GATM (P50440) review notes

Gene: GATM (HGNC:4175), synonym AGAT. UniProt P50440, "Glycine amidinotransferase, mitochondrial".
EC 2.1.4.1. L-arginine:glycine amidinotransferase / transamidinase.

Core catalytic function

• AGAT catalyzes the committed/rate-limiting step of creatine biosynthesis:
  L-arginine + glycine -> guanidinoacetate (GAA) + L-ornithine (Rhea:13201). GAA is then
  methylated by GAMT to form creatine.
  PMID:9218780
• Catalytic mechanism: ping-pong, catalytic triad Cys-His-Asp; amidino-cysteine covalent
  intermediate at Cys407 (mature numbering). Active site residues His303, Asp254, Asp305, etc.
  PMID:9218780
• New fold ("basket") with 5-fold pseudosymmetry of betabeta-alphabeta modules.
  PMID:9218780
• Purified human kidney enzyme: dimer ~89 kDa, subunits ~44 kDa; Km ~2.5 mM for both arginine
  and glycine (UniProt lists Km 2 uM / 3 uM from later work).
  PMID:3800397
• Mutagenesis + crystallography confirming catalytic residues and mechanism.
  PMID:9266688 (substrate binding and catalysis; mutagenesis of Asp170, Glu233, Asp254, His303, Asp305, Arg322, Ser355, Cys407, Cys410).

Substrate promiscuity (moonlighting / side reactions)

• Human GATM also accepts GABA, beta-alanine and taurine as amidino acceptors, producing
  guanidinobutyrate (GBA), guanidinopropionate (GPA) and taurocyamine (TC) respectively, with
  decreasing preference; glycine remains the main substrate.
  PMID:36543883
  PMID:36543883
  These appear as additional CATALYTIC ACTIVITY entries in UniProt (Rhea 75939/75943/75947).
  This justifies the broader parent MF "amidinotransferase activity" (GO:0015067) as IDA in GOA.

Localization

• Mitochondrial enzyme; canonical isoform 1 has a cleaved N-terminal mitochondrial transit
  peptide (1-43) and localizes to the mitochondrial intermembrane space / inner-membrane
  intermembrane side. IDA placement in intermembrane space (MGI, PMID:9218780).
  UniProt: "Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side.
  Note=Probably attached to the outer side of the inner membrane." Isoform 2 = cytoplasmic.
• GOA also has C:mitochondrion (IDA HPA, HTP) - consistent broader location.
• C:extracellular exosome (HDA, PMID:23533145, prostatic-secretion exosome proteomics) is a
  high-throughput proteomics co-purification; not a site of catalytic function. Over-annotation
  / non-core.

Tissue expression and regulation

• Expressed broadly; highest in kidney; also liver, pancreas (exocrine acinar cells), heart,
  brain, lung, salivary gland, skeletal muscle. HPA group-enriched kidney/liver/pancreas.
  [UniProt TISSUE SPECIFICITY: "highest expression in kidney"]
  PMID:28844881
• Feedback repression of AGAT by creatine (classic; not directly in cached abstracts but a
  well-established regulatory feature). Induction: elevated in failing myocardium (PMID:16820567),
  decreased in IUGR placenta (PMID:16125225). Not GO-annotated; record as biology only.

Disease

• Cerebral creatine deficiency syndrome 3 (CCDS3 / AGAT deficiency, MIM:612718): autosomal
  recessive; intellectual disability/developmental delay, speech delay, severe brain creatine
  depletion; many develop myopathy. Treatable with oral creatine.
  PMID:26490222
  PMID:26490222
  PMID:27233232
  Many loss-of-activity missense variants characterized in PMID:27233232 (IDA glycine
  amidinotransferase activity supported by variant assays).
• Fanconi renotubular syndrome 1 (FRTS1, MIM:134600): autosomal DOMINANT; a distinct,
  gain-of-toxicity mechanism - specific GATM missense variants (e.g. P320S, T336A/I, P341L)
  cause GATM protein AGGREGATION in mitochondria, abnormal/elongated mitochondria, ROS,
  NLRP3 inflammasome activation, proximal tubulopathy and progressive kidney failure
  (PMID:29654216). This is a toxic-aggregation gain of function, NOT loss of catalytic activity.

