CPS1 (carbamoyl-phosphate synthase [ammonia], mitochondrial) is a ~1500-residue multidomain enzyme of the mitochondrial matrix that catalyzes the first and rate-limiting committed step of the urea cycle in ureotelic animals: the ATP-dependent condensation of ammonia and bicarbonate into carbamoyl phosphate (NH4+ + HCO3- + 2 ATP -> carbamoyl phosphate + 2 ADP + phosphate + 2 H+; EC 6.3.4.16). It is highly expressed in liver and small intestine, where it initiates hepatic detoxification of ammonia derived from amino acid catabolism. Unlike the cytosolic glutamine-dependent CPS II (part of CAD) that feeds pyrimidine biosynthesis, CPS1 uses free ammonia rather than glutamine; its ancestral glutamine amidotransferase domain is catalytically defective (the catalytic cysteine is replaced by Ser294). CPS1 is an allosteric enzyme with an absolute requirement for the activator N-acetyl-L-glutamate (NAG), which binds the C-terminal MGS-like domain and, together with nucleotide binding, drives long-range conformational changes that build the intramolecular tunnel through which the labile carbamate intermediate migrates between the two ATP-grasp phosphorylation sites; in the absence of NAG the enzyme retains <=2% of its maximal activity. Catalysis also requires the ionic activators potassium and magnesium. The enzyme behaves in solution as a monomer-dimer equilibrium in which the monomer predominates. Loss-of-function variants cause the autosomal recessive urea-cycle disorder carbamoyl phosphate synthetase 1 deficiency (CPS1D), which presents most severely as neonatal hyperammonemia with high mortality and neurological sequelae.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred carbamoyl-phosphate synthase (ammonia) activity. This is the correct, specific core molecular function of CPS1 and is directly supported by biochemical characterization of the recombinant human enzyme. Reason: This is the well-established core catalytic function of CPS1 (EC 6.3.4.16), the ammonia-dependent carbamoyl-phosphate synthetase of the urea cycle. The IBA annotation is at the correct level of specificity. Supporting Evidence: PMID:23649895 The kinetic and molecular properties of recombinant CPS1 are essentially the same as for natural human CPS1. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic annotation to cytoplasm. CPS1 is a mitochondrial-matrix protein; cytoplasm is far too general and does not capture the specific compartment. Reason: CPS1 is imported into the mitochondrion via an N-terminal transit peptide and functions in the mitochondrial matrix, not the general cytoplasm. The more specific and accurate location GO:0005759 mitochondrial matrix is separately annotated (TAS). Replace the over-general cytoplasm term with mitochondrial matrix. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH COMPARTMENT OR COMPLEX MISMATCH Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:15897806 carbamoyl phosphate synthase-1 (CPS-1), an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0006541 L-glutamine metabolic process | IBA GO_REF:0000033 | REMOVE | Summary: Phylogenetic annotation to glutamine metabolic process, inherited from the glutamine-dependent CPS family ancestor. Human CPS1 does not use glutamine. Reason: CPS1 is ammonia-dependent, not glutamine-dependent. Its ancestral glutamine amidotransferase (GATase) domain is catalytically defective, with the key catalytic cysteine replaced by serine (Ser294), so CPS1 does not hydrolyze or metabolize glutamine. This IBA term reflects the broader CPS family (which includes glutamine-hydrolyzing CPS II) rather than the specific human enzyme. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE PSEUDO OR SUBACTIVITY LOSS Sources checked: GO_REF:0000033 Β· PAN-GO phylogenetic inference (CPS family tree) SUPPORTS SOURCE BUT NOT TARGET Glutamine metabolism is a genuine property of glutamine-dependent CPS family members (e.g. CPS II/CAD), but human CPS1 has lost the glutaminase sub-activity (catalytic Cys->Ser294) and uses free ammonia. Supporting Evidence: PMID:26592762 The inability of human CPS1 to use glutamine is explained by the replacement by serine (Ser294) in this enzyme of the key catalytic cysteine of the catalytic triad |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic annotation to the glutamine-hydrolyzing carbamoyl-phosphate synthase activity. This is the activity of the distinct cytosolic CPS II (CAD) enzyme of pyrimidine biosynthesis, not of CPS1. Reason: GO:0004088 uses L-glutamine (plus water) as the nitrogen donor; this is the activity of glutamine-dependent CPS II/CAD. Human CPS1 uses free ammonia and has a defective glutaminase domain, so this term is incorrect for CPS1. The essence (carbamoyl phosphate synthetase activity) is sound but the specific subtype is wrong; replace with the ammonia-dependent activity GO:0004087. