Existing Annotations Review

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 · 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 · 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 β 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.

Core Functions

CPS1 catalyzes the first, committed and rate-limiting step of the urea cycle: the ATP-dependent, ammonia-utilizing synthesis of carbamoyl phosphate from ammonia and bicarbonate, using 2 ATP. This ammonia detoxification reaction occurs in the hepatic (and intestinal) mitochondrial matrix and has an absolute allosteric requirement for the activator N-acetyl-L-glutamate.

Molecular Function:

carbamoyl-phosphate synthase (ammonia) activity

Directly Involved In:

urea cycle carbamoyl phosphate biosynthetic process

Cellular Locations:

mitochondrial matrix

Substrates:

ammonium hydrogencarbonate ATP

Supporting Evidence:

PMID:23649895
The kinetic and molecular properties of recombinant CPS1 are essentially the same as for natural human CPS1.
PMID:26592762
Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain enzyme, catalyzes the first step of ammonia detoxification to urea requiring N-acetyl-L-glutamate (NAG) as essential activator

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12620389

Novel raf kinase protein-protein interactions found by an exhaustive yeast two-hybrid analysis.

PMID:14718356

Relationship between carbamoyl-phosphate synthetase genotype and systemic vascular function.

PMID:15161933

Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins.

PMID:15897806

Release of the mitochondrial enzyme carbamoyl phosphate synthase under septic conditions.

PMID:18063578

The layered structure of human mitochondrial DNA nucleoids.

PMID:1840546

Cloning and sequence of a cDNA encoding human carbamyl phosphate synthetase I: molecular analysis of hyperammonemia.

PMID:20031578

Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine in a healthy population: a genome-wide evaluation of 13 974 participants in the Women's Genome Health Study.

PMID:20618440

Proteomic and biochemical analysis of 14-3-3-binding proteins during C2-ceramide-induced apoptosis.

PMID:21120950

Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations.

PMID:23649895

Molecular characterization of carbamoyl-phosphate synthetase (CPS1) deficiency using human recombinant CPS1 as a key tool.

PMID:24813853

Understanding carbamoyl phosphate synthetase (CPS1) deficiency by using the recombinantly purified human enzyme: effects of CPS1 mutations that concentrate in a central domain of unknown function.

PMID:26592762

Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.

PMID:34800366

Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.

PMID:6249820

Human carbamylphosphate synthetase I. Stabilization, purification, and partial characterization of the enzyme from human liver.

PMID:7416778

Detection of carbamyl phosphate synthetase 1 deficiency using duodenal biopsy samples.

PMID:8486760

Carbamyl phosphate synthetase I deficiency. One base substitution in an exon of the CPS I gene causes a 9-basepair deletion due to aberrant splicing.

PMID:9711878

Prenatal diagnosis of carbamoyl phosphate synthetase I deficiency by identification of a missense mutation in CPS1.

Reactome:R-HSA-70555

2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]

Reactome:R-HSA-70635

Urea cycle

Reactome:R-HSA-9955504

SIRT5 deglutarylates CPS1

Reactome:R-HSA-9955543

CPS1 variants don't synthesize carbamoyl phosphate

Reactome:R-HSA-9959874

CPS1 gene expression

Deep Research

Falcon

(CPS1-deep-research-falcon.md)

Comprehensive Functional Annotation of Human CPS1 (Carbamoyl-Phosphate Synthase 1, Mitochondrial) Falcon Edison Scientific Literature 44 citations 1 artifacts 2026-07-05T13:24:21.724934

Edison artifact artifact-00 (text/markdown)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Functional Annotation of Human CPS1 (Carbamoyl-Phosphate Synthase 1, Mitochondrial)

Gene and Protein Identity

CPS1 (gene symbol: CPS1; UniProt accession: P31327; ENSG00000021826) encodes carbamoyl-phosphate synthase [ammonia], mitochondrial (also known as carbamoyl-phosphate synthetase I, CPSase I; EC 6.3.4.16). The gene is located on human chromosome 2q35 and comprises 38 exons (dong2024clinicalfeaturesand pages 5-6). The CPS1 protein is synthesized as a 1,500-amino acid precursor, with an N-terminal mitochondrial targeting sequence of approximately 38 residues that is cleaved upon import into the mitochondrial matrix, yielding a mature enzyme of 1,462 residues (~160 kDa) (fernandez2015usingrecombinanthuman pages 71-77, fernandez2015usingrecombinanthuman pages 106-110, fernandez2015usingrecombinanthuman pages 85-89). CPS1 is expressed exclusively in hepatocytes and enterocytes (liver and small intestine), where it constitutes an extraordinarily abundant enzyme, comprising 10–25% of the total mitochondrial matrix protein in liver (pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2, fernandez2015usingrecombinanthuman pages 37-41).

The summary table below provides a quick-reference overview of CPS1's key properties:

