GATM (AGAT; L-arginine:glycine amidinotransferase, EC 2.1.4.1) is the first and rate-limiting enzyme of creatine biosynthesis. It catalyzes the transfer of the amidino group of L-arginine onto the amino group of glycine to yield guanidinoacetate and L-ornithine; guanidinoacetate is subsequently methylated by GAMT to form creatine. The mature enzyme is a homodimer with a five-fold pseudosymmetric basket fold and a buried active site that uses a Cys-His-Asp catalytic triad and an amidino-cysteine covalent intermediate (ping-pong mechanism). Although glycine is the strongly preferred acceptor, the enzyme is promiscuous and can also amidinate GABA, beta-alanine and taurine to produce guanidinobutyrate, guanidinopropionate and taurocyamine. The canonical mitochondrial isoform carries a cleavable N-terminal transit peptide and localizes to the mitochondrial intermembrane space, attached to the intermembrane side of the inner membrane; an alternatively spliced isoform is cytoplasmic. GATM is expressed broadly with highest levels in kidney, and is also abundant in liver, pancreas (exocrine acinar cells), heart, brain and skeletal muscle, supplying creatine to high-energy-demand tissues for ATP buffering. Loss-of-function variants cause autosomal-recessive cerebral creatine deficiency syndrome 3 (AGAT deficiency), a treatable disorder of brain creatine depletion presenting with intellectual disability, speech delay and myopathy, whereas distinct dominant aggregation-prone variants cause Fanconi renotubular syndrome 1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005758
mitochondrial intermembrane space
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) propagation of the mitochondrial intermembrane space localization, consistent with the experimentally determined human localization and the conserved mitochondrial targeting of the amidinotransferase family.
Reason: The canonical isoform is a mitochondrial enzyme localized to the intermembrane space (attached to the intermembrane side of the inner membrane). This is the correct core location and is independently supported by an IDA annotation (PMID:9218780).
|
|
GO:0006601
creatine biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) propagation of involvement in creatine biosynthesis, the canonical and best-established biological role of GATM/AGAT.
Reason: GATM catalyzes the committed, rate-limiting step of creatine biosynthesis (formation of guanidinoacetate). This is a core biological process for the gene.
Supporting Evidence:
PMID:9218780
L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine.
|
|
GO:0015068
glycine amidinotransferase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) propagation of glycine amidinotransferase activity, the defining catalytic activity of GATM.
Reason: This is the core molecular function of GATM, directly demonstrated experimentally in human enzyme (EXP/IDA in multiple references) and conserved across the family.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: Cytoplasmic location derived by UniProt subcellular-location mapping, reflecting the cytoplasmic splice isoform (P50440-2) rather than the canonical mitochondrial enzyme.
Reason: UniProt annotates isoform 2 as cytoplasmic, so this term is not wrong, but the core, catalytically characterized form is the mitochondrial intermembrane-space enzyme. Retain as non-core (isoform-specific) localization.
|
|
GO:0005743
mitochondrial inner membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Mitochondrial inner membrane location from UniProt subcellular-location mapping; the enzyme is a peripheral membrane protein on the intermembrane side of the inner membrane.
Reason: Consistent with the UniProt subcellular location (Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side). The functionally most specific term is mitochondrial intermembrane space; this inner-membrane term is an accurate, slightly different facet of the same location.
|
|
GO:0015067
amidinotransferase activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Parent amidinotransferase activity assigned via InterPro2GO from the amidinotransferase family signature.
Reason: Accurate but less specific than glycine amidinotransferase activity. The broader parent is genuinely appropriate because GATM is promiscuous, also amidinating GABA, beta-alanine and taurine. Retained; the specific GO:0015068 term is the primary core function.
|
|
GO:0015068
glycine amidinotransferase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Glycine amidinotransferase activity inferred electronically from Rhea/EC:2.1.4.1 mapping.
Reason: Correct core molecular function, redundant with the experimental annotations for the same term but valid as an automated EC/Rhea-based assignment.
|
|
GO:0005515
protein binding
|
IPI
PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... |
MARK AS OVER ANNOTATED |
Summary: Generic protein binding annotations from a large-scale neurodegenerative-disease interactome/Y2H screen, covering 13 prey partners.