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE PSEUDO OR SUBACTIVITY LOSS Sources checked: GO_REF:0000033 Β· PAN-GO phylogenetic inference (CPS family tree) SUPPORTS SOURCE BUT NOT TARGET The glutamine-hydrolyzing subtype (GO:0004088) is correct for glutamine-dependent CPS family members but not for human CPS1, which is ammonia-dependent; the ammonia subtype GO:0004087 is the correct term. Proposed replacements: carbamoyl-phosphate synthase (ammonia) activity Supporting Evidence: PMID:26592762 Glutamine is utilized as the endogenous source of ammonia by all types of CPS31464748 except CPS12 |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of the correct core catalytic activity of CPS1. Reason: Correct core molecular function, consistent with experimental and phylogenetic annotations of the same term. |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO electronic annotation to the glutamine-hydrolyzing CPS activity, transferred from the shared CPS domain architecture. This subtype belongs to CPS II, not CPS1. Reason: Same issue as the IBA GO:0004088 annotation: human CPS1 is ammonia-dependent with a defective glutaminase domain and cannot hydrolyze glutamine. Replace with the ammonia-dependent activity GO:0004087. Proposed replacements: carbamoyl-phosphate synthase (ammonia) activity Supporting Evidence: PMID:26592762 The inability of human CPS1 to use glutamine is explained by the replacement by serine (Ser294) in this enzyme of the key catalytic cysteine of the catalytic triad |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of ATP binding. CPS1 has two ATP-grasp phosphorylation domains and consumes 2 ATP per catalytic cycle; ATP binding is a genuine and required molecular activity. Reason: ATP binding is directly supported by the catalytic mechanism (two ATP-grasp domains, L1 and L3) and by kinetic characterization (KM for ATP measured). This is a real, core-supporting cofactor/substrate activity. Supporting Evidence: PMID:26592762 the adenine ring sandwiched between the central Ξ² sheets of the B and C subdomains (for the boundaries between the A, B and C subdomains, see Supplementary Fig. 2), as is characteristic for the ATP-grasp fold |
| GO:0005730 nucleolus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic annotation to nucleolus derived from the UniProt subcellular location vocabulary. UniProt records a nucleus/nucleolus location from a large-scale spatial proteomics study, but the enzyme's function is in the mitochondrial matrix. Reason: A nucleus/nucleolus localization is reported in UniProt (from PMID:22002106) and is separately supported by an IDA annotation, so it is retained, but it is a secondary/moonlighting localization unrelated to the core ureagenesis function of CPS1, which occurs in the mitochondrial matrix. |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation to mitochondrion, the correct organelle. CPS1 is a mitochondrial-matrix protein. Reason: Correct organelle-level localization; consistent with the more specific mitochondrial matrix annotations and with the N-terminal mitochondrial transit peptide. Retained as a valid (if less specific) location. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic annotation to plasma membrane. UniProt records a cell-membrane / hepatocyte cell-surface location inferred by similarity to the mouse ortholog. Reason: A cell-surface / plasma-membrane location is reported in UniProt as a peripheral membrane protein on the extracellular side (by similarity to mouse Q8C196, "cell surface of hepatocytes"). This is a reported secondary localization, not the compartment where the core catalytic function occurs. Keep as non-core rather than remove, since it is corroborated in UniProt. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO electronic annotation to de novo pyrimidine biosynthesis, transferred from the shared CPS domain architecture. Pyrimidine biosynthesis is the role of the cytosolic glutamine-dependent CPS II (CAD), not CPS1. Reason: In humans, carbamoyl phosphate for pyrimidine biosynthesis is made by the cytosolic CPS II activity of the multifunctional CAD protein, not by mitochondrial CPS1. CPS1-derived carbamoyl phosphate is committed to the urea cycle. This term is a domain-based over-annotation transferred from the broader CPS family. Supporting Evidence: PMID:26592762 Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain enzyme, catalyzes the first step of ammonia detoxification to urea |
| GO:0006541 L-glutamine metabolic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO electronic annotation to glutamine metabolic process, inherited from the glutamine-dependent CPS family. Human CPS1 does not use glutamine. Reason: Same rationale as the IBA GO:0006541 annotation: CPS1 is ammonia-dependent and has a defective glutaminase domain (Cys->Ser294), so it does not participate in glutamine metabolism. Supporting Evidence: PMID:26592762 The inability of human CPS1 to use glutamine is explained by the replacement by serine (Ser294) in this enzyme of the key catalytic cysteine of the catalytic triad |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: Electronic annotation to metal ion binding. CPS1 uses Mg2+ (coordinated to ADP at both phosphorylation sites) and K+ as essential ionic activators. Reason: Metal ion binding is genuine: catalysis requires magnesium (coordinating the nucleotides) and potassium (coordinated in the L1 K-loop). This broad term is an acceptable parent; the more specific potassium ion binding is separately annotated with experimental evidence. Supporting Evidence: PMID:26592762 CPS1 affinities for its essential ionic activators potassium and magnesium are increased importantly by NAG |
| GO:0090407 organophosphate biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning electronic annotation to the very broad organophosphate biosynthetic process. Carbamoyl phosphate is an organophosphate, so this is not wrong, but it is far more general than the specific process CPS1 performs. Reason: The product carbamoyl phosphate is technically an organophosphate, so the term is not incorrect, but it is uninformatively broad. The specific process is better captured by GO:0070409 carbamoyl phosphate biosynthetic process, which is separately and experimentally annotated. Proposed replacements: carbamoyl phosphate biosynthetic process |