GO annotation assessment summary

Core:
- MF: glycine amidinotransferase activity (GO:0015068) - EXP/IDA, multiple papers. ACCEPT (core).
- BP: creatine biosynthetic process (GO:0006601) - IDA/IBA. ACCEPT (core).
- CC: mitochondrial intermembrane space (GO:0005758) - IDA. ACCEPT (core location).

Supporting/peripheral:
- amidinotransferase activity (GO:0015067) parent MF - ACCEPT as accurate parent (promiscuous
side activities). Keep.
- mitochondrial inner membrane (GO:0005743) IEA SubCell - ACCEPT/keep (UniProt subcellular).
- mitochondrion (GO:0005739) IDA/HTP - ACCEPT (broader true location).
- cytoplasm (GO:0005737) IEA SubCell - reflects cytoplasmic isoform 2; KEEP_AS_NON_CORE.
- positive regulation of cold-induced thermogenesis (GO:0120162) ISS/IEA from mouse Adipo-Gatm
KO (PMID:28844881) - real mouse phenotype but a tissue/context-specific downstream consequence
of creatine synthesis, not a core human function. KEEP_AS_NON_CORE.
- learning or memory (GO:0007611) IMP CAFA (PMID:26490222) - downstream of brain creatine
depletion; over-reach from a clinical ID phenotype. MARK_AS_OVER_ANNOTATED.
- muscle atrophy (GO:0014889) IMP CAFA (PMID:26490222) - downstream myopathy consequence;
over-annotation. MARK_AS_OVER_ANNOTATED.
- extracellular exosome (GO:0070062) HDA (PMID:23533145) - HTP co-purification; over-annotation.
- protein binding (GO:0005515) IPI x13 (PMID:32814053) - uninformative; this is the
Haenig/neurodegeneration interactome map. MARK_AS_OVER_ANNOTATED (avoid bare protein binding).
- acts_upstream_of_or_within creatine biosynthetic process (GO:0006601) IDA - same as core BP,
weaker qualifier; ACCEPT.

References to cite: 9218780, 3800397, 9266688, 36543883, 27233232, 26490222, 28844881,
23533145, 32814053, 34800366, plus GO_REFs and Reactome already in stub.

QA re-review 2026-07-23 (conservative)

Re-validated GATM-ai-review.yaml: ai-gene-review validate returns "✓ Valid", no
warnings. Audited all 25 annotations plus core_functions. No changes made — the review is
biologically and curatorially sound.

Checks performed:
- protein binding (GO:0005515, IPI, PMID:32814053) is correctly MARK_AS_OVER_ANNOTATED,
not ACCEPT (bare protein binding from an HT interactome; no defined GATM complex). OK.
- All 10 cited PMIDs are cached; every supporting_text verifies as a verbatim
(whitespace-normalized) substring of its cached publication. Labels match GOA terms.
- No action/reason contradictions found; MARK_AS_OVER_ANNOTATED / KEEP_AS_NON_CORE reasons
each give positive justification (learning-or-memory & muscle-atrophy are distal disease
consequences; cold-induced thermogenesis is tissue/context-specific mouse phenotype;
extracellular exosome is HT co-purification).
- core_functions ids are all in the correct GO aspect: GO:0015068 & GO:0015067 (MF),
GO:0006601 (BP, directly_involved_in), GO:0005758 (CC, locations). Core glycine
amidinotransferase activity → creatine biosynthesis in the mitochondrial IMS is captured
as core and not over-generalized; the parent GO:0015067 as a second core_function is
justified by the experimentally documented promiscuity (PMID:36543883).
- Left alone (conservative): all EXP/IDA/IMP experimental annotations retained per their
authors; no REMOVE issued; no existing-annotation term ids rewritten.