Reason: Protein binding (GO:0005515) is uninformative and does not capture a defined molecular function. These IPI calls come from a high-throughput interactome map and none of the listed partners corresponds to an established, functionally meaningful GATM complex. Per curation guidelines, bare protein binding should not be carried as a core function.
|
|
GO:0120162
positive regulation of cold-induced thermogenesis
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Positive regulation of cold-induced thermogenesis transferred electronically from the mouse ortholog (Gatm), based on adipocyte-specific knockout phenotypes.
Reason: This reflects a genuine but tissue- and context-specific downstream consequence of adipocyte creatine synthesis demonstrated in mouse (fat-specific Gatm knockout impairs diet-induced/adaptive thermogenesis). It is a physiological role of creatine energetics, not a core molecular/biological function of the human enzyme; retain as non-core.
Supporting Evidence:
PMID:28844881
we have inactivated the first and rate-limiting enzyme of creatine biosynthesis, glycine amidinotransferase (GATM), selectively in fat (Adipo-Gatm KO).
|
|
GO:0006601
creatine biosynthetic process
|
IEA
GO_REF:0000041 |
ACCEPT |
Summary: Creatine biosynthetic process inferred electronically from UniPathway mapping.
Reason: Correct core biological process, consistent with the curated and experimental annotations for the same term.
|
|
GO:0005739
mitochondrion
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: Mitochondrial localization from immunofluorescence (HPA), a broader but accurate compartment assignment.
Reason: Directly observed mitochondrial localization. Less specific than mitochondrial intermembrane space but correct; retained as supporting localization evidence.
|
|
GO:0005758
mitochondrial intermembrane space
|
TAS
Reactome:R-HSA-71275 |
ACCEPT |
Summary: Mitochondrial intermembrane space localization asserted by Reactome (creatine metabolism pathway).
Reason: Same core location as the IDA and IBA annotations; traceable author statement consistent with the experimentally established localization.
|
|
GO:0015068
glycine amidinotransferase activity
|
EXP
PMID:36543883 Guanidino acid hydrolysis by the human enzyme annotated as a... |
ACCEPT |
Summary: Experimental demonstration that purified recombinant human GATM amidinates glycine (and, less efficiently, GABA/beta-alanine/taurine), with glycine as the preferred acceptor.
Reason: Direct experimental support for the defining catalytic activity; this is the core molecular function of the gene.
Supporting Evidence:
PMID:36543883
human GATM had the highest activity with glycine, but also GABA, β-alanine and taurine were accepted as substrates with decreasing preference
|
|
GO:0015068
glycine amidinotransferase activity
|
EXP
PMID:3800397 The purification and characterization of human kidney L-argi... |
ACCEPT |
Summary: Purification and biochemical characterization of human kidney transamidinase establishing its amidinotransferase activity and dimeric structure.
Reason: Classic experimental support for the core catalytic activity of human AGAT.
Supporting Evidence:
PMID:3800397
Human kidney transamidinase is a dimer with a molecular mass of 89,000 Da and subunit masses of 44,000 Da. The Km for arginine and glycine were both 2.5 mM
|
|
GO:0015068
glycine amidinotransferase activity
|
EXP
PMID:9266688 Substrate binding and catalysis by L-arginine:glycine amidin... |
ACCEPT |
Summary: Mutagenesis and crystallographic study confirming the catalytic activity and active-site residues of human AGAT.
Reason: Direct experimental and structural support for the core glycine amidinotransferase activity, including identification of catalytic residues whose mutation abolishes activity.
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: Mitochondrial localization from a high-throughput high-confidence human mitochondrial proteome study.
Reason: Consistent with the established mitochondrial localization; high-throughput evidence corroborating the more specific intermembrane-space assignment.
|
|
GO:0015067
amidinotransferase activity
|
IDA
PMID:36543883 Guanidino acid hydrolysis by the human enzyme annotated as a... |
ACCEPT |
Summary: Direct experimental demonstration of broader amidinotransferase activity, since human GATM amidinates multiple acceptors (glycine, GABA, beta-alanine, taurine).
Reason: The parent term is justified by the experimentally observed substrate promiscuity. The most specific core activity is glycine amidinotransferase activity (GO:0015068); this broader term legitimately captures the side reactions.
Supporting Evidence:
PMID:36543883
human GATM had the highest activity with glycine, but also GABA, β-alanine and taurine were accepted as substrates with decreasing preference
|
|
GO:0120162
positive regulation of cold-induced thermogenesis
|
ISS
PMID:28844881 Genetic Depletion of Adipocyte Creatine Metabolism Inhibits ... |
KEEP AS NON CORE |
Summary: Positive regulation of cold-induced thermogenesis inferred by sequence/orthology from the mouse Gatm adipocyte-knockout phenotype.