Property	Summary
Gene name	CPS1 (carbamoyl-phosphate synthase 1) (OpenTargets Search: -CPS1, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2)
Protein name	Carbamoyl-phosphate synthase [ammonia], mitochondrial; carbamoyl-phosphate synthetase I; CPSase I (OpenTargets Search: -CPS1, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2)
EC number	EC 6.3.4.16 (OpenTargets Search: -CPS1, fernandez2015usingrecombinanthuman pages 71-77)
UniProt ID	P31327 (OpenTargets Search: -CPS1)
Organism	Homo sapiens (Human) (OpenTargets Search: -CPS1)
Molecular weight	~160 kDa mature mitochondrial enzyme (fernandez2015usingrecombinanthuman pages 71-77, fernandez2015usingrecombinanthuman pages 37-41)
Precursor length	1500 aa precursor with N-terminal mitochondrial targeting sequence (pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2)
Mature length	1462 aa after cleavage of ~38 aa transit peptide upon mitochondrial import (fernandez2015usingrecombinanthuman pages 106-110, fernandez2015usingrecombinanthuman pages 85-89)
Subcellular localization	Mitochondrial matrix; a substantial fraction also associates in clusters near the inner mitochondrial membrane with NAGS and OTC (fernandez2015usingrecombinanthuman pages 37-41, haskins2021mitochondrialenzymesof pages 2-3, haskins2021mitochondrialenzymesof pages 1-2)
Tissue expression	Expressed predominantly in hepatocytes and enterocytes (liver and small intestine) (pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2, fernandez2015usingrecombinanthuman pages 106-110)
Substrates	2 ATP + NH3 + HCO3-; CPS1 uses free ammonia rather than glutamine (fernandez2015usingrecombinanthuman pages 37-41, fernandez2015usingrecombinanthuman pages 71-77, fernandez2015usingrecombinanthuman pages 24-31)
Products	Carbamoyl phosphate + 2 ADP + Pi (fernandez2015usingrecombinanthuman pages 37-41, fernandez2015usingrecombinanthuman pages 71-77)
Primary biochemical function	Catalyzes the first and rate-limiting step of the urea cycle, producing carbamoyl phosphate for conversion with ornithine to citrulline by OTC (fernandez2015usingrecombinanthuman pages 37-41, yao2020smallmoleculeinhibition pages 1-3)
Catalytic mechanism	Three-step mechanism with carboxyphosphate and carbamate intermediates; two distinct phosphorylation sites for bicarbonate and carbamate phosphorylation (fernandez2015usingrecombinanthuman pages 37-41, fernandez2015usingrecombinanthuman pages 41-44)
Allosteric activator	N-acetyl-L-glutamate (NAG) is an essential allosteric activator; CPS1 is inactive without it (fernandez2015usingrecombinanthuman pages 41-44, nakagawa2009sirt5deacetylatescarbamoyl pages 3-4, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2)
Key regulatory modification: SIRT5 deacetylation	SIRT5 deacetylates and activates CPS1 in the mitochondrial matrix, especially during fasting/calorie restriction, promoting ammonia detoxification (nakagawa2009sirt5deacetylatescarbamoyl pages 3-4, nakagawa2009sirt5deacetylatescarbamoyl pages 7-8, nakagawa2009sirt5deacetylatescarbamoyl pages 6-7)
Key regulatory modification: O-GlcNAcylation	O-GlcNAcylation regulates CPS1 activity in a nutrient-sensitive manner; reported sites include Thr109, Thr110, Thr1078 that enhance catalytic efficiency for ammonia, while aging/dietary studies also identify nutrient-responsive O-GlcNAc regulation affecting ureagenesis (soria2022oglcnacylationenhancescps1 pages 4-4, soria2022oglcnacylationenhancescps1 pages 6-7, wu2022regulationofthe pages 1-2, wu2022regulationofthe pages 2-5)
Structural/domain features	Multidomain enzyme with bicarbonate-phosphorylation and carbamate-phosphorylation domains plus a C-terminal allosteric NAG-binding domain and integrating/unknown-function subdomain (fernandez2015usingrecombinanthuman pages 106-110, fernandez2015usingrecombinanthuman pages 41-44)
Disease association: inherited disorder	CPS1 deficiency (OMIM 237300), an autosomal recessive urea-cycle disorder causing severe hyperammonemia; neonatal and late-onset forms are reported (dong2024clinicalfeaturesand pages 1-2, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2)
Clinical features/statistics in recent cohorts	In a 2024 Chinese series of 7 patients, peak ammonia ranged 160-1000 umol/L; 4 died and 3 survived with treatment; 10 of 12 variants identified were novel (dong2024clinicalfeaturesand pages 4-5)
Typical treatment/management	Ammonia scavengers (sodium phenylbutyrate, sodium benzoate), arginine, low-protein diet, hemodialysis in crises, and sometimes liver transplantation (dong2024clinicalfeaturesand pages 4-5, wang2023clinicalandgenetic pages 3-5)
Disease association: cancer	CPS1 can be downregulated in hepatocellular carcinoma via promoter DNA methylation, but is upregulated in several other cancers where it supports pyrimidine synthesis and tumor growth (liu2011dnamethylationsuppresses pages 4-6, hajaj2023fromtheinside pages 4-5)
Real-world/therapeutic relevance	CPS1 is a candidate target in hyperammonemia and oncology; small-molecule inhibition in primary human hepatocytes reduces urea production and affects pyrimidine metabolism (yao2020smallmoleculeinhibition pages 8-8, yao2020smallmoleculeinhibition pages 1-3)
PDB structure codes	5DOT (apo human CPS1 used as structural reference), 5DOU (human CPS1 structure), 6UEL (CPS1 in complex with allosteric inhibitor H3B-193 at 1.90 A resolution) (haskins2021mitochondrialenzymesof pages 1-2, yao2020smallmoleculeinhibition pages 14-15)

Table: This table summarizes the verified identity, biochemical function, regulation, localization, disease relevance, and structural resources for human CPS1 (UniProt P31327). It is useful as a compact reference for the main facts needed in a functional-annotation report.

Enzymatic Reaction and Catalytic Mechanism

CPS1 catalyzes the first and rate-limiting step of the urea cycle: the ATP-dependent synthesis of carbamoyl phosphate from ammonia, bicarbonate, and two molecules of ATP (fernandez2015usingrecombinanthuman pages 71-77, yao2020smallmoleculeinhibition pages 1-3). The overall reaction is:

2 ATP + NH₃ + HCO₃⁻ → carbamoyl phosphate + 2 ADP + Pᵢ

This reaction proceeds through a three-step catalytic mechanism involving two unstable intermediates (fernandez2015usingrecombinanthuman pages 37-41, fernandez2015usingrecombinanthuman pages 41-44):

Bicarbonate phosphorylation: The first ATP molecule phosphorylates bicarbonate at the N-terminal phosphorylation domain, forming the highly reactive intermediate carboxyphosphate (also referred to as "active CO₂").
Carbamate formation: Ammonia reacts with carboxyphosphate to form carbamate, releasing inorganic phosphate.
Carbamate phosphorylation: The second ATP molecule phosphorylates carbamate at the C-terminal phosphorylation domain, producing the final product, carbamoyl phosphate.

