Ghosh, A. (deposition date: 2021-08-23, release date: 2021-11-03, Last modification date: 2023-10-18)

Primary citation

Ghosh, A.,Niland, C.N.,Cahill, S.M.,Karadkhelkar, N.M.,Schramm, V.L.
Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 angstrom Resolution.
J.Am.Chem.Soc., 143:18325-18330, 2021

PubMed Abstract: Human methionine adenosyltransferase MAT2A provides -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 Mg, Al, and F. MgF is trapped as a PO mimic in a structure with malonate filling the pyrophosphate site. NMR demonstrates that MgF and AlF are bound by MAT2A as mimics of the departing phosphoryl group. Crystallographic analysis reveals a planar MgF acting to mimic a phosphoryl (PO) leaving group. The modeled transition state with PO 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.

PubMed: 34668717
DOI: 10.1021/jacs.1c09328

Experimental method

X-RAY DIFFRACTION (1.07 Å)