| GO:0005515 protein binding | IPI PMID:12620389 Novel raf kinase protein-protein interactions found by an ex... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a high-throughput yeast two-hybrid screen for Raf kinase interactors (A-Raf / C-Raf bait). Uninformative and not a defined functional partnership. Reason: Per curation guidelines, bare protein binding is uninformative about molecular function. The interaction derives from an exhaustive Raf two-hybrid screen (CPS1 as one of many hits) with no established functional consequence for ureagenesis. Retained only as a low-value, non-core annotation. Supporting Evidence: PMID:12620389 We have performed an exhaustive unbiased yeast two-hybrid analysis to identify interaction partners of two human Raf kinase isoforms, A-Raf and C-Raf, using their N-terminal regulatory domain as "bait." |
| GO:0005515 protein binding | IPI PMID:15161933 Comprehensive proteomic analysis of interphase and mitotic 1... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a comprehensive 14-3-3 affinity-capture proteomics screen. Uninformative and a large-scale-screen hit rather than a defined functional interaction. Reason: Bare protein binding is uninformative. CPS1 was identified among many proteins binding 14-3-3 in a global proteomics screen with no demonstrated functional role in ureagenesis. Retained only as a low-value, non-core annotation. Supporting Evidence: PMID:15161933 Here we describe a global proteomics analysis to identify proteins that bind to 14-3-3s during interphase and mitosis. |
| GO:0005515 protein binding | IPI PMID:20618440 Proteomic and biochemical analysis of 14-3-3-binding protein... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a 14-3-3-binding proteomics study during ceramide-induced apoptosis. Uninformative screen-derived interaction. Reason: Bare protein binding is uninformative about molecular function, and the interaction comes from a large-scale 14-3-3 proteomics/affinity study. Retained only as a low-value, non-core annotation. Supporting Evidence: PMID:20618440 A combination of tandem affinity purification and liquid chromatography-tandem MS techniques identified 15 proteins involved in cell survival processes whose 14-3-3-binding status changed during C2-ceramide-induced apoptosis. |
| GO:0000050 urea cycle | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl-Compara ortholog-transfer annotation to the urea cycle, the core biological process of CPS1. Reason: CPS1 catalyzes the first committed step of the urea cycle; this is a core biological-process annotation, corroborated by TAS and NAS annotations to the same term. Supporting Evidence: PMID:1840546 Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis. |
| GO:0001889 liver development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl-Compara ortholog-transfer annotation to liver development. CPS1 is highly expressed in liver but is a metabolic enzyme, not a developmental regulator. Reason: This is a tissue/physiological-context transfer from rodent orthologs reflecting hepatic expression, not a demonstrated role of CPS1 in liver morphogenesis. Not a core function; keep as non-core. |
| GO:0004175 endopeptidase activity | IEA GO_REF:0000107 | REMOVE | Summary: Ensembl-Compara ortholog-transfer annotation to endopeptidase activity. CPS1 is a ligase (EC 6.3.4.16), not a protease; this is biologically implausible. Reason: Endopeptidase activity (hydrolysis of internal peptide bonds) is incompatible with the known ligase function and structure of CPS1. This is a spurious ortholog-transfer artifact with no supporting evidence. Supporting Evidence: PMID:23649895 The kinetic and molecular properties of recombinant CPS1 are essentially the same as for natural human CPS1. |
| GO:0005509 calcium ion binding | IEA GO_REF:0000107 | REMOVE | Summary: Ensembl-Compara ortholog-transfer annotation to calcium ion binding. CPS1's catalytically relevant ions are potassium and magnesium, not calcium. Reason: There is no evidence that CPS1 binds calcium as a functional ligand. Its essential ionic activators are K+ and Mg2+. This is a spurious ortholog transfer. Supporting Evidence: PMID:26592762 CPS1 affinities for its essential ionic activators potassium and magnesium are increased importantly by NAG |
| GO:0005543 phospholipid binding | IEA GO_REF:0000107 | REMOVE | Summary: Ensembl-Compara ortholog-transfer annotation to phospholipid binding. No evidence that the matrix enzyme CPS1 binds phospholipids as part of its function. Reason: CPS1 is a soluble mitochondrial-matrix ligase with no phospholipid-binding function established in the literature; this is a spurious ortholog-transfer artifact. |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000107 | MODIFY | Summary: Ortholog-transfer annotation to mitochondrial inner membrane. CPS1 is a soluble matrix protein; it may associate with the matrix face of the inner membrane but functions in the matrix. Reason: CPS1 is characterized as a soluble mitochondrial-matrix enzyme, not an integral inner-membrane protein. The more accurate location is the mitochondrial matrix (GO:0005759), which is separately annotated with TAS evidence. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0005829 cytosol | IEA GO_REF:0000107 | REMOVE | Summary: Ortholog-transfer annotation to cytosol. CPS1 functions in the mitochondrial matrix, not the cytosol. Reason: CPS1 carries an N-terminal mitochondrial transit peptide and functions in the matrix. A cytosolic location contradicts the established mitochondrial localization; this ortholog-transfer term is inappropriate for the core enzyme. (Any transient cytosolic pool during import is not a functional location.) Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0007494 midgut development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer annotation to midgut development, reflecting intestinal expression of CPS1 in model organisms. Not a demonstrated developmental role. Reason: CPS1 is expressed in the small intestine, but this term reflects a tissue-context ortholog transfer rather than a role in gut morphogenesis. Not a core function; keep as non-core. |