The two reactive intermediates (carboxyphosphate and carbamate) are shielded from water as they migrate between the two phosphorylation centers through an intraenzymatic pathway (fernandez2015usingrecombinanthuman pages 41-44). An important kinetic feature is that the intraenzymatic reversible reaction between ATP and bicarbonate occurs much faster than the overall reaction, representing a rapid equilibrium step followed by slower ammonia incorporation (fernandez2015usingrecombinanthuman pages 37-41).

A critical distinction from CPS2 (the cytosolic carbamoyl phosphate synthetase II, part of the CAD multienzymatic complex involved in pyrimidine biosynthesis) is that CPS1 uses free ammonia directly as its nitrogen source, rather than glutamine (fernandez2015usingrecombinanthuman pages 24-31). CPS1 possesses an approximately 100-fold higher affinity for ammonia compared to bacterial CPS, making it well-suited for detoxification of ammonia at portal blood concentrations (fernandez2015usingrecombinanthuman pages 37-41).

Domain Architecture and Structural Biology

CPS1 is a multidomain enzyme organized as a single polypeptide chain with fused subunit domains that can be functionally divided into a small subunit region (~40 kDa) and a large subunit region (~120 kDa) (fernandez2015usingrecombinanthuman pages 106-110, fernandez2015usingrecombinanthuman pages 41-44). The large subunit region functions as a pseudohomodimer, containing two homologous ~60 kDa halves, each consisting of an ~45 kDa phosphorylation domain followed by an ~15 kDa domain:

N-terminal phosphorylation domain: Catalyzes bicarbonate phosphorylation (the "ATP A" domain).
C-terminal phosphorylation domain: Catalyzes carbamate phosphorylation (the "ATP B" domain).
Integrating domain (UFSD): A ~17.7 kDa subdomain (residues 822–973) connecting the two phosphorylation domains; it has no substrate sites or catalytic components but contains an allosteric pocket exploited by small-molecule inhibitors (fernandez2015usingrecombinanthuman pages 106-110, yao2020smallmoleculeinhibition pages 5-7).
Allosteric/regulatory domain (ASD): The C-terminal ~20 kDa domain (residues 1354–1500) binds the essential allosteric activator N-acetyl-L-glutamate (NAG) and controls the enzyme's on/off state (fernandez2015usingrecombinanthuman pages 106-110, fernandez2015usingrecombinanthuman pages 133-137).

The crystal structure of human CPS1 has been determined, with key depositions in the Protein Data Bank including PDB 5DOT (apo form), 5DOU (liganded form), and 6UEL (CPS1 in complex with the allosteric inhibitor H3B-193, resolved at 1.90 Å) (yao2020smallmoleculeinhibition pages 5-7, yao2020smallmoleculeinhibition pages 14-15). The co-crystal structure of CPS1 with H3B-193 revealed a previously unknown allosteric pocket located between the integrating and ATP A domains, approximately 10 Å wide at its opening and 24 Å deep, lined with hydrophobic residues (M656, V664, F809, L813, I851). Binding of the inhibitor induces a conformational change in the flexible K-loop (residues V653–H659), which flips out of the ATP binding pocket to stabilize the inhibitor (yao2020smallmoleculeinhibition pages 5-7).

Subcellular Localization and Supramolecular Organization

CPS1 resides in the mitochondrial matrix after cleavage of its N-terminal targeting peptide (fernandez2015usingrecombinanthuman pages 85-89, fernandez2015usingrecombinanthuman pages 37-41). Elegant studies using super-resolution gated stimulation emission depletion (gSTED) microscopy and biochemical fractionation have demonstrated that CPS1, together with N-acetylglutamate synthase (NAGS) and ornithine transcarbamylase (OTC), forms dynamic nanoclusters at the inner mitochondrial membrane (IMM) rather than functioning as isolated soluble matrix enzymes (haskins2021mitochondrialenzymesof pages 2-3, haskins2021mitochondrialenzymesof pages 1-2, haskins2021mitochondrialenzymesof pages 11-13). Approximately 35% of CPS1 and 30% of OTC partition with the IMM fraction, and these proteins co-immunoprecipitate (haskins2021mitochondrialenzymesof pages 11-13). The clusters measure 100–150 nm and contain multiple urea cycle enzymes, facilitating efficient channeling of the unstable intermediate carbamoyl phosphate and potentially increasing pathway flux up to 100-fold through increased local enzyme and metabolite concentrations (haskins2021mitochondrialenzymesof pages 13-14). The mammalian-specific "variable segment" of NAGS mediates the interaction between NAGS and CPS1 within these clusters (haskins2021mitochondrialenzymesof pages 1-2). Surface amino acid mutations in CPS1 and OTC that do not affect catalytic activity or protein stability can nonetheless impair ureagenesis by disrupting these enzyme–enzyme interactions, underscoring the functional importance of the supramolecular organization (haskins2021mitochondrialenzymesof pages 5-7, haskins2021mitochondrialenzymesof pages 7-10).

Metabolic Pathway Context

The Urea Cycle

CPS1 catalyzes the first committed step of the urea cycle, which consists of five enzymatic reactions: CPS1 → OTC → argininosuccinate synthetase (ASS1) → argininosuccinate lyase (ASL) → arginase (ARG1) (mitchell2009geneticvariationin pages 2-3, yao2020smallmoleculeinhibition pages 1-3). The carbamoyl phosphate produced by CPS1 is immediately transferred to OTC, which combines it with ornithine to form citrulline—the first specific intermediate of the urea cycle (fernandez2015usingrecombinanthuman pages 37-41, haskins2021mitochondrialenzymesof pages 2-3). The urea cycle is the only mammalian pathway capable of efficiently converting ammonia into urea, sufficient to detoxify tens of grams of ammonia daily (zhu2026ureacycledysregulation pages 5-7). In the liver, the urea cycle operates as a high-capacity system for ammonia removal in periportal hepatocytes, complementing the high-affinity glutamine synthetase system in perivenous hepatocytes (fernandez2015usingrecombinanthuman pages 37-41).