Reason: Same context-specific downstream role as the IEA annotation for this term: adipocyte creatine synthesis supports adaptive/diet-induced thermogenesis in mouse. A legitimate physiological consequence of creatine energetics, but not a core function of the enzyme; retain as non-core.
Supporting Evidence:
PMID:28844881
these data suggest that adipose tissue Gatm and creatine energetics support adaptive thermogenesis in response to environmental cold.
|
|
GO:0007611
learning or memory
|
IMP
PMID:26490222 Arginine:glycine amidinotransferase (AGAT) deficiency: Clini... |
MARK AS OVER ANNOTATED |
Summary: Learning or memory assigned (CAFA) from the cognitive impairment seen in AGAT-deficiency patients.
Reason: The clinical phenotype is intellectual disability/developmental delay arising from severe brain creatine depletion. Annotating GATM directly to learning or memory over-reaches from a distal, secondary consequence of loss of creatine and does not reflect a molecular or cellular role of the enzyme in this process. The core process is creatine biosynthesis.
Supporting Evidence:
PMID:26490222
15 patients diagnosed between 16 months and 25 years of life had intellectual disability/developmental delay (IDD).
|
|
GO:0014889
muscle atrophy
|
IMP
PMID:26490222 Arginine:glycine amidinotransferase (AGAT) deficiency: Clini... |
MARK AS OVER ANNOTATED |
Summary: Muscle atrophy assigned (CAFA) from the myopathy/muscle weakness seen in AGAT-deficiency patients.
Reason: Myopathy/proximal muscle weakness in AGAT deficiency is a downstream consequence of systemic creatine depletion, not evidence that GATM participates in a muscle-atrophy process per se. This is an over-annotation derived from a disease phenotype; the core process is creatine biosynthesis.
Supporting Evidence:
PMID:26490222
8 patients also had myopathy/proximal muscle weakness.
|
|
GO:0015068
glycine amidinotransferase activity
|
IDA
PMID:27233232 Arginine-Glycine Amidinotransferase Deficiency and Functiona... |
ACCEPT |
Summary: Direct assay of glycine amidinotransferase activity used to functionally characterize pathogenic GATM missense variants (several retaining 0% of wild-type activity).
Reason: Strong experimental support for the core catalytic activity, with variant assays linking loss of this activity to AGAT-deficiency pathogenicity.
Supporting Evidence:
PMID:27233232
We found seven missense variants retaining 0% of wild-type GATM activity indicating putative pathogenicity.
|
|
GO:0070062
extracellular exosome
|
HDA
PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... |
MARK AS OVER ANNOTATED |
Summary: Extracellular exosome localization from a high-throughput proteomic study of exosomes in expressed prostatic secretions.
Reason: GATM is a mitochondrial intermembrane-space enzyme; detection in an exosome proteomics dataset is a high-throughput co-purification and does not reflect a functional extracellular/exosomal location. Over-annotation; not a core localization.
|
|
GO:0005758
mitochondrial intermembrane space
|
IDA
PMID:9218780 Crystal structure and mechanism of human L-arginine:glycine ... |
ACCEPT |
Summary: Direct (IDA) assignment of GATM to the mitochondrial intermembrane space, the core functional location of the enzyme.
Reason: Experimentally supported, most-specific correct localization. This is the core cellular location where the enzyme performs creatine precursor synthesis.
Supporting Evidence:
PMID:9218780
a mitochondrial enzyme involved in creatine biosynthesis
|
|
GO:0006601
creatine biosynthetic process
|
IDA
PMID:9218780 Crystal structure and mechanism of human L-arginine:glycine ... |
ACCEPT |
Summary: Direct evidence linking GATM activity to creatine biosynthesis (formation of the immediate creatine precursor guanidinoacetate).
Reason: Core biological process for the gene. Captured with the same evidence as the enables/MF and involved_in/BP annotations; the acts_upstream_of_or_within qualifier is acceptable.
Supporting Evidence:
PMID:9218780
L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine.
|
|
GO:0015068
glycine amidinotransferase activity
|
IDA
PMID:9218780 Crystal structure and mechanism of human L-arginine:glycine ... |
ACCEPT |
Summary: Direct (IDA) annotation of glycine amidinotransferase activity from the crystal-structure and mechanism study of the human enzyme.
