Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 Å Resolution

Overview

Journal J Am Chem Soc

Publisher American Chemical Society

Specialty Chemistry

Date 2021 Oct 20

PMID 34668717

Citations 1

Authors

Agnidipta Ghosh

Courtney N Niland

Sean M Cahill

Nishant M Karadkhelkar

Vern L Schramm

Affiliations

Soon will be listed here.

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.

Citing Articles

Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Adenosine Deaminase.

Balasubramani S, Schwartz S J Phys Chem B. 2022; 126(29):5413-5420.

PMID: 35830574 PMC: 9444332. DOI: 10.1021/acs.jpcb.2c03251.

References

Wang W, Cho H, Kim R, Jancarik J, Yokota H, Nguyen H . Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. J Mol Biol. 2002; 319(2):421-31. DOI: 10.1016/S0022-2836(02)00324-8. View

Ghosh A, Shuman S, Lima C . The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Mol Cell. 2008; 32(4):478-90. PMC: 2645342. DOI: 10.1016/j.molcel.2008.09.021. View

Gohara D, Di Cera E . Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem. 2016; 291(40):20840-20848. PMC: 5076497. DOI: 10.1074/jbc.R116.737833. View

Firestone R, Schramm V . The Transition-State Structure for Human MAT2A from Isotope Effects. J Am Chem Soc. 2017; 139(39):13754-13760. PMC: 5674783. DOI: 10.1021/jacs.7b05803. View

Matte A, Tari L, Delbaere L . How do kinases transfer phosphoryl groups?. Structure. 1998; 6(4):413-9. DOI: 10.1016/s0969-2126(98)00043-4. View

Motojima F, Izumi A, Nuylert A, Zhai Z, Dadashipour M, Shichida S . R-hydroxynitrile lyase from the cyanogenic millipede, Chamberlinius hualienensis-A new entry to the carrier protein family Lipocalines. FEBS J. 2020; 288(5):1679-1695. PMC: 7983990. DOI: 10.1111/febs.15490. View

Bossi R, Negri A, Tedeschi G, Mattevi A . Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis. Biochemistry. 2002; 41(9):3018-24. DOI: 10.1021/bi015939r. View

Ge M, Molt Jr R, Jenkins H, Blackburn G, Jin Y, Antson A . Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor. ACS Catal. 2021; 11(5):2769-2773. PMC: 7944477. DOI: 10.1021/acscatal.0c04500. View

Desiderio C, Cavallaro R, De Rossi A, Danselmi F, Fuso A, Scarpa S . Evaluation of chemical and diastereoisomeric stability of S-adenosylmethionine in aqueous solution by capillary electrophoresis. J Pharm Biomed Anal. 2005; 38(3):449-56. DOI: 10.1016/j.jpba.2005.01.041. View

10.

Graham D, Lowe P, Grime G, Marsh M, Rittinger K, Smerdon S . MgF(3)(-) as a transition state analog of phosphoryl transfer. Chem Biol. 2002; 9(3):375-81. DOI: 10.1016/s1074-5521(02)00112-6. View

11.

Laughlin L, Reed G . The monovalent cation requirement of rabbit muscle pyruvate kinase is eliminated by substitution of lysine for glutamate 117. Arch Biochem Biophys. 1998; 348(2):262-7. DOI: 10.1006/abbi.1997.0448. View

12.

Quinlan C, Kaiser S, Bolanos B, Nowlin D, Grantner R, Karlicek-Bryant S . Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A. Nat Chem Biol. 2017; 13(7):785-792. DOI: 10.1038/nchembio.2384. View

13.

Guillen Schlippe Y, Hedstrom L . A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Arch Biochem Biophys. 2004; 433(1):266-78. DOI: 10.1016/j.abb.2004.09.018. View

14.

Mowat C, Moysey R, Miles C, Leys D, Doherty M, Taylor P . Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase. Biochemistry. 2001; 40(41):12292-8. DOI: 10.1021/bi011360h. View

15.

Maldonado L, Arsene D, Mato J, Lu S . Methionine adenosyltransferases in cancers: Mechanisms of dysregulation and implications for therapy. Exp Biol Med (Maywood). 2017; 243(2):107-117. PMC: 5788143. DOI: 10.1177/1535370217740860. View

16.

Murray B, Antonyuk S, Marina A, Lu S, Mato J, Hasnain S . Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes. Proc Natl Acad Sci U S A. 2016; 113(8):2104-9. PMC: 4776477. DOI: 10.1073/pnas.1510959113. View

17.

Lucic M, Svistunenko D, Wilson M, Chaplin A, Davy B, Ebrahim A . Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe =O Formation. Angew Chem Int Ed Engl. 2020; 59(48):21656-21662. PMC: 7756461. DOI: 10.1002/anie.202008622. View

18.

Schlichting I, Reinstein J . pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog. Nat Struct Biol. 1999; 6(8):721-3. DOI: 10.1038/11485. View

19.

Nagao M, Oyanagi K . Genetic analysis of isolated persistent hypermethioninemia with dominant inheritance. Acta Paediatr Jpn. 1997; 39(5):601-6. DOI: 10.1111/j.1442-200x.1997.tb03648.x. View

20.

Blackburn G, Williams N, Gamblin S, Smerdon S . Comment on "The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction". Science. 2003; 301(5637):1184; author reply 1184. DOI: 10.1126/science.1085796. View