Connection to Pyrimidine Biosynthesis

Beyond the urea cycle, carbamoyl phosphate produced by CPS1 can leak from mitochondria to the cytosol, where it serves as a substrate for pyrimidine biosynthesis via the cytosolic CAD enzyme complex (CPS2/ATCase/DHOase). This alternative metabolic fate is particularly significant in cancer cells with high CPS1 expression, where increased carbamoyl phosphate production fuels nucleotide synthesis to support rapid proliferation (hajaj2023fromtheinside pages 4-5).

Regulation of CPS1 Activity

Allosteric Activation by N-Acetylglutamate (NAG)

CPS1 is essentially inactive without its obligate allosteric activator, N-acetyl-L-glutamate (NAG), which is synthesized by NAGS from acetyl-CoA and glutamate (nakagawa2009sirt5deacetylatescarbamoyl pages 3-4, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2). NAG binds to the C-terminal allosteric domain and is required for the enzyme to adopt a catalytically competent conformation. This allosteric regulation provides the primary on/off switch for flux through the urea cycle (fernandez2015usingrecombinanthuman pages 133-137).

Post-Translational Regulation by SIRT5

The mitochondrial sirtuin SIRT5, an NAD⁺-dependent deacetylase localized to the mitochondrial matrix, was identified as a specific regulator of CPS1 (nakagawa2009sirt5deacetylatescarbamoyl pages 1-2, nakagawa2009sirt5deacetylatescarbamoyl pages 3-4). SIRT5 deacetylates CPS1, increasing its enzymatic activity. During fasting and calorie restriction, mitochondrial NAD⁺ levels rise approximately two-fold, upregulating SIRT5 activity and thereby promoting CPS1 deacetylation and ammonia disposal (nakagawa2009sirt5deacetylatescarbamoyl pages 5-6, nakagawa2009sirt5deacetylatescarbamoyl pages 6-7). SIRT5 knockout mice exhibit significantly elevated blood ammonia levels following fasting, demonstrating the physiological importance of this regulatory mechanism (nakagawa2009sirt5deacetylatescarbamoyl pages 6-7). This regulation is specific to SIRT5, as other mitochondrial sirtuins (SIRT3, SIRT4) do not affect CPS1 activity (nakagawa2009sirt5deacetylatescarbamoyl pages 3-4).

Post-Translational Regulation by O-GlcNAcylation

O-linked N-acetylglucosamine glycosylation (O-GlcNAcylation) represents another layer of nutrient-responsive CPS1 regulation. Two studies have provided complementary but mechanistically distinct findings:

Soria et al. (2022, Nature Communications) demonstrated that O-GlcNAcylation at specific threonine residues (Thr109, Thr110, and Thr1078) enhances CPS1 catalytic efficiency for ammonia and promotes ureagenesis. Pharmacological inhibition of O-GlcNAcase (OGA) with Thiamet-G increased CPS1 O-GlcNAcylation and reduced hyperammonemia in mouse models of both genetic (propionic acidemia) and acquired (thioacetamide-induced liver failure) liver diseases (soria2022oglcnacylationenhancescps1 pages 4-4, soria2022oglcnacylationenhancescps1 pages 6-7, soria2022oglcnacylationenhancescps1 pages 7-8).
Wu et al. (2022, Journal of Molecular Cell Biology) found that global O-GlcNAc levels increase in aged tissues, with CPS1 being among the most heavily O-GlcNAcylated proteins in aged liver. In their model, high glucose stimulates CPS1 O-GlcNAcylation and inhibits CPS1 activity, while calorie restriction reverses CPS1 O-GlcNAcylation. The O-GlcNAcylation site Ser537 was identified as important for regulation (wu2022regulationofthe pages 1-2, wu2022regulationofthe pages 2-5, wu2022regulationofthe pages 5-6).

These findings collectively position CPS1 O-GlcNAcylation as a nutrient-sensing mechanism linking dietary status and aging to urea cycle regulation, though the opposing functional effects reported may reflect context-dependent or site-specific modifications (wu2022regulationofthe pages 7-9).

Additional Post-Translational Modifications

Beyond acetylation and O-GlcNAcylation, CPS1 has been found to undergo malonylation, succinylation, fatty acylation, and nitration, which generally have neutral or negative effects on enzyme activity (soria2022oglcnacylationenhancescps1 pages 6-7). Phosphorylation sites on CPS1, including pY590, pY852, and pY1450, have been mapped to binding domains for NAG, substrates, and dimer interfaces, suggesting additional regulatory inputs (evidence from phosphoproteomic studies).

Disease Associations

CPS1 Deficiency (OMIM 237300)

CPS1 deficiency (CPS1D) is a rare autosomal recessive inborn error of the urea cycle characterized by severe hyperammonemia (dong2024clinicalfeaturesand pages 1-2, pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2). The disease presents in two clinical forms:

Early-onset (neonatal): Manifests within the first days of life with poor feeding, vomiting, lethargy, seizures, and rapidly progressive encephalopathy. Without treatment, neonatal-onset CPS1D is typically lethal (dong2024clinicalfeaturesand pages 4-5, dong2024clinicalfeaturesand pages 1-2).
Late-onset: Presents from childhood to adulthood with variable severity, including developmental delay, psychiatric symptoms, and metabolic crises triggered by high-protein intake or acute illness (dong2024clinicalfeaturesand pages 4-5, wang2023clinicalandgenetic pages 3-5).

