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, Ξ²-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, Ξ²-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. |
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Download this section (compressed HTML)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.
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