Reason: Core molecular function, supported by structural characterization of the catalytic mechanism (Cys-His-Asp triad, amidino-cysteine intermediate).
Supporting Evidence:
PMID:9218780
A reaction mechanism with a catalytic triad Cys-His-Asp is proposed on the basis of substrate and product bound states.
|
Q: Is the broad amidinotransferase promiscuity (GABA, beta-alanine, taurine) physiologically significant in vivo, or is it primarily an in vitro side reaction with little flux under normal conditions?
Q: By what mechanism does the FRTS1 aggregation-prone gain-of-toxicity of specific GATM variants cause proximal tubulopathy, and how does it relate (if at all) to loss of catalytic activity?
Experiment: Quantify in vivo flux of GATM toward the non-canonical guanidino acids (guanidinobutyrate, guanidinopropionate, taurocyamine) in human/mouse tissues using stable-isotope tracing, to determine whether the promiscuous activities contribute meaningfully to metabolite pools.
Hypothesis: The non-glycine amidinotransferase side reactions are minor relative to guanidinoacetate synthesis under physiological conditions.
Experiment: Use structure-guided mutants that selectively impair GATM aggregation (FRTS1 variants) while preserving catalytic activity to dissociate the toxic-aggregation phenotype from enzymatic loss of function in proximal tubule cell models.
Hypothesis: FRTS1 pathology is driven by mitochondrial protein aggregation and downstream stress, not by loss of creatine synthesis.
Gene: GATM (HGNC:4175), synonym AGAT. UniProt P50440, "Glycine amidinotransferase, mitochondrial".
EC 2.1.4.1. L-arginine:glycine amidinotransferase / transamidinase.
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.
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.
id: P50440
gene_symbol: GATM
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
GATM (AGAT; L-arginine:glycine amidinotransferase, EC 2.1.4.1) is the first and
rate-limiting enzyme of creatine biosynthesis. It catalyzes the transfer of the
amidino group of L-arginine onto the amino group of glycine to yield guanidinoacetate
and L-ornithine; guanidinoacetate is subsequently methylated by GAMT to form creatine.
The mature enzyme is a homodimer with a five-fold pseudosymmetric basket fold and a
buried active site that uses a Cys-His-Asp catalytic triad and an amidino-cysteine
covalent intermediate (ping-pong mechanism). Although glycine is the strongly preferred
acceptor, the enzyme is promiscuous and can also amidinate GABA, beta-alanine and taurine
to produce guanidinobutyrate, guanidinopropionate and taurocyamine. The canonical
mitochondrial isoform carries a cleavable N-terminal transit peptide and localizes to the
mitochondrial intermembrane space, attached to the intermembrane side of the inner
membrane; an alternatively spliced isoform is cytoplasmic. GATM is expressed broadly with
highest levels in kidney, and is also abundant in liver, pancreas (exocrine acinar cells),
heart, brain and skeletal muscle, supplying creatine to high-energy-demand tissues for
ATP buffering. Loss-of-function variants cause autosomal-recessive cerebral creatine
deficiency syndrome 3 (AGAT deficiency), a treatable disorder of brain creatine depletion
presenting with intellectual disability, speech delay and myopathy, whereas distinct
dominant aggregation-prone variants cause Fanconi renotubular syndrome 1.
alternative_products:
- name: 1 (Mitochondrial)
id: P50440-1
- name: 2 (Cytoplasmic)
id: P50440-2
sequence_note: VSP_000235
- name: '3'
id: P50440-3
sequence_note: VSP_039871
existing_annotations:
- term:
id: GO:0005758
label: mitochondrial intermembrane space
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetic (IBA) propagation of the mitochondrial intermembrane space localization,
consistent with the experimentally determined human localization and the conserved
mitochondrial targeting of the amidinotransferase family.
action: ACCEPT
reason: >-
The canonical isoform is a mitochondrial enzyme localized to the intermembrane space
(attached to the intermembrane side of the inner membrane). This is the correct core
location and is independently supported by an IDA annotation (PMID:9218780).
- term:
id: GO:0006601
label: creatine biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetic (IBA) propagation of involvement in creatine biosynthesis, the canonical
and best-established biological role of GATM/AGAT.
action: ACCEPT
reason: >-
GATM catalyzes the committed, rate-limiting step of creatine biosynthesis (formation of
guanidinoacetate). This is a core biological process for the gene.
supported_by:
- reference_id: PMID:9218780
supporting_text: >-
L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine
biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine.
