S-adenosylmethionine (SAM) cycle — SAM synthesis / transmethylation / SAH hydrolysis (MAT1A/GNMT/AHCY); hypermethioninemias

The S-adenosylmethionine (SAM) arm of the methionine cycle generates and recycles the universal biological methyl donor. Methionine adenosyltransferase (liver MAT1A; extrahepatic MAT2A) condenses L-methionine with ATP to form S-adenosyl-L-methionine (SAM). SAM then donates its methyl group in the many transmethylation reactions of SAM-dependent methyltransferases — of which glycine N-methyltransferase (GNMT), the abundant hepatic enzyme methylating glycine to sarcosine, is the major regulator of the SAM:SAH ratio (cellular methylation capacity) — each producing S-adenosyl-L-homocysteine (SAH). Adenosylhomocysteinase (AHCY, SAH hydrolase) then hydrolyses SAH to L-homocysteine + adenosine, relieving the potent SAH product-inhibition of methyltransferases. Homocysteine is then either remethylated back to methionine (methionine synthase MTR / betaine-homocysteine methyltransferase), closing the cycle, or committed to transsulfuration (CBS) toward cysteine — reactions curated in the homocysteine-metabolism module. Inherited defects of the three SAM-arm enzymes all cause hypermethioninemia: MAT1A (MAT I/III deficiency, usually benign, severe forms with CNS demyelination), GNMT (GNMT deficiency, mild hepatopathy), and AHCY (S-adenosylhomocysteine hydrolase / SAHH deficiency, with elevated SAH/SAM, myopathy, developmental delay and liver disease).

MODULE:sam_cycleDRAFTMetabolic Pathwaymodules/sam_cycle.yaml
L-methionine cycleGO:0033353
GO:0033353
L-methionine cycle
The module is grounded in the GO L-methionine cycle (GO:0033353): SAM synthesis, transmethylation to SAH, and SAH hydrolysis to homocysteine.
file:modules/methionine_cycle.yaml
Methionine (SAM) cycle module (abstract, taxon-neutral)
This is the concrete, human-gene-grounded SAM-arm complement to the taxon-neutral abstract methionine_cycle module (which additionally encodes the SBO/ChEBI regulatory layer, e.g. SAM's opposite regulation of MAT-I vs MAT-III); homocysteine fate (remethylation/transsulfuration) is in the homocysteine_metabolism module.
file:human/MAT1A/MAT1A-ai-review.yaml
MAT1A gene review (human)
The SAM-synthesis step (UniProtKB:Q00266, GO:0004478) matches the completed human MAT1A review.
file:human/GNMT/GNMT-ai-review.yaml
GNMT gene review (human)
The SAM-consuming transmethylation / SAM:SAH-regulating step (UniProtKB:Q14749, GO:0017174) matches the completed human GNMT review.
file:human/AHCY/AHCY-ai-review.yaml
AHCY gene review (human)
The SAH-hydrolysis step (UniProtKB:P23526, GO:0004013) matches the completed human AHCY review.
4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:sam_cycle deep-research report alongside the module YAML.

Leaf nodes lacking representative members

every leaf node grounds to a representative protein.

Template conformance

every declared conforms_to bundle matches its template motif.

Gene-review completeness (3/3 grounded genes reviewed)

3 complete review(s) · 0 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
AHCY P23526
GNMT Q14749
MAT1A Q00266

Details

Context
cytosolGO:0005829
S-adenosylmethionine (SAM) cycle (SAM arm)Metabolic Pathwaysam_cycle
L-methionine cycleGO:0033353
Context
cytosolGO:0005829