| GO:0009410 response to xenobiotic stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to stimulus" annotation from rodent expression studies. Reflects regulation of CPS1 abundance, not a core molecular role. Reason: These transferred physiological-context terms describe conditions under which CPS1 expression changes rather than the enzyme's molecular function. Keep as non-core. |
| GO:0009636 response to toxic substance | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to toxic substance" annotation. Context/expression transfer, not a core function. Reason: Physiological-context term transferred from orthologs; describes regulation of CPS1 rather than its molecular activity. Keep as non-core. |
| GO:0010043 response to zinc ion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to zinc ion" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; not a demonstrated molecular role of human CPS1. Keep as non-core. |
| GO:0014075 response to amine | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to amine" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; describes conditions affecting CPS1 rather than its molecular activity. Keep as non-core. |
| GO:0016595 glutamate binding | IEA GO_REF:0000107 | MODIFY | Summary: Ortholog-transfer annotation to glutamate binding. CPS1's allosteric activator is N-acetyl-L-glutamate (a modified amino acid), not free glutamate. Reason: The functionally important ligand of CPS1's C-terminal allosteric domain is N-acetyl-L-glutamate (NAG), not free L-glutamate. Binding of the modified amino acid NAG is more accurately captured by GO:0072341 modified amino acid binding. The generic glutamate binding term mischaracterizes the actual allosteric ligand. Proposed replacements: modified amino acid binding Supporting Evidence: PMID:26592762 NAG binding to CPS1 as observed in the crystal structure appears to genuinely reflect the binding of this effector to the enzyme in vivo. |
| GO:0032094 response to food | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to food" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting dietary regulation of CPS1 abundance; not a core molecular function. Keep as non-core. |
| GO:0032496 response to lipopolysaccharide | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Ortholog-transfer "response to lipopolysaccharide" annotation. Context transfer reflecting altered CPS1 levels/release under septic conditions, not a core function. Reason: Reflects the observation that CPS1 abundance/release changes under LPS/septic conditions (see PMID:15897806), which is a downstream biomarker phenomenon rather than CPS1 executing an LPS-response function. Harmonized with the IDA annotation to the same term, which is also marked as over-annotated. |
| GO:0032991 protein-containing complex | IEA GO_REF:0000107 | REMOVE | Summary: Ortholog-transfer annotation to the generic protein-containing complex. CPS1 acts predominantly as a monomer (monomer-dimer equilibrium); it is not a constitutive subunit of a defined complex. Reason: CPS1 functions as a monomer (with a weak monomer-dimer equilibrium) rather than as part of a stable protein complex, and no specific complex is defined. The generic protein-containing complex term is uninformative and not supported. Supporting Evidence: PMID:26592762 the behavior of human CPS1 in solution as a monomer-dimer system in rapid equilibrium in which the monomer predominates |
| GO:0033762 response to glucagon | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to glucagon" annotation. Context/expression transfer, not a core function. Reason: Reflects hormonal regulation of CPS1 expression transferred from rodent orthologs; not a core molecular function. Keep as non-core. |
| GO:0034201 response to oleic acid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to oleic acid" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; not a demonstrated molecular function of human CPS1. Keep as non-core. |
| GO:0042594 response to starvation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to starvation" annotation. Fasting increases CPS1 glutarylation and urea-cycle flux, but this is a regulatory context, not a core molecular function. Reason: Reflects fasting/starvation regulation of ureagenesis and CPS1 acylation rather than a distinct molecular function. Keep as non-core. |
| GO:0043200 response to amino acid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to amino acid" annotation. Context/expression transfer reflecting dietary-protein regulation of ureagenesis. Reason: Transferred physiological-context term reflecting protein/amino-acid-load regulation of the urea cycle; not a core molecular function. Keep as non-core. |
| GO:0044344 cellular response to fibroblast growth factor stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "cellular response to FGF" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; not a demonstrated molecular role of human CPS1. Keep as non-core. |