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) propagation of glycine amidinotransferase activity, the defining
catalytic activity of GATM.
action: ACCEPT
reason: >-
This is the core molecular function of GATM, directly demonstrated experimentally in
human enzyme (EXP/IDA in multiple references) and conserved across the family.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Cytoplasmic location derived by UniProt subcellular-location mapping, reflecting the
cytoplasmic splice isoform (P50440-2) rather than the canonical mitochondrial enzyme.
action: KEEP_AS_NON_CORE
reason: >-
UniProt annotates isoform 2 as cytoplasmic, so this term is not wrong, but the core,
catalytically characterized form is the mitochondrial intermembrane-space enzyme.
Retain as non-core (isoform-specific) localization.
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Mitochondrial inner membrane location from UniProt subcellular-location mapping; the
enzyme is a peripheral membrane protein on the intermembrane side of the inner membrane.
action: ACCEPT
reason: >-
Consistent with the UniProt subcellular location (Mitochondrion inner membrane;
Peripheral membrane protein; Intermembrane side). The functionally most specific term
is mitochondrial intermembrane space; this inner-membrane term is an accurate, slightly
different facet of the same location.
- term:
id: GO:0015067
label: amidinotransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
Parent amidinotransferase activity assigned via InterPro2GO from the amidinotransferase
family signature.
action: ACCEPT
reason: >-
Accurate but less specific than glycine amidinotransferase activity. The broader parent
is genuinely appropriate because GATM is promiscuous, also amidinating GABA, beta-alanine
and taurine. Retained; the specific GO:0015068 term is the primary core function.
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Glycine amidinotransferase activity inferred electronically from Rhea/EC:2.1.4.1 mapping.
action: ACCEPT
reason: >-
Correct core molecular function, redundant with the experimental annotations for the same
term but valid as an automated EC/Rhea-based assignment.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32814053
qualifier: enables
review:
summary: >-
Generic protein binding annotations from a large-scale neurodegenerative-disease
interactome/Y2H screen, covering 13 prey partners.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Protein binding (GO:0005515) is uninformative and does not capture a defined molecular
function. These IPI calls come from a high-throughput interactome map and none of the
listed partners corresponds to an established, functionally meaningful GATM complex.
Per curation guidelines, bare protein binding should not be carried as a core function.
- term:
id: GO:0120162
label: positive regulation of cold-induced thermogenesis
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: >-
Positive regulation of cold-induced thermogenesis transferred electronically from the
mouse ortholog (Gatm), based on adipocyte-specific knockout phenotypes.
action: KEEP_AS_NON_CORE
reason: >-
This reflects a genuine but tissue- and context-specific downstream consequence of
adipocyte creatine synthesis demonstrated in mouse (fat-specific Gatm knockout impairs
diet-induced/adaptive thermogenesis). It is a physiological role of creatine energetics,
not a core molecular/biological function of the human enzyme; retain as non-core.
supported_by:
- reference_id: PMID:28844881
supporting_text: >-
we have inactivated the first and rate-limiting enzyme of creatine biosynthesis,
glycine amidinotransferase (GATM), selectively in fat (Adipo-Gatm KO).
- term:
id: GO:0006601
label: creatine biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000041
qualifier: involved_in
review:
summary: >-
Creatine biosynthetic process inferred electronically from UniPathway mapping.
action: ACCEPT
reason: >-
Correct core biological process, consistent with the curated and experimental
annotations for the same term.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: GO_REF:0000052
qualifier: located_in
review:
summary: >-
Mitochondrial localization from immunofluorescence (HPA), a broader but accurate
compartment assignment.
action: ACCEPT
reason: >-
Directly observed mitochondrial localization. Less specific than mitochondrial
intermembrane space but correct; retained as supporting localization evidence.
- term:
id: GO:0005758
label: mitochondrial intermembrane space
evidence_type: TAS
original_reference_id: Reactome:R-HSA-71275
qualifier: located_in
review:
summary: >-
Mitochondrial intermembrane space localization asserted by Reactome (creatine
metabolism pathway).
action: ACCEPT
reason: >-
Same core location as the IDA and IBA annotations; traceable author statement consistent
with the experimentally established localization.
