S-Adenosylmethionine synthetase enzyme

S-Adenosylmethionine synthetase (EC 2.5.1.6), also known as methionine adenosyltransferase (MAT), is an enzyme that creates S-adenosylmethionine (also known as AdoMet, SAM or SAMe) by reacting methionine (a non-polar amino acid) and ATP (the basic currency of energy).

Function

AdoMet is a methyl donor for transmethylation. It gives away its methyl group and is also the propylamino donor in polyamine biosynthesis. S-adenosylmethionine synthesis can be considered the rate-limiting step of the methionine cycle.

As a methyl donor SAM allows DNA methylation. Once DNA is methylated, it switches the genes off and therefore, S-adenosylmethionine can be considered to control gene expression.

SAM is also involved in gene transcription, cell proliferation, and production of secondary metabolites. Hence SAM synthetase is fast becoming a drug target, in particular for the following diseases: depression, dementia, vacuolar myelopathy, liver injury, migraine, osteoarthritis, and as a potential cancer chemopreventive agent.

This article discusses the protein domains that make up the SAM synthetase enzyme and how these domains contribute to its function. More specifically, this article explores the shared pseudo-3-fold symmetry that makes the domains well-adapted to their functions.

This enzyme catalyses the following chemical reaction

ATP + L-methionine + H₂O

\rightleftharpoons

phosphate + diphosphate + S-adenosyl-L-methionine

Conserved motifs in the 3'UTR of MAT2A mRNA

A computational comparative analysis of vertebrate genome sequences have identified a cluster of 6 conserved hairpin motifs in the 3'UTR of the MAT2A messenger RNA (mRNA) transcript. The predicted hairpins (named A-F) have strong evolutionary conservation and 3 of the predicted RNA structures (hairpins A, C and D) have been confirmed by in-line probing analysis. No structural changes were observed for any of the hairpins in the presence of metabolites SAM, S-adenosylhomocysteine or L-Methionine. They are proposed to be involved in transcript stability and their functionality is currently under investigation.

Protein overview

The S-adenosylmethionine synthetase enzyme is found in almost every organism bar parasites which obtain AdoMet from their host. Isoenzymes are found in bacteria, budding yeast and even in mammalian mitochondria. Most MATs are homo-oligomers and the majority are tetramers. The monomers are organised into three domains formed by nonconsecutive stretches of the sequence, and the subunits interact through a large flat hydrophobic surface to form the dimers.

S-adenosylmethionine synthetase N terminal domain

S-adenosylmethionine synthetase with ADP

Identifiers

Symbol

S-AdoMet_synt_N

1mxa / SCOPe / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

In molecular biology the protein domain S-adenosylmethionine synthetase N terminal domain is found at the N-terminal of the enzyme.

N terminal domain function

The N terminal domain is well conserved across different species. This may be due to its important function in substrate and cation binding. The residues involved in methionine binding are found in the N-terminal domain.

N terminal domain structure

The N terminal region contains two alpha helices and four beta strands.

S-adenosylmethionine synthetase Central domain

S-adenosylmethionine synthetase with ADP

Identifiers

Symbol

S-AdoMet_synt_M

1mxa / SCOPe / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Central terminal domain function

The precise function of the central domain has not been fully elucidated, but it is thought to be important in aiding catalysis.

Central domain structure

The central region contains two alpha helices and four beta strands.

S-adenosylmethionine synthetase, C terminal domain

S-adenosylmethionine synthetase, C-terminal domain

Methionine adenosyltransferase in a complex ADP and l-methionine.

Identifiers

Symbol

S-AdoMet_synt_C

1mxa / SCOPe / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

In molecular biology, the protein domain S-adenosylmethionine synthetase, C-terminal domain refers to the C terminus of the S-adenosylmethionine synthetase

C terminal domain function

The function of the C-terminal domain has been experimentally determined as being important for cytoplasmic localisation. The residues are scattered along the C-terminal domain sequence however once the protein folds, they position themselves closely together.

C terminal domain structure

The C-terminal domains contains two alpha-helices and four beta-strands.