| GO:0044877 protein-containing complex binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer annotation to protein-containing complex binding. Generic and uninformative for CPS1, a predominantly monomeric enzyme. Reason: No specific complex-binding function of CPS1 is established; this generic transferred term is uninformative. Keep as non-core rather than assert a defined functional interaction. |
| GO:0048545 response to steroid hormone | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to steroid hormone" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting hormonal regulation of CPS1 expression; not a core molecular function. Keep as non-core. |
| GO:0051384 response to glucocorticoid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to glucocorticoid" annotation. Context/expression transfer, not a core function. Reason: Reflects glucocorticoid regulation of CPS1 expression transferred from rodent orthologs; not a core molecular function. Keep as non-core. |
| GO:0051591 response to cAMP | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to cAMP" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting cAMP-mediated regulation of CPS1; not a core molecular function. Keep as non-core. |
| GO:0055081 monoatomic anion homeostasis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer annotation to monoatomic anion homeostasis. Not a recognized function of CPS1. Reason: This transferred term does not correspond to any established CPS1 function (its substrate bicarbonate is a polyatomic anion, and CPS1 is not an ion transporter/homeostasis factor). Weak transfer; keep as non-core rather than assert a role. |
| GO:0060416 response to growth hormone | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to growth hormone" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting hormonal regulation of CPS1 expression; not a core molecular function. Keep as non-core. |
| GO:0070365 hepatocyte differentiation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "hepatocyte differentiation" annotation. CPS1 is a hepatocyte marker and highly expressed in differentiated hepatocytes, but is a metabolic enzyme rather than a differentiation driver. Reason: CPS1 is a marker of differentiated hepatocytes rather than a demonstrated regulator of hepatocyte differentiation; this reflects expression context. Keep as non-core. |
| GO:0071320 cellular response to cAMP | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "cellular response to cAMP" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting cAMP-mediated regulation of CPS1; not a core molecular function. Keep as non-core. |
| GO:0071377 cellular response to glucagon stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "cellular response to glucagon stimulus" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term reflecting glucagon regulation of ureagenesis/CPS1; not a core molecular function. Keep as non-core. |
| GO:0071400 cellular response to oleic acid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "cellular response to oleic acid" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; not a demonstrated molecular function of human CPS1. Keep as non-core. |
| GO:0071548 response to dexamethasone | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to dexamethasone" annotation. Context/expression transfer reflecting glucocorticoid induction of CPS1. Reason: Transferred physiological-context term reflecting glucocorticoid (dexamethasone) induction of CPS1 expression; not a core molecular function. Keep as non-core. |
| GO:0097305 response to alcohol | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ortholog-transfer "response to alcohol" annotation. Context/expression transfer, not a core function. Reason: Transferred physiological-context term; not a demonstrated molecular function of human CPS1. Keep as non-core. |
| GO:0000050 urea cycle | TAS Reactome:R-HSA-70635 | ACCEPT | Summary: Reactome traceable-author-statement annotation of CPS1 in the urea cycle, the core biological process. Reason: CPS1 catalyzes the first committed step of the urea cycle; this is a core, well-supported biological-process annotation. Supporting Evidence: PMID:1840546 Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis. |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | EXP PMID:6249820 Human carbamylphosphate synthetase I. Stabilization, purific... | ACCEPT | Summary: Experimental demonstration of carbamoyl-phosphate synthase (ammonia) activity from purified human liver CPS1, including Michaelis constants for NH4+, HCO3-, MgATP, and the activator N-acetyl-L-glutamate. Reason: Direct experimental evidence for the core catalytic function using the purified human enzyme. This is the central molecular function of CPS1. Supporting Evidence: PMID:6249820 The apparent Michaelis constants for NH4+, HCO3-, MgATP, and the activator, N-acetyl-L-glutamic acid, were 0.8, 6.7, 1.1, and 0.1 mM, respectively. |
| GO:0005730 nucleolus | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Immunofluorescence-based (IDA) annotation to nucleolus. UniProt records a nucleus/nucleolus localization from large-scale spatial proteomics, but the catalytic function is in the mitochondrial matrix. Reason: A nucleus/nucleolus localization is reported in UniProt (PMID:22002106) and supported here by immunofluorescence curation, so it is retained; however it is a secondary localization unrelated to CPS1's core ureagenesis function in the mitochondrial matrix. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9955543 | ACCEPT | Summary: Reactome TAS annotation to the mitochondrial matrix, the correct functional location of CPS1. Reason: The mitochondrial matrix is the established site of CPS1 catalysis and is the correct, specific cellular location. Core localization. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9955504 | ACCEPT | Summary: Reactome TAS annotation (SIRT5 deglutarylation of CPS1) to the mitochondrial matrix, the correct functional location. Reason: Correct, specific core cellular location; consistent with all other matrix annotations. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | EXP PMID:23649895 Molecular characterization of carbamoyl-phosphate synthetase... | ACCEPT | Summary: Experimental demonstration of the core catalytic activity using recombinant human CPS1, with full kinetic characterization; this is one of the two references anchoring the EC 6.3.4.16 assignment in UniProt. Reason: Direct experimental evidence for the ammonia-dependent carbamoyl-phosphate synthase activity of recombinant human CPS1. Core molecular function. Supporting Evidence: PMID:23649895 The kinetic and molecular properties of recombinant CPS1 are essentially the same as for natural human CPS1. |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | EXP PMID:24813853 Understanding carbamoyl phosphate synthetase (CPS1) deficien... | ACCEPT | Summary: Experimental characterization of recombinant human CPS1 catalytic activity (and the effect of clinical mutations on Vmax/Km); this is the second reference anchoring the EC 6.3.4.16 assignment in UniProt. Reason: Direct experimental evidence for the core catalytic function of human CPS1. Core molecular function. Supporting Evidence: PMID:24813853 the majority of the mutations also decreased from modestly to very drastically the specific activity of the fraction of the enzyme that remained soluble and that could be purified, apparently because they decreased V(max) |
| GO:0005886 plasma membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Sequence-similarity (ISS) annotation to plasma membrane, consistent with the UniProt cell-surface location inferred from the mouse ortholog. Reason: A hepatocyte cell-surface / plasma-membrane location is reported in UniProt (by similarity to mouse Q8C196). This is a reported secondary localization, not the compartment of the core catalytic function. Keep as non-core. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: High-throughput mitochondrial-proteome evidence localizing CPS1 to the mitochondrion, the correct organelle. Reason: Consistent with the established mitochondrial-matrix localization; a valid (organelle-level) location annotation. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0030955 potassium ion binding | EXP PMID:26592762 Structure of human carbamoyl phosphate synthetase: decipheri... | ACCEPT | Summary: Experimental/structural evidence that CPS1 coordinates a potassium ion in the L1 K-loop; potassium is an essential ionic activator of the bicarbonate phosphorylation step. Reason: The crystal structure shows a coordinated potassium ion in the K-loop of the bicarbonate-phosphorylating domain, and potassium is required for catalysis. This is a genuine, functionally important cofactor-binding activity. Supporting Evidence: PMID:26592762 being fully structured, having at its center a coordinated potassium ion (thus the name K-loop) |
| GO:0036094 small molecule binding | EXP PMID:26592762 Structure of human carbamoyl phosphate synthetase: decipheri... | MODIFY | Summary: Experimental annotation to the very broad "small molecule binding" from the structural study, which resolved ADP, NAG, potassium and magnesium binding. Reason: "Small molecule binding" is uninformatively broad. The structure specifically resolves binding of the allosteric activator N-acetyl-L-glutamate (a modified amino acid); more informative and specific terms (NAG/modified amino acid binding, ATP binding, potassium/metal ion binding) are separately annotated. Replace with the specific modified amino acid (NAG) binding term. Proposed replacements: modified amino acid binding Supporting Evidence: PMID:26592762 One NAG molecule was found sitting with full occupancy in each subunit of ligand-bound CPS1 |
| GO:0046872 metal ion binding | EXP PMID:26592762 Structure of human carbamoyl phosphate synthetase: decipheri... | ACCEPT | Summary: Experimental/structural evidence for metal ion binding (magnesium coordinating ADP; potassium in the K-loop) in the active enzyme. Reason: Metal ion binding is directly supported by the structure (Mg2+ coordinated to the nucleotides and a coordinated K+); these ions are essential ionic activators of catalysis. Supporting Evidence: PMID:26592762 besides having also two bound magnesium ions, hosted a potassium ion coordinated to its K-loop |
| GO:0042311 vasodilation | IMP PMID:14718356 Relationship between carbamoyl-phosphate synthetase genotype... | MARK AS OVER ANNOTATED | Summary: Annotation to vasodilation from a study associating a CPS1 coding polymorphism (T1405N) with nitric-oxide-mediated forearm vasodilation. This is an indirect, downstream physiological consequence, not a molecular function of the enzyme. Reason: CPS1 influences vascular NO indirectly, by supplying carbamoyl phosphate for citrulline/arginine synthesis; the study is a genotype-phenotype association of a polymorphism with vascular reactivity, not evidence that CPS1 executes a vasodilation process. This is an over-annotation of a distal physiological effect. Supporting Evidence: PMID:14718356 a polymorphism in the gene encoding carbamoyl-phosphate synthetase 1 influences nitric oxide production as well as vascular smooth muscle reactivity. |