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: EXP
original_reference_id: PMID:36543883
qualifier: enables
review:
summary: >-
Experimental demonstration that purified recombinant human GATM amidinates glycine
(and, less efficiently, GABA/beta-alanine/taurine), with glycine as the preferred acceptor.
action: ACCEPT
reason: >-
Direct experimental support for the defining catalytic activity; this is the core
molecular function of the gene.
supported_by:
- reference_id: PMID:36543883
supporting_text: >-
human GATM had the highest activity with glycine, but also GABA, β-alanine and taurine
were accepted as substrates with decreasing preference
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: EXP
original_reference_id: PMID:3800397
qualifier: enables
review:
summary: >-
Purification and biochemical characterization of human kidney transamidinase establishing
its amidinotransferase activity and dimeric structure.
action: ACCEPT
reason: >-
Classic experimental support for the core catalytic activity of human AGAT.
supported_by:
- reference_id: PMID:3800397
supporting_text: >-
Human kidney transamidinase is a dimer with a molecular mass of 89,000 Da and subunit
masses of 44,000 Da. The Km for arginine and glycine were both 2.5 mM
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: EXP
original_reference_id: PMID:9266688
qualifier: enables
review:
summary: >-
Mutagenesis and crystallographic study confirming the catalytic activity and active-site
residues of human AGAT.
action: ACCEPT
reason: >-
Direct experimental and structural support for the core glycine amidinotransferase
activity, including identification of catalytic residues whose mutation abolishes activity.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: >-
Mitochondrial localization from a high-throughput high-confidence human mitochondrial
proteome study.
action: ACCEPT
reason: >-
Consistent with the established mitochondrial localization; high-throughput evidence
corroborating the more specific intermembrane-space assignment.
- term:
id: GO:0015067
label: amidinotransferase activity
evidence_type: IDA
original_reference_id: PMID:36543883
qualifier: enables
review:
summary: >-
Direct experimental demonstration of broader amidinotransferase activity, since human
GATM amidinates multiple acceptors (glycine, GABA, beta-alanine, taurine).
action: ACCEPT
reason: >-
The parent term is justified by the experimentally observed substrate promiscuity. The
most specific core activity is glycine amidinotransferase activity (GO:0015068); this
broader term legitimately captures the side reactions.
supported_by:
- reference_id: PMID:36543883
supporting_text: >-
human GATM had the highest activity with glycine, but also GABA, β-alanine and taurine
were accepted as substrates with decreasing preference
- term:
id: GO:0120162
label: positive regulation of cold-induced thermogenesis
evidence_type: ISS
original_reference_id: PMID:28844881
qualifier: involved_in
review:
summary: >-
Positive regulation of cold-induced thermogenesis inferred by sequence/orthology from the
mouse Gatm adipocyte-knockout phenotype.
action: KEEP_AS_NON_CORE
reason: >-
Same context-specific downstream role as the IEA annotation for this term: adipocyte
creatine synthesis supports adaptive/diet-induced thermogenesis in mouse. A legitimate
physiological consequence of creatine energetics, but not a core function of the enzyme;
retain as non-core.
supported_by:
- reference_id: PMID:28844881
supporting_text: >-
these data suggest that adipose tissue Gatm and creatine energetics support adaptive
thermogenesis in response to environmental cold.
- term:
id: GO:0007611
label: learning or memory
evidence_type: IMP
original_reference_id: PMID:26490222
qualifier: involved_in
review:
summary: >-
Learning or memory assigned (CAFA) from the cognitive impairment seen in AGAT-deficiency
patients.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The clinical phenotype is intellectual disability/developmental delay arising from severe
brain creatine depletion. Annotating GATM directly to learning or memory over-reaches
from a distal, secondary consequence of loss of creatine and does not reflect a molecular
or cellular role of the enzyme in this process. The core process is creatine biosynthesis.
supported_by:
- reference_id: PMID:26490222
supporting_text: >-
15 patients diagnosed between 16 months and 25 years of life had intellectual
disability/developmental delay (IDD).
- term:
id: GO:0014889
label: muscle atrophy
evidence_type: IMP
original_reference_id: PMID:26490222
qualifier: involved_in
review:
summary: >-
Muscle atrophy assigned (CAFA) from the myopathy/muscle weakness seen in AGAT-deficiency
patients.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Myopathy/proximal muscle weakness in AGAT deficiency is a downstream consequence of
systemic creatine depletion, not evidence that GATM participates in a muscle-atrophy
process per se. This is an over-annotation derived from a disease phenotype; the core
process is creatine biosynthesis.
supported_by:
- reference_id: PMID:26490222
supporting_text: >-
8 patients also had myopathy/proximal muscle weakness.