In a 2024 cohort of seven Chinese patients, peak blood ammonia levels ranged from 160 to 1,000 µmol/L, with low citrulline and arginine levels being characteristic biochemical findings. Four of seven patients died, and 10 of 12 identified CPS1 variants were novel, highlighting the broad mutation spectrum without hotspot variants (dong2024clinicalfeaturesand pages 4-5, dong2024clinicalfeaturesand pages 5-6). Treatment modalities include ammonia scavengers (sodium phenylbutyrate, sodium benzoate), arginine supplementation, low-protein diet, hemodialysis during acute crises, and liver transplantation as definitive therapy (dong2024clinicalfeaturesand pages 4-5, wang2023clinicalandgenetic pages 3-5). Some patients may respond to N-carbamyl-L-glutamate (NCG), a stable NAG analog that can activate residual CPS1 enzyme activity (fernandez2015usingrecombinanthuman pages 133-137).

CPS1 is also associated with hyperammonemia, kidney failure, venous thromboembolism, and skeletal abnormalities through genetic association studies (OpenTargets Search: -CPS1).

CPS1 in Cancer

CPS1 exhibits a paradoxical dual role in cancer. In hepatocellular carcinoma (HCC), CPS1 expression is frequently suppressed through DNA methylation of CpG dinucleotides near the transcription start site. In 80.6% of 36 HCC tumor samples examined, CPS1 mRNA levels were significantly lower than in noncancerous tissue (liu2011dnamethylationsuppresses pages 4-6). In non-alcoholic fatty liver disease (NAFLD/NASH), CPS1 mRNA levels are decreased by 30–40% on average, contributing to impaired urea production and hyperammonemia (zhu2026ureacycledysregulation pages 5-7).

Conversely, CPS1 is upregulated in multiple extrahepatic cancers including rectal, stomach, melanoma, sarcoma, lung carcinoma, glioma, glioblastoma, and B-cell lymphoma (hajaj2023fromtheinside pages 4-5). In these contexts, elevated CPS1 activity increases carbamoyl phosphate production, which leaks from mitochondria to the cytosol and serves as substrate for pyrimidine biosynthesis, supporting tumor cell proliferation. Silencing CPS1 in such cancer cells results in cell death through pyrimidine depletion both in vitro and in vivo (hajaj2023fromtheinside pages 4-5). The first small-molecule CPS1 inhibitor, H3B-120 (IC₅₀ ~1.5 µM), was identified through high-throughput screening and demonstrated cellular activity in blocking both urea cycle function and pyrimidine biosynthesis support in primary human hepatocytes, establishing CPS1 as a druggable oncology target (yao2020smallmoleculeinhibition pages 4-5, yao2020smallmoleculeinhibition pages 1-3).

Conclusions

CPS1 is a highly abundant mitochondrial matrix enzyme that catalyzes the first and rate-limiting reaction of the urea cycle, converting ammonia, bicarbonate, and two ATP molecules into carbamoyl phosphate through a three-step mechanism involving carboxyphosphate and carbamate intermediates. The enzyme absolutely requires N-acetylglutamate as an allosteric activator and is further regulated by multiple post-translational modifications including SIRT5-mediated deacetylation and O-GlcNAcylation, which link its activity to nutritional status and aging. CPS1, together with NAGS and OTC, forms dynamic nanoclusters at the inner mitochondrial membrane that facilitate efficient substrate channeling. Deficiency of CPS1 causes severe hyperammonemia with high morbidity and mortality, while its aberrant expression in cancer—either suppressed in HCC or upregulated in extrahepatic tumors—contributes to metabolic reprogramming. The availability of high-resolution crystal structures and the identification of druggable allosteric pockets position CPS1 as an active area of both basic and translational research.