References

Horikawa S, Sasuga J, Shimizu K, Ozasa H, Tsukada K (August 1990). "Molecular cloning and nucleotide sequence of cDNA encoding the rat kidney S-adenosylmethionine synthetase". J. Biol. Chem. 265 (23): 13683–6. doi:10.1016/S0021-9258(18)77403-6. PMID 1696256.
Markham GD, Pajares MA (2009). "Structure-function relationships in methionine adenosyltransferases". Cell Mol Life Sci. 66 (4): 636–48. doi:10.1007/s00018-008-8516-1. PMC 2643306. PMID 18953685.
^ Reytor E, Pérez-Miguelsanz J, Alvarez L, Pérez-Sala D, Pajares MA (2009). "Conformational signals in the C-terminal domain of methionine adenosyltransferase I/III determine its nucleocytoplasmic distribution". FASEB J. 23 (10): 3347–60. doi:10.1096/fj.09-130187. hdl:10261/55151. PMID 19497982. S2CID 25548921.
Yoon S, Lee W, Kim M, Kim TD, Ryu Y (2012). "Structural and functional characterization of S-adenosylmethionine (SAM) synthetase from Pichia ciferrii". Bioprocess Biosyst Eng. 35 (1–2): 173–81. doi:10.1007/s00449-011-0640-x. PMID 21989639. S2CID 40318843.
Kamarthapu V, Rao KV, Srinivas PN, Reddy GB, Reddy VD (2008). "Structural and kinetic properties of Bacillus subtilis S-adenosylmethionine synthetase expressed in Escherichia coli". Biochim Biophys Acta. 1784 (12): 1949–58. doi:10.1016/j.bbapap.2008.06.006. PMID 18634909.
^ Takusagawa F, Kamitori S, Misaki S, Markham GD (1996). "Crystal structure of S-adenosylmethionine synthetase". J Biol Chem. 271 (1): 136–47. doi:10.1074/jbc.271.1.136. PMID 8550549.
^ Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS (November 2011). "New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes". Genome Res. 21 (11): 1929–43. doi:10.1101/gr.112516.110. PMC 3205577. PMID 21994249.
^ Garrido F, Estrela S, Alves C, Sánchez-Pérez GF, Sillero A, Pajares MA (2011). "Refolding and characterization of methionine adenosyltransferase from Euglena gracilis". Protein Expr Purif. 79 (1): 128–36. doi:10.1016/j.pep.2011.05.004. hdl:10261/55441. PMID 21605677.

External links

Methionine+adenosyltransferase at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
EC 2.5.1.6

Metabolism: Protein metabolism, synthesis and catabolism enzymes

Essential amino acids are in Capitals

K→acetyl-CoA

LYSINE→	Saccharopine dehydrogenase Glutaryl-CoA dehydrogenase
LEUCINE→	3-Hydroxybutyryl-CoA dehydrogenase Branched-chain amino acid aminotransferase Branched-chain alpha-keto acid dehydrogenase complex Enoyl-CoA hydratase HMG-CoA lyase HMG-CoA reductase Isovaleryl coenzyme A dehydrogenase α-Ketoisocaproate dioxygenase Leucine 2,3-aminomutase Methylcrotonyl-CoA carboxylase Methylglutaconyl-CoA hydratase (See Template:Leucine metabolism in humans – this diagram does not include the pathway for β-leucine synthesis via leucine 2,3-aminomutase)
TRYPTOPHAN→	Indoleamine 2,3-dioxygenase/Tryptophan 2,3-dioxygenase Arylformamidase Kynureninase 3-hydroxyanthranilate oxidase Aminocarboxymuconate-semialdehyde decarboxylase Aminomuconate-semialdehyde dehydrogenase
PHENYLALANINE→tyrosine→	(see below)

G→pyruvate
→citrate

glycine→serine→	Serine hydroxymethyltransferase Serine dehydratase glycine→creatine: Guanidinoacetate N-methyltransferase Creatine kinase
alanine→	Alanine transaminase
cysteine→	D-cysteine desulfhydrase
threonine→	L-threonine dehydrogenase

G→glutamate→
α-ketoglutarate

HISTIDINE→	Histidine ammonia-lyase Urocanate hydratase Formiminotransferase cyclodeaminase
proline→	Proline oxidase Pyrroline-5-carboxylate reductase 1-Pyrroline-5-carboxylate dehydrogenase/ALDH4A1 PYCR1
arginine→	Ornithine aminotransferase Ornithine decarboxylase Agmatinase
→alpha-ketoglutarate→TCA	Glutamate dehydrogenase
Other	cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase Glutathione synthetase Gamma-glutamyl transpeptidase glutamate→glutamine: Glutamine synthetase Glutaminase

G→propionyl-CoA→
succinyl-CoA

VALINE→	Branched-chain amino acid aminotransferase Branched-chain alpha-keto acid dehydrogenase complex Enoyl-CoA hydratase 3-hydroxyisobutyryl-CoA hydrolase 3-hydroxyisobutyrate dehydrogenase Methylmalonate semialdehyde dehydrogenase
ISOLEUCINE→	Branched-chain amino acid aminotransferase Branched-chain alpha-keto acid dehydrogenase complex 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
METHIONINE→	generation of homocysteine: Methionine adenosyltransferase Adenosylhomocysteinase regeneration of methionine: Methionine synthase/Homocysteine methyltransferase Betaine-homocysteine methyltransferase conversion to cysteine: Cystathionine beta synthase Cystathionine gamma-lyase
THREONINE→	Threonine aldolase
→succinyl-CoA→TCA	Propionyl-CoA carboxylase Methylmalonyl CoA epimerase Methylmalonyl-CoA mutase

G→fumarate

PHENYLALANINE→tyrosine→

tyrosine→melanin: Tyrosinase

G→oxaloacetate

asparagine→aspartate→	Asparaginase/Asparagine synthetase Aspartate transaminase

v t e Transferases: alkyl and aryl (EC 2.5)
2.5.1	Dimethylallyltranstransferase Thiaminase I Methionine adenosyltransferase Riboflavin synthase Dihydropteroate synthase Spermidine synthase Glutathione S-transferase Farnesyl-diphosphate farnesyltransferase Spermine synthase Alkylglycerone phosphate synthase Farnesyltransferase Geranylgeranyltransferase type 1 Porphobilinogen deaminase

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Diffusion-limited enzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

This article incorporates text from the public domain Pfam and InterPro: IPR022630 Categories: