Methionine adenosyltransferase

 

In biological systems, methyl groups are transferred from a small number of donors to a large number of acceptors. S-adenosylmethionine (AdoMet) is the most widespread of these donors, and is synthesised solely by the action of AdoMet synthase.

The catalytic site of this enzyme, found in a cleft between two subunits, conducts an unusual reaction pathway where a triphosphate chain is cleaved from ATP as AdoMet is formed and the triphosphate is hydrolysed to diphosphate and phosphate before the product is released. There are three similar domains arranged around a pseudo-threefold symmetry axis.

 

Reference Protein and Structure

Sequence
P31153 UniProt (2.5.1.6) IPR002133 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
5a1i - The structure of Humab MAT2A in complex with SAMe, Adenosine, Methionine and PPNP. (1.09 Å) PDBe PDBsum 5a1i
Catalytic CATH Domains
3.30.300.10 CATHdb (see all for 5a1i)
Cofactors
Magnesium(2+) (2), Potassium(1+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:2.5.1.6)

ATP(4-)
CHEBI:30616ChEBI
+
water
CHEBI:15377ChEBI
+
L-methionine zwitterion
CHEBI:57844ChEBI
→
S-adenosyl-L-methionine zwitterion
CHEBI:59789ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: S-adenosyl-L-methionine synthetase, S-adenosylmethionine synthase, S-adenosylmethionine synthetase, ATP-methionine adenosyltransferase, AdoMet synthetase, Adenosylmethionine synthetase, Methionine S-adenosyltransferase, Methionine-activating enzyme,

Enzyme Mechanism

Introduction

The reaction involves the cleavage of the triphosphate chain from ATP, in forming the product, and hydrolysis of the PPPi moiety to PPi and Pi before the AdoMet product is released.

Mechanistic studies have shown the AdoMet forming reaction to follow an SN2 mechanism, with the S atom of methionine attacking the C5 atom of ATP directly. His29 acts as a general acid, activated by the surrounding basic backbone amide groups, towards the O5' as the C5'-O5' bond cleaves. Simultaneously, the methionine sulphur attacks the developing cation. This reaction is followed by the hydrolysis of triphosphate to phosphate and pyrophosphate, providing energy for the removal of the reaction product from the active site.

The reaction requires divalent metal cations for activity, two binding sites have been identified both by structural information and EPR studies.

Catalytic Residues Roles

UniProt PDB* (5a1i)
His29 His29A Acts as a general acid/base by abstratcing donating a proton to the triphosphate leaving group. It returns to its initial protonation step through the abstraction of a proton from water. proton acceptor, proton donor
Asp31 Asp31A Binds Mg(II) ion metal ligand, electrostatic stabiliser
Lys32 (main-N), Asp31 Lys32A (main-N), Asp31A main chain amides help stabilise the anionic His29 electrostatic stabiliser
Glu57, Asp258, Ala259 (main-C) Glu57A, Asp258A, Ala259A (main-C) Binds K(I) ion. metal ligand
Lys181, Arg264, Lys265, Lys285 Lys181A, Arg264A, Lys265A, Lys285A Stabilises the negative charges on the triphosphate moiety. electrostatic stabiliser
Phe250, Glu70 Phe250A, Glu70A Guides the steric outcome of the reaction. steric role
Lys289, Asp291 Lys289A, Asp291A Helps bind and stabilise the intermediates. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, overall reactant used, dephosphorylation, overall product formed, intermediate formation, proton transfer, rate-determining step, hydrolysis, intermediate collapse, intermediate terminated, native state of enzyme regenerated