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: IDA
original_reference_id: PMID:27233232
qualifier: enables
review:
summary: >-
Direct assay of glycine amidinotransferase activity used to functionally characterize
pathogenic GATM missense variants (several retaining 0% of wild-type activity).
action: ACCEPT
reason: >-
Strong experimental support for the core catalytic activity, with variant assays linking
loss of this activity to AGAT-deficiency pathogenicity.
supported_by:
- reference_id: PMID:27233232
supporting_text: >-
We found seven missense variants retaining 0% of wild-type GATM activity indicating
putative pathogenicity.
- term:
id: GO:0070062
label: extracellular exosome
evidence_type: HDA
original_reference_id: PMID:23533145
qualifier: located_in
review:
summary: >-
Extracellular exosome localization from a high-throughput proteomic study of exosomes in
expressed prostatic secretions.
action: MARK_AS_OVER_ANNOTATED
reason: >-
GATM is a mitochondrial intermembrane-space enzyme; detection in an exosome proteomics
dataset is a high-throughput co-purification and does not reflect a functional
extracellular/exosomal location. Over-annotation; not a core localization.
- term:
id: GO:0005758
label: mitochondrial intermembrane space
evidence_type: IDA
original_reference_id: PMID:9218780
qualifier: located_in
review:
summary: >-
Direct (IDA) assignment of GATM to the mitochondrial intermembrane space, the core
functional location of the enzyme.
action: ACCEPT
reason: >-
Experimentally supported, most-specific correct localization. This is the core cellular
location where the enzyme performs creatine precursor synthesis.
supported_by:
- reference_id: PMID:9218780
supporting_text: >-
a mitochondrial enzyme involved in creatine biosynthesis
- term:
id: GO:0006601
label: creatine biosynthetic process
evidence_type: IDA
original_reference_id: PMID:9218780
qualifier: acts_upstream_of_or_within
review:
summary: >-
Direct evidence linking GATM activity to creatine biosynthesis (formation of the immediate
creatine precursor guanidinoacetate).
action: ACCEPT
reason: >-
Core biological process for the gene. Captured with the same evidence as the enables/MF
and involved_in/BP annotations; the acts_upstream_of_or_within qualifier is acceptable.
supported_by:
- reference_id: PMID:9218780
supporting_text: >-
L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine
biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine.
- term:
id: GO:0015068
label: glycine amidinotransferase activity
evidence_type: IDA
original_reference_id: PMID:9218780
qualifier: enables
review:
summary: >-
Direct (IDA) annotation of glycine amidinotransferase activity from the crystal-structure
and mechanism study of the human enzyme.
action: ACCEPT
reason: >-
Core molecular function, supported by structural characterization of the catalytic
mechanism (Cys-His-Asp triad, amidino-cysteine intermediate).
supported_by:
- reference_id: PMID:9218780
supporting_text: >-
A reaction mechanism with a catalytic triad Cys-His-Asp is proposed on the basis of
substrate and product bound states.
core_functions:
- description: >-
Glycine amidinotransferase activity: transfers the amidino group of L-arginine to glycine,
producing guanidinoacetate and L-ornithine - the committed, rate-limiting step of creatine
biosynthesis - acting in the mitochondrial intermembrane space.
molecular_function:
id: GO:0015068
label: glycine amidinotransferase activity
directly_involved_in:
- id: GO:0006601
label: creatine biosynthetic process
locations:
- id: GO:0005758
label: mitochondrial intermembrane space
substrates:
- id: CHEBI:32682
label: L-arginine
- id: CHEBI:57305
label: glycine
supported_by:
- reference_id: PMID:9218780
supporting_text: >-
L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine
biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine.