The SAM arm of the methionine cycle grounded to the human enzymes MAT1A (UniProtKB:Q00266, GO:0004478, EC 2.5.1.6), GNMT (Q14749, GO:0017174, EC 2.1.1.20) and AHCY (P23526, GO:0004013, EC 3.13.2.1). GO molecular-function terms were taken from the human GOA records; Reactome reaction ids and titles were verified against the local reactome cache. The MAT node uses a PANTHER family selector (PTHR11964) generic over MAT1A (liver) and MAT2A (extrahepatic); GNMT and AHCY use their own family selectors. GNMT is the representative transmethylation step, but SAM is used by hundreds of SAM-dependent methyltransferases (DNA/protein/small-molecule), all producing SAH that AHCY must clear; GNMT's special role is regulatory (buffering the SAM:SAH ratio, inhibited by 5-methyl-THF). This module is the concrete, human-gene-grounded SAM-arm complement to the pre-existing taxon-neutral abstract methionine_cycle module (which encodes the SBO/ChEBI regulatory wiring, e.g. SAM competitively inhibiting MAT-I but allosterically activating MAT-III); the fate of the homocysteine produced here — remethylation to methionine (MTR/BHMT, closing the cycle) or transsulfuration to cysteine (CBS) — is curated in the homocysteine_metabolism module (CTH/MTHFR/MTR/MTRR/MMACHC + CBS). Disorders: all three enzymes cause hypermethioninemia — MAT1A (MAT I/III deficiency), GNMT (GNMT deficiency), AHCY (SAHH deficiency).

Connections

mat_step -> gnmt_step Provides Input For
SAM from MAT is the methyl donor consumed by GNMT (and other methyltransferases).
gnmt_step -> ahcy_step Provides Input For
The SAH produced by transmethylation is hydrolysed by AHCY.
Part 1: SAM synthesis
L-methionine + ATP to S-adenosyl-L-methionine + Pi + PPiReactionmat_step

Annotons

MAT1A/MAT2A: methionine adenosyltransferase
mat_activity
Participant: Family: Methionine adenosyltransferase family (MAT1A/MAT2A)
Family:
Methionine adenosyltransferase family (MAT1A/MAT2A)PANTHER:PTHR11964
Representative Members: MAT1A (human, liver isoform)UniProtKB:Q00266

Function

methionine adenosyltransferase activityGO:0004478
Substrates: L-methionine ATP
Products: S-adenosyl-L-methionine (SAM) phosphate + diphosphate

Locations

cytosolGO:0005829

Synthesises SAM, the universal methyl donor and committed entry to the cycle. MAT1A (liver MAT-I/MAT-III) deficiency -> hypermethioninemia; MAT2A is the extrahepatic isoform. (SAM oppositely regulates MAT-I vs MAT-III — see the abstract methionine_cycle module's regulatory layer.)

Part 2: transmethylation (SAM -> SAH; SAM:SAH-ratio regulation)
S-adenosyl-L-methionine + glycine to S-adenosyl-L-homocysteine + sarcosineReactiongnmt_step

Annotons

GNMT: glycine N-methyltransferase (regulatory SAM-consumer)
gnmt_activity
Participant: Family: Glycine N-methyltransferase family (GNMT)
Family:
Glycine N-methyltransferase family (GNMT)PANTHER:PTHR16458
Representative Members: GNMT (human)UniProtKB:Q14749

Function

glycine N-methyltransferase activityGO:0017174
Substrates: S-adenosyl-L-methionine (SAM) glycine
Products: S-adenosyl-L-homocysteine (SAH) sarcosine (N-methylglycine)

Locations

cytosolGO:0005829

Representative and regulatory SAM-dependent methyltransferase: methylates glycine to sarcosine, disposing of excess SAM to buffer the SAM:SAH ratio (cellular methylation capacity). All SAM-dependent methyltransferases feed SAH to the next step. GNMT deficiency -> hypermethioninemia.

Part 3: SAH hydrolysis (relieves methyltransferase inhibition)
S-adenosyl-L-homocysteine + H2O to L-homocysteine + adenosineReactionahcy_step

Annotons

AHCY: adenosylhomocysteinase (SAH hydrolase)
ahcy_activity
Participant: Family: Adenosylhomocysteinase family (AHCY)
Family:
Adenosylhomocysteinase family (AHCY)PANTHER:PTHR23420
Representative Members: AHCY (human)UniProtKB:P23526

Function

adenosylhomocysteinase activityGO:0004013
Substrates: S-adenosyl-L-homocysteine (SAH) water
Products: L-homocysteine adenosine

Locations

cytosolGO:0005829

Hydrolyses SAH to homocysteine + adenosine, clearing the SAH generated by every methyltransferase (SAH is a potent product-inhibitor). Its product homocysteine re-enters remethylation (MTR) or transsulfuration (CBS). SAHH deficiency -> hypermethioninemia with elevated SAH/SAM.