References

  1. Murray B et al. (2016), Proc Natl Acad Sci U S A, 113, 2104-2109. Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes. DOI:10.1073/pnas.1510959113. PMID:26858410.
  2. Liu Y et al. (2016), Frontiers of Chemical Science and Engineering, 10, 238-244. Functional characterization of a thermostable methionine adenosyltransferase from Thermus thermophilus HB27. DOI:10.1007/s11705-016-1566-2.
  3. Markham GD et al. (2009), Arch Biochem Biophys, 492, 82-92. An investigation of the catalytic mechanism of S-adenosylmethionine synthetase by QM/MM calculations. DOI:10.1016/j.abb.2009.08.010. PMID:19699176.
  4. Komoto J et al. (2004), Biochemistry, 43, 1821-1831. Crystal Structure of theS-Adenosylmethionine Synthetase Ternary Complex:  A Novel Catalytic Mechanism ofS-Adenosylmethionine Synthesis from ATP and Met†,‡. DOI:10.1021/bi035611t. PMID:14967023.
  5. Taylor JC et al. (1999), J Biol Chem, 274, 32909-32914. The Bifunctional Active Site of S-Adenosylmethionine Synthetase: ROLES OF THE ACTIVE SITE ASPARTATES. DOI:10.1074/jbc.274.46.32909. PMID:10551856.
  6. Takusagawa F et al. (1996), Biochemistry, 35, 2586-2596. Structure and Function ofS-Adenosylmethionine Synthetase:  Crystal Structures ofS-Adenosylmethionine Synthetase with ADP, BrADP, and PPiat 2.8 Å Resolution†,‡. DOI:10.1021/bi952604z. PMID:8611562.
  7. Takusagawa F et al. (1996), J Biol Chem, 271, 136-147. Crystal structure of S-adenosylmethionine synthetase. DOI:10.2210/pdb1xra/pdb. PMID:8550549.
  8. Fu Z et al. (1996), J Biomol Struct Dyn, 13, 727-739. Flexible Loop in the Structure of S-Adenosylmethionine Synthetase Crystallized in the Tetragonal Modification. DOI:10.1080/07391102.1996.10508887. PMID:8723769.

Step 1. The C5'-O5' bond of ATP dissociates, the phosphate of the leaving group deprotonates His29, the anionic histidine is stabilised by the main chain amides of Lys32 and Asp31. A simultaneous change in the ribose ring conformation from C4'-exo to C3'-endo occurs, and the SD of methionine makes a nucleophilic attack on the C5' to form S-adenosylmethionine. His29 deprotonates the leaving group in an overall nucleophilic substitution reaction.

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Catalytic Residues Roles

Residue Roles
Glu57A metal ligand
Ala259A (main-C) metal ligand
Asp258A metal ligand, electrostatic stabiliser, steric role
Glu70A electrostatic stabiliser, steric role
Lys289A electrostatic stabiliser
Phe250A steric role
Lys285A electrostatic stabiliser
Lys265A electrostatic stabiliser
Lys181A electrostatic stabiliser
Arg264A electrostatic stabiliser
Asp31A metal ligand, electrostatic stabiliser
Lys32A (main-N) electrostatic stabiliser
Asp291A electrostatic stabiliser
His29A proton donor

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, dephosphorylation, overall product formed, intermediate formation, proton transfer, rate-determining step

Step 2. Triphosphate hydrolyses to form diphosphate and monophosphate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp31A electrostatic stabiliser
Lys32A (main-N) electrostatic stabiliser
Lys181A electrostatic stabiliser
Lys289A electrostatic stabiliser
Lys285A electrostatic stabiliser
Lys265A electrostatic stabiliser
Arg264A electrostatic stabiliser
Glu57A metal ligand
Ala259A (main-C) metal ligand
Asp258A metal ligand
Asp31A metal ligand
Asp291A electrostatic stabiliser
His29A proton acceptor

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall reactant used, hydrolysis, intermediate collapse, overall product formed, intermediate terminated, dephosphorylation, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. The C5'-O5' bond of ATP dissociates, the phosphate of the leaving group deprotonates His29, the anionic histidine is stabilised by the main chain amides of Lys32 and Asp31. A simultaneous change in the ribose ring conformation from C4'-exo to C3'-endo occurs, and the SD of methionine makes a nucleophilic attack on the C5' to form S-adenosylmethionine. His29 deprotonates the leaving group in an overall nucleophilic substitution reaction.

Step 2. Triphosphate hydrolyses to form diphosphate and monophosphate.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Sophie T. Williams, James W. Murray, Craig Porter, Katherine Ferris