References

(dong2024clinicalfeaturesand pages 5-6): Hui Dong, Tian Sang, Xue Ma, Jinqing Song, Zhehui Chen, Huiting Zhang, Ying Jin, Mengqiu Li, Dingding Dong, Liying Sun, Zhijun Zhu, Yao Zhang, and Yanling Yang. Clinical features and cps1 variants in chinese patients with carbamoyl phosphate synthetase 1 deficiency. BMC Pediatrics, Aug 2024. URL: https://doi.org/10.1186/s12887-024-05005-5, doi:10.1186/s12887-024-05005-5. This article has 5 citations and is from a peer-reviewed journal.
(fernandez2015usingrecombinanthuman pages 71-77): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(fernandez2015usingrecombinanthuman pages 106-110): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(fernandez2015usingrecombinanthuman pages 85-89): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(pekkala2010understandingcarbamoyl‐phosphatesynthetase pages 1-2): Satu Pekkala, Ana I. Martínez, Belén Barcelona, Igor Yefimenko, Ulrich Finckh, Vicente Rubio, and Javier Cervera. Understanding carbamoyl‐phosphate synthetase i (cps1) deficiency by using expression studies and structure‐based analysis. Human Mutation, 31:801-808, Jul 2010. URL: https://doi.org/10.1002/humu.21272, doi:10.1002/humu.21272. This article has 50 citations and is from a domain leading peer-reviewed journal.
(fernandez2015usingrecombinanthuman pages 37-41): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(OpenTargets Search: -CPS1): Open Targets Query (-CPS1, 9 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.
(haskins2021mitochondrialenzymesof pages 2-3): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(haskins2021mitochondrialenzymesof pages 1-2): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(fernandez2015usingrecombinanthuman pages 24-31): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(yao2020smallmoleculeinhibition pages 1-3): Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, and David M. Bolduc. Small molecule inhibition of cps1 activity through an allosteric pocket. Cell Chemical Biology, 27:259-268.e5, Mar 2020. URL: https://doi.org/10.1016/j.chembiol.2020.01.009, doi:10.1016/j.chembiol.2020.01.009. This article has 41 citations and is from a domain leading peer-reviewed journal.
(fernandez2015usingrecombinanthuman pages 41-44): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(nakagawa2009sirt5deacetylatescarbamoyl pages 3-4): Takashi Nakagawa, David J. Lomb, Marcia C. Haigis, and Leonard Guarente. Sirt5 deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell, 137:560-570, May 2009. URL: https://doi.org/10.1016/j.cell.2009.02.026, doi:10.1016/j.cell.2009.02.026. This article has 992 citations and is from a highest quality peer-reviewed journal.
(nakagawa2009sirt5deacetylatescarbamoyl pages 7-8): Takashi Nakagawa, David J. Lomb, Marcia C. Haigis, and Leonard Guarente. Sirt5 deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell, 137:560-570, May 2009. URL: https://doi.org/10.1016/j.cell.2009.02.026, doi:10.1016/j.cell.2009.02.026. This article has 992 citations and is from a highest quality peer-reviewed journal.
(nakagawa2009sirt5deacetylatescarbamoyl pages 6-7): Takashi Nakagawa, David J. Lomb, Marcia C. Haigis, and Leonard Guarente. Sirt5 deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell, 137:560-570, May 2009. URL: https://doi.org/10.1016/j.cell.2009.02.026, doi:10.1016/j.cell.2009.02.026. This article has 992 citations and is from a highest quality peer-reviewed journal.
(soria2022oglcnacylationenhancescps1 pages 4-4): Leandro R. Soria, Georgios Makris, Alfonso M. D’Alessio, Angela De Angelis, Iolanda Boffa, Veronica M. Pravata, Véronique Rüfenacht, Sergio Attanasio, Edoardo Nusco, Paola Arena, Andrew T. Ferenbach, Debora Paris, Paola Cuomo, Andrea Motta, Matthew Nitzahn, Gerald S. Lipshutz, Ainhoa Martínez-Pizarro, Eva Richard, Lourdes R. Desviat, Johannes Häberle, Daan M. F. van Aalten, and Nicola Brunetti-Pierri. O-glcnacylation enhances cps1 catalytic efficiency for ammonia and promotes ureagenesis. Nature Communications, Sep 2022. URL: https://doi.org/10.1038/s41467-022-32904-x, doi:10.1038/s41467-022-32904-x. This article has 23 citations and is from a highest quality peer-reviewed journal.
(soria2022oglcnacylationenhancescps1 pages 6-7): Leandro R. Soria, Georgios Makris, Alfonso M. D’Alessio, Angela De Angelis, Iolanda Boffa, Veronica M. Pravata, Véronique Rüfenacht, Sergio Attanasio, Edoardo Nusco, Paola Arena, Andrew T. Ferenbach, Debora Paris, Paola Cuomo, Andrea Motta, Matthew Nitzahn, Gerald S. Lipshutz, Ainhoa Martínez-Pizarro, Eva Richard, Lourdes R. Desviat, Johannes Häberle, Daan M. F. van Aalten, and Nicola Brunetti-Pierri. O-glcnacylation enhances cps1 catalytic efficiency for ammonia and promotes ureagenesis. Nature Communications, Sep 2022. URL: https://doi.org/10.1038/s41467-022-32904-x, doi:10.1038/s41467-022-32904-x. This article has 23 citations and is from a highest quality peer-reviewed journal.
(wu2022regulationofthe pages 1-2): Jing Wu, Jiayu Liu, Kalina Lapenta, Reina Desrouleaux, Min-Dian Li, and Xiaoyong Yang. Regulation of the urea cycle by cps1 o-glcnacylation in response to dietary restriction and aging. Journal of Molecular Cell Biology, Mar 2022. URL: https://doi.org/10.1093/jmcb/mjac016, doi:10.1093/jmcb/mjac016. This article has 17 citations and is from a peer-reviewed journal.
(wu2022regulationofthe pages 2-5): Jing Wu, Jiayu Liu, Kalina Lapenta, Reina Desrouleaux, Min-Dian Li, and Xiaoyong Yang. Regulation of the urea cycle by cps1 o-glcnacylation in response to dietary restriction and aging. Journal of Molecular Cell Biology, Mar 2022. URL: https://doi.org/10.1093/jmcb/mjac016, doi:10.1093/jmcb/mjac016. This article has 17 citations and is from a peer-reviewed journal.
(dong2024clinicalfeaturesand pages 1-2): Hui Dong, Tian Sang, Xue Ma, Jinqing Song, Zhehui Chen, Huiting Zhang, Ying Jin, Mengqiu Li, Dingding Dong, Liying Sun, Zhijun Zhu, Yao Zhang, and Yanling Yang. Clinical features and cps1 variants in chinese patients with carbamoyl phosphate synthetase 1 deficiency. BMC Pediatrics, Aug 2024. URL: https://doi.org/10.1186/s12887-024-05005-5, doi:10.1186/s12887-024-05005-5. This article has 5 citations and is from a peer-reviewed journal.
(dong2024clinicalfeaturesand pages 4-5): Hui Dong, Tian Sang, Xue Ma, Jinqing Song, Zhehui Chen, Huiting Zhang, Ying Jin, Mengqiu Li, Dingding Dong, Liying Sun, Zhijun Zhu, Yao Zhang, and Yanling Yang. Clinical features and cps1 variants in chinese patients with carbamoyl phosphate synthetase 1 deficiency. BMC Pediatrics, Aug 2024. URL: https://doi.org/10.1186/s12887-024-05005-5, doi:10.1186/s12887-024-05005-5. This article has 5 citations and is from a peer-reviewed journal.
(wang2023clinicalandgenetic pages 3-5): Shangyu Wang, Jinglin Chen, Xiaoqi Zhu, Tingting Huang, Haifeng Xu, Guohuan Ying, Hao Qian, Wenxin Lin, Yiehen Tung, Kaleem Ullah Khan, Hu Guo, Guo Zheng, Haiying Lu, and Gang Zhang. Clinical and genetic analysis of a case of late onset carbamoyl phosphate synthase i deficiency caused by cps1 mutation and literature review. BMC Medical Genomics, Jun 2023. URL: https://doi.org/10.1186/s12920-023-01569-w, doi:10.1186/s12920-023-01569-w. This article has 10 citations and is from a peer-reviewed journal.
(liu2011dnamethylationsuppresses pages 4-6): Hongyan Liu, Huijia Dong, Keith Robertson, and Chen Liu. Dna methylation suppresses expression of the urea cycle enzyme carbamoyl phosphate synthetase 1 (cps1) in human hepatocellular carcinoma. The American journal of pathology, 178 2:652-61, Feb 2011. URL: https://doi.org/10.1016/j.ajpath.2010.10.023, doi:10.1016/j.ajpath.2010.10.023. This article has 133 citations.
(hajaj2023fromtheinside pages 4-5): Emma Hajaj, Sabina Pozzi, and Ayelet Erez. From the inside out: exposing the roles of urea cycle enzymes in tumors and their micro and macro environments. Cold Spring Harbor perspectives in medicine, 14:a041538, Sep 2024. URL: https://doi.org/10.1101/cshperspect.a041538, doi:10.1101/cshperspect.a041538. This article has 12 citations and is from a peer-reviewed journal.
(yao2020smallmoleculeinhibition pages 8-8): Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, and David M. Bolduc. Small molecule inhibition of cps1 activity through an allosteric pocket. Cell Chemical Biology, 27:259-268.e5, Mar 2020. URL: https://doi.org/10.1016/j.chembiol.2020.01.009, doi:10.1016/j.chembiol.2020.01.009. This article has 41 citations and is from a domain leading peer-reviewed journal.
(yao2020smallmoleculeinhibition pages 14-15): Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, and David M. Bolduc. Small molecule inhibition of cps1 activity through an allosteric pocket. Cell Chemical Biology, 27:259-268.e5, Mar 2020. URL: https://doi.org/10.1016/j.chembiol.2020.01.009, doi:10.1016/j.chembiol.2020.01.009. This article has 41 citations and is from a domain leading peer-reviewed journal.
(yao2020smallmoleculeinhibition pages 5-7): Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, and David M. Bolduc. Small molecule inhibition of cps1 activity through an allosteric pocket. Cell Chemical Biology, 27:259-268.e5, Mar 2020. URL: https://doi.org/10.1016/j.chembiol.2020.01.009, doi:10.1016/j.chembiol.2020.01.009. This article has 41 citations and is from a domain leading peer-reviewed journal.
(fernandez2015usingrecombinanthuman pages 133-137): CARMEN DÍEZ FERNÁNDEZ. USING RECOMBINANT HUMAN CARBAMOYL PHOSPHATE SYNTHETASE 1 (CPS1) FOR STUDYING THIS ENZYME'S FUNCTION, REGULATION, PATHOLOGY AND STRUCTURE. PhD thesis, Universitat Politecnica de Valencia, 2015. URL: https://doi.org/10.4995/thesis/10251/52855, doi:10.4995/thesis/10251/52855.
(haskins2021mitochondrialenzymesof pages 11-13): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(haskins2021mitochondrialenzymesof pages 13-14): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(haskins2021mitochondrialenzymesof pages 5-7): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(haskins2021mitochondrialenzymesof pages 7-10): Nantaporn Haskins, Shivaprasad Bhuvanendran, Claudio Anselmi, Anna Gams, Tomas Kanholm, Kristen M. Kocher, Jonathan LoTempio, Kylie I. Krohmaly, Danielle Sohai, Nathaniel Stearrett, Erin Bonner, Mendel Tuchman, Hiroki Morizono, Jyoti K. Jaiswal, and Ljubica Caldovic. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Frontiers in Physiology, Jan 2021. URL: https://doi.org/10.3389/fphys.2020.542950, doi:10.3389/fphys.2020.542950. This article has 40 citations.
(mitchell2009geneticvariationin pages 2-3): Sabrina Mitchell, Clint Ellingson, Thomas Coyne, Lynn Hall, Meaghan Neill, Natalie Christian, Catherine Higham, Steven F. Dobrowolski, Mendel Tuchman, and Marshall Summar. Genetic variation in the urea cycle: a model resource for investigating key candidate genes for common diseases. Human Mutation, 30:56-60, Jan 2009. URL: https://doi.org/10.1002/humu.20813, doi:10.1002/humu.20813. This article has 57 citations and is from a domain leading peer-reviewed journal.
(zhu2026ureacycledysregulation pages 5-7): Boying Zhu, Chaoyang Wang, Peng Liu, Zhifeng Qu, Ran Qi, Shengjiang Chen, and Huanzhang Niu. Urea cycle dysregulation and arginine pathways in the pathogenesis of nafld and nash (review). International Journal of Molecular Medicine, 58:1-21, Jun 2026. URL: https://doi.org/10.3892/ijmm.2026.5886, doi:10.3892/ijmm.2026.5886. This article has 0 citations and is from a peer-reviewed journal.
(nakagawa2009sirt5deacetylatescarbamoyl pages 1-2): Takashi Nakagawa, David J. Lomb, Marcia C. Haigis, and Leonard Guarente. Sirt5 deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell, 137:560-570, May 2009. URL: https://doi.org/10.1016/j.cell.2009.02.026, doi:10.1016/j.cell.2009.02.026. This article has 992 citations and is from a highest quality peer-reviewed journal.
(nakagawa2009sirt5deacetylatescarbamoyl pages 5-6): Takashi Nakagawa, David J. Lomb, Marcia C. Haigis, and Leonard Guarente. Sirt5 deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell, 137:560-570, May 2009. URL: https://doi.org/10.1016/j.cell.2009.02.026, doi:10.1016/j.cell.2009.02.026. This article has 992 citations and is from a highest quality peer-reviewed journal.
(soria2022oglcnacylationenhancescps1 pages 7-8): Leandro R. Soria, Georgios Makris, Alfonso M. D’Alessio, Angela De Angelis, Iolanda Boffa, Veronica M. Pravata, Véronique Rüfenacht, Sergio Attanasio, Edoardo Nusco, Paola Arena, Andrew T. Ferenbach, Debora Paris, Paola Cuomo, Andrea Motta, Matthew Nitzahn, Gerald S. Lipshutz, Ainhoa Martínez-Pizarro, Eva Richard, Lourdes R. Desviat, Johannes Häberle, Daan M. F. van Aalten, and Nicola Brunetti-Pierri. O-glcnacylation enhances cps1 catalytic efficiency for ammonia and promotes ureagenesis. Nature Communications, Sep 2022. URL: https://doi.org/10.1038/s41467-022-32904-x, doi:10.1038/s41467-022-32904-x. This article has 23 citations and is from a highest quality peer-reviewed journal.
(wu2022regulationofthe pages 5-6): Jing Wu, Jiayu Liu, Kalina Lapenta, Reina Desrouleaux, Min-Dian Li, and Xiaoyong Yang. Regulation of the urea cycle by cps1 o-glcnacylation in response to dietary restriction and aging. Journal of Molecular Cell Biology, Mar 2022. URL: https://doi.org/10.1093/jmcb/mjac016, doi:10.1093/jmcb/mjac016. This article has 17 citations and is from a peer-reviewed journal.
(wu2022regulationofthe pages 7-9): Jing Wu, Jiayu Liu, Kalina Lapenta, Reina Desrouleaux, Min-Dian Li, and Xiaoyong Yang. Regulation of the urea cycle by cps1 o-glcnacylation in response to dietary restriction and aging. Journal of Molecular Cell Biology, Mar 2022. URL: https://doi.org/10.1093/jmcb/mjac016, doi:10.1093/jmcb/mjac016. This article has 17 citations and is from a peer-reviewed journal.
(yao2020smallmoleculeinhibition pages 4-5): Shihua Yao, Tuong-Vi Nguyen, Alan Rolfe, Anant A. Agrawal, Jiyuan Ke, Shouyong Peng, Federico Colombo, Sean Yu, Patricia Bouchard, Jiayi Wu, Kuan-Chun Huang, Xingfeng Bao, Kiyoyuki Omoto, Anand Selvaraj, Lihua Yu, Stephanos Ioannidis, Frédéric H. Vaillancourt, Ping Zhu, Nicholas A. Larsen, and David M. Bolduc. Small molecule inhibition of cps1 activity through an allosteric pocket. Cell Chemical Biology, 27:259-268.e5, Mar 2020. URL: https://doi.org/10.1016/j.chembiol.2020.01.009, doi:10.1016/j.chembiol.2020.01.009. This article has 41 citations and is from a domain leading peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