- reference_id: PMID:36543883
supporting_text: >-
human GATM had the highest activity with glycine, but also GABA, β-alanine and taurine
were accepted as substrates with decreasing preference
- description: >-
Broader amidinotransferase activity reflecting the enzyme's substrate promiscuity: in
addition to glycine, GATM amidinates GABA, beta-alanine and taurine to form guanidinobutyrate,
guanidinopropionate and taurocyamine, respectively.
molecular_function:
id: GO:0015067
label: amidinotransferase activity
locations:
- id: GO:0005758
label: mitochondrial intermembrane space
supported_by:
- reference_id: PMID:36543883
supporting_text: >-
we further show that the identified guanidino acid substrates were produced by the
promiscuous action of human glycine amidinotransferase
suggested_questions:
- question: >-
Is the broad amidinotransferase promiscuity (GABA, beta-alanine, taurine) physiologically
significant in vivo, or is it primarily an in vitro side reaction with little flux under
normal conditions?
- question: >-
By what mechanism does the FRTS1 aggregation-prone gain-of-toxicity of specific GATM variants
cause proximal tubulopathy, and how does it relate (if at all) to loss of catalytic activity?
suggested_experiments:
- description: >-
Quantify in vivo flux of GATM toward the non-canonical guanidino acids (guanidinobutyrate,
guanidinopropionate, taurocyamine) in human/mouse tissues using stable-isotope tracing, to
determine whether the promiscuous activities contribute meaningfully to metabolite pools.
hypothesis: >-
The non-glycine amidinotransferase side reactions are minor relative to guanidinoacetate
synthesis under physiological conditions.
- description: >-
Use structure-guided mutants that selectively impair GATM aggregation (FRTS1 variants) while
preserving catalytic activity to dissociate the toxic-aggregation phenotype from enzymatic
loss of function in proximal tubule cell models.
hypothesis: >-
FRTS1 pathology is driven by mitochondrial protein aggregation and downstream stress, not by
loss of creatine synthesis.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000041
title: Gene Ontology annotation based on UniPathway vocabulary mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary
mapping, accompanied by conservative changes to GO terms applied by UniProt
findings: []
- id: GO_REF:0000052
title: Gene Ontology annotation based on curation of immunofluorescence data
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to orthologs
using Ensembl Compara
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:23533145
title: In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions
in urine.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
High-throughput exosome proteomics; supports only an incidental co-purification, not a
functional extracellular location for this mitochondrial enzyme.
- id: PMID:26490222
title: 'Arginine:glycine amidinotransferase (AGAT) deficiency: Clinical features and long term
outcomes in 16 patients diagnosed worldwide.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Clinical cohort establishing AGAT deficiency as a treatable creatine-deficiency disorder
(intellectual disability, myopathy); used (via CAFA) for the learning/memory and muscle
atrophy annotations, which are downstream disease consequences rather than core functions.
- id: PMID:27233232
title: Arginine-Glycine Amidinotransferase Deficiency and Functional Characterization of
Missense Variants in GATM.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Functional assays of GATM missense variants directly measuring glycine amidinotransferase
activity; supports the core MF annotation and links activity loss to pathogenicity.
- id: PMID:28844881
title: Genetic Depletion of Adipocyte Creatine Metabolism Inhibits Diet-Induced Thermogenesis
and Drives Obesity.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Mouse adipocyte-specific Gatm knockout; basis for the cold-induced thermogenesis
annotations. Establishes a tissue-specific physiological role of creatine energetics,
retained as non-core for the human gene.
- id: PMID:32814053
title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers
Widespread Protein Aggregation in Affected Brains.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Large-scale interactome/Y2H map; source of 13 uninformative protein binding IPI
annotations. No defined functional GATM complex established.
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular
context.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: High-confidence mitochondrial proteome; corroborates mitochondrial localization.
- id: PMID:36543883
title: Guanidino acid hydrolysis by the human enzyme annotated as agmatinase.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Demonstrates purified human GATM amidinates glycine (preferred) plus GABA, beta-alanine and
taurine; supports both the specific and parent amidinotransferase MF annotations.
- id: PMID:3800397
title: The purification and characterization of human kidney L-arginine:glycine
amidinotransferase.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Classic purification/characterization of human AGAT as a dimeric transamidinase; supports
the core catalytic activity.
- id: PMID:9218780
title: 'Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a
mitochondrial enzyme involved in creatine biosynthesis.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Crystal structure and mechanism; supports the core MF, the creatine biosynthetic process,
and the mitochondrial intermembrane space localization.
- id: PMID:9266688
title: Substrate binding and catalysis by L-arginine:glycine amidinotransferase--a mutagenesis
and crystallographic study.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Mutagenesis/crystallography defining catalytic residues; supports the core glycine
amidinotransferase activity.
- id: Reactome:R-HSA-71275
title: Creatine metabolism
findings: []