| GO:0070409 carbamoyl phosphate biosynthetic process | IMP PMID:21120950 Molecular defects in human carbamoy phosphate synthetase I: ... | ACCEPT | Summary: Mutant-phenotype evidence that CPS1 is required for carbamoyl phosphate biosynthesis, from the large CPS1D mutational-spectrum study. Reason: Carbamoyl phosphate biosynthesis is the direct product-forming process of CPS1, and loss-of-function CPS1 mutations abolish it (causing hyperammonemia). Core biological process, at an appropriate level of specificity. Supporting Evidence: PMID:21120950 Deficiency of carbamoyl phosphate synthetase I (CPSI) results in hyperammonemia ranging from neonatally lethal to environmentally induced adult-onset disease. |
| GO:0071242 cellular response to ammonium ion | IMP PMID:21120950 Molecular defects in human carbamoy phosphate synthetase I: ... | KEEP AS NON CORE | Summary: Annotation to cellular response to ammonium ion from the CPS1D mutational study. CPS1 consumes ammonia as a substrate for detoxification. Reason: CPS1 uses ammonia as its nitrogen substrate, and its loss causes hyperammonemia, so participation in the cellular handling/detoxification of ammonium is reasonable. This is better regarded as a physiological framing of the core urea-cycle role than a distinct core function; keep as non-core. Supporting Evidence: PMID:21120950 Deficiency of carbamoyl phosphate synthetase I (CPSI) results in hyperammonemia |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-70555 | ACCEPT | Summary: Reactome TAS annotation to the mitochondrial matrix (the CPS1 reaction event), the correct functional location. Reason: Correct, specific core cellular location for the site of the CPS1-catalyzed reaction. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9959874 | ACCEPT | Summary: Reactome TAS annotation to the mitochondrial matrix (CPS1 gene-expression event context), the correct functional location. Reason: Correct, specific core cellular location; consistent with all other matrix annotations. Supporting Evidence: PMID:15897806 an abundant enzyme of the hepatic urea cycle, which is normally located in the mitochondrial matrix. |
| GO:0050667 homocysteine metabolic process | IDA PMID:20031578 Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma... | REMOVE | Summary: Annotation to homocysteine metabolic process attributed to a genome-wide association study that linked a CPS1 SNP (rs7422339) to plasma homocysteine levels. There is no direct evidence that CPS1 acts in homocysteine metabolism. Reason: The cited paper is a GWAS reporting a statistical association between a common CPS1 variant and plasma homocysteine concentration in women; it does not demonstrate that CPS1 participates in homocysteine metabolism, and the IDA evidence code is misapplied. The urea cycle and one-carbon/homocysteine pathways intersect only indirectly. This is an over-interpretation of a GWAS signal. Supporting Evidence: PMID:20031578 we found novel associations with CPS1 (2q34; rs7422339; P=1.9 x 10(-11)) |
| GO:0072341 modified amino acid binding | IDA PMID:20031578 Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma... | ACCEPT | Summary: Annotation to modified amino acid binding attributed to the homocysteine GWAS paper. The cited reference does not demonstrate direct ligand binding, but the molecular function is nonetheless correct for CPS1 for a different reason: the enzyme binds the modified amino acid N-acetyl-L-glutamate as its essential allosteric activator. Reason: Modified amino acid binding is a genuine and functionally central activity of CPS1, whose obligatory allosteric activator N-acetyl-L-glutamate (an N-acetylated amino acid) binds a dedicated pocket in the C-terminal MGS-like domain, as shown structurally. Although the original GWAS reference is a weak basis, the term itself is correct and well supported by structural/biochemical data. Accept (supporting evidence re-anchored to the structural study). Supporting Evidence: PMID:26592762 One NAG molecule was found sitting with full occupancy in each subunit of ligand-bound CPS1 |
| GO:0070409 carbamoyl phosphate biosynthetic process | IMP PMID:7416778 Detection of carbamyl phosphate synthetase 1 deficiency usin... | ACCEPT | Summary: Mutant/deficiency-phenotype evidence (reduced CPS1 activity in duodenal biopsy of a hyperammonemic patient) that CPS1 is required for carbamoyl phosphate biosynthesis. Reason: Reduced CPS1 activity in patient tissue with hyperammonemia supports CPS1's required role in carbamoyl phosphate biosynthesis. Core biological process. Supporting Evidence: PMID:7416778 All enzyme levels were normal except N-acetyl glutamate-dependent carbamyl phosphate synthetase 1 (CPS1) which was half the mean activity in normal control specimens. |
| GO:0000050 urea cycle | NAS PMID:1840546 Cloning and sequence of a cDNA encoding human carbamyl phosp... | ACCEPT | Summary: Non-traceable author statement that CPS1 is the first enzyme of urea synthesis, from the human CPS1 cDNA cloning paper. Reason: CPS1's role in the urea cycle is a core, well-established biological process, here asserted from the cloning/sequence characterization of human CPS1. Supporting Evidence: PMID:1840546 Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis. |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IMP PMID:8486760 Carbamyl phosphate synthetase I deficiency. One base substit... | ACCEPT | Summary: Mutant-phenotype evidence (a splicing mutation causing a 9-bp in-frame deletion, with markedly reduced CPS1 mRNA/protein) that links loss of CPS1 to its ammonia-dependent synthetase function. Reason: A disease-causing CPS1 mutation abolishing normal CPS1 supports the enzyme's core carbamoyl-phosphate synthase (ammonia) activity. Core molecular function. Supporting Evidence: PMID:8486760 Northern and Western blots revealed a marked decrease in CPS I mRNA and enzyme protein |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IMP PMID:9711878 Prenatal diagnosis of carbamoyl phosphate synthetase I defic... | ACCEPT | Summary: Mutant-phenotype evidence: a homozygous Thr544Met missense mutation causing severe (lethal) CPS1 deficiency, supporting CPS1's core synthetase function. Reason: A disease-causing CPS1 missense mutation (Thr544Met, which structurally raises the Km for bicarbonate) causing severe CPS1 deficiency supports the core ammonia-dependent carbamoyl-phosphate synthase activity of CPS1. Supporting Evidence: PMID:9711878 Direct sequencing of the complete CPS1 coding region revealed a disease-associated homozygous Thr544Met mutation in CPS1. |