dong2024clinicalfeaturesand pages 5-6
dong2024clinicalfeaturesand pages 4-5
fernandez2015usingrecombinanthuman pages 41-44
fernandez2015usingrecombinanthuman pages 37-41
fernandez2015usingrecombinanthuman pages 24-31
yao2020smallmoleculeinhibition pages 5-7
haskins2021mitochondrialenzymesof pages 11-13
haskins2021mitochondrialenzymesof pages 13-14
haskins2021mitochondrialenzymesof pages 1-2
zhu2026ureacycledysregulation pages 5-7
hajaj2023fromtheinside pages 4-5
fernandez2015usingrecombinanthuman pages 133-137
wu2022regulationofthe pages 7-9
liu2011dnamethylationsuppresses pages 4-6
fernandez2015usingrecombinanthuman pages 71-77
fernandez2015usingrecombinanthuman pages 106-110
fernandez2015usingrecombinanthuman pages 85-89
haskins2021mitochondrialenzymesof pages 2-3
yao2020smallmoleculeinhibition pages 1-3
wu2022regulationofthe pages 1-2
wu2022regulationofthe pages 2-5
dong2024clinicalfeaturesand pages 1-2
wang2023clinicalandgenetic pages 3-5
yao2020smallmoleculeinhibition pages 8-8
yao2020smallmoleculeinhibition pages 14-15
haskins2021mitochondrialenzymesof pages 5-7
haskins2021mitochondrialenzymesof pages 7-10
mitchell2009geneticvariationin pages 2-3
wu2022regulationofthe pages 5-6
yao2020smallmoleculeinhibition pages 4-5
ammonia
https://doi.org/10.1186/s12887-024-05005-5,
https://doi.org/10.4995/thesis/10251/52855,
https://doi.org/10.1002/humu.21272,
https://doi.org/10.3389/fphys.2020.542950,
https://doi.org/10.1016/j.chembiol.2020.01.009,
https://doi.org/10.1016/j.cell.2009.02.026,
https://doi.org/10.1038/s41467-022-32904-x,
https://doi.org/10.1093/jmcb/mjac016,
https://doi.org/10.1186/s12920-023-01569-w,
https://doi.org/10.1016/j.ajpath.2010.10.023,
https://doi.org/10.1101/cshperspect.a041538,
https://doi.org/10.1002/humu.20813,
https://doi.org/10.3892/ijmm.2026.5886,