| GO:0019240 L-citrulline biosynthetic process | NAS PMID:14718356 Relationship between carbamoyl-phosphate synthetase genotype... | MARK AS OVER ANNOTATED | Summary: Non-traceable statement associating CPS1 with citrulline formation, from the vascular-function polymorphism study. CPS1 does not itself synthesize citrulline; it makes carbamoyl phosphate, the precursor that OTC then combines with ornithine to form citrulline. Reason: CPS1's product (carbamoyl phosphate) feeds citrulline biosynthesis, but the committed citrulline-forming reaction is catalyzed by ornithine transcarbamylase (OTC), not CPS1. Annotating CPS1 to L-citrulline biosynthetic process over-extends its role to a downstream step it does not catalyze; the term is loosely (NAS) asserted in a vascular-genetics paper. Supporting Evidence: PMID:14718356 the enzyme catalyzing the rate-limiting step in l-citrulline formation |
| GO:0019433 triglyceride catabolic process | IMP PMID:9711878 Prenatal diagnosis of carbamoyl phosphate synthetase I defic... | UNDECIDED | Summary: Annotation to triglyceride catabolic process attributed to an IMP in PMID:9711878. The cached record for this paper is abstract-only (full_text_available: false), and the abstract concerns a urea-cycle-defect (CPS1D) missense mutation with no triglyceride-catabolism content; there is no known biochemical basis linking CPS1 (a mitochondrial urea-cycle ligase) to triglyceride catabolism. Reason: This is an experimental (IMP) annotation whose full text is not available in the cache, so per project guidelines it should not be REMOVE'd on the basis of the abstract alone. The annotation looks biologically implausible / likely misassigned, but adjudication is deferred pending the GOA source line or full text; a curator with access should verify what phenotype the IMP actually supports. Supporting Evidence: PMID:9711878 Carbamoyl phosphate synthetase I (CPS1) deficiency is an autosomal recessive metabolic disorder affecting the first enzymatic step of urea cycle. |
| GO:0032496 response to lipopolysaccharide | IDA PMID:15897806 Release of the mitochondrial enzyme carbamoyl phosphate synt... | MARK AS OVER ANNOTATED | Summary: Annotation to response to LPS from a study showing that CPS1 is fragmented and released into the circulation under septic (LPS) conditions as a candidate biomarker of hepatic mitochondrial injury. Reason: The observation is that CPS1 protein is cleaved and released during endotoxemia (making it a serum biomarker), not that CPS1 executes a functional response to LPS. This is a downstream biomarker phenomenon rather than a biological process in which CPS1 participates; it over-annotates the enzyme's role. Supporting Evidence: PMID:15897806 We suggest that circulating CPS-1 might serve as a novel serum marker indicating mitochondrial impairment of the liver and/or the small intestine in critically ill patients. |
| GO:0042645 mitochondrial nucleoid | IDA PMID:18063578 The layered structure of human mitochondrial DNA nucleoids. | MARK AS OVER ANNOTATED | Summary: Annotation to mitochondrial nucleoid from a study that biochemically purified mtDNA nucleoids. CPS1 is among the abundant matrix proteins that co-purify with native nucleoids, but the study notes several such metabolic proteins do not cross-link to mtDNA. Reason: CPS1 is an extremely abundant matrix protein that can co-purify with native nucleoid preparations, but the paper explicitly notes that several metabolic proteins identified in native nucleoids were not observed to cross-link to mtDNA, indicating co-purification rather than genuine nucleoid association. The core functional location of CPS1 is the mitochondrial matrix; nucleoid localization is likely a preparation artifact and is over-annotated. Supporting Evidence: PMID:18063578 Several other metabolic proteins and chaperones identified in native nucleoids, including ATAD3, were not observed to cross-link to mtDNA. |
| GO:0046209 nitric oxide metabolic process | IMP PMID:14718356 Relationship between carbamoyl-phosphate synthetase genotype... | MARK AS OVER ANNOTATED | Summary: Annotation to nitric oxide metabolic process from the CPS1-polymorphism vascular-function study. CPS1 affects NO only indirectly, by supplying carbamoyl phosphate for the citrulline/arginine precursor pool. Reason: The link to NO is indirect and pathway-level: CPS1 provides carbamoyl phosphate for citrulline -> arginine, the NO precursor, and a coding polymorphism was statistically associated with NO metabolites and vasodilation. CPS1 does not itself synthesize or metabolize nitric oxide; this over-annotates a distal metabolic consequence. Supporting Evidence: PMID:14718356 a polymorphism in the gene encoding carbamoyl-phosphate synthetase 1 influences nitric oxide production as well as vascular smooth muscle reactivity. |
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