📚 Additional Documentation

Notes

(CPS1-notes.md)

CPS1 (human, P31327) review notes

Deep research: falcon run polled (~12 min) but did NOT land before review; grounded instead in
UniProt (P31327), seeded GOA, cached publications, and the dismech CPS1D disorder file.

Core biology (verified)

~1500-aa mitochondrial-matrix multidomain enzyme; catalyzes the FIRST committed step of the urea
cycle: NH4+ + HCO3- + 2 ATP -> carbamoyl phosphate + 2 ADP + Pi + 2 H+ (EC 6.3.4.16).
[UniProt P31327 CATALYTIC ACTIVITY; Rhea:RHEA:18029]
Glutamine-INDEPENDENT (ammonia-dependent). "Glutamine is utilized as the endogenous source of
ammonia by all types of CPS except CPS1. 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." PMID:26592762
UniProt: "The type-1 glutamine amidotransferase domain is defective."
ABSOLUTE requirement for the allosteric activator N-acetyl-L-glutamate (NAG). Without NAG, activity
is <=2% of NAG-saturated. PMID:26592762
NAG binds the C-terminal L4 (MGS-like) domain. [UniProt BINDING 1391..1449 N-acetyl-L-glutamate]
Ionic activators: potassium and magnesium; K+ coordinated in L1 K-loop, Mg2+ coordinates ADP.
[PMID:26802762... PMID:26592762 "having at its center a coordinated potassium ion (thus the name K-loop)"; "CPS1 affinities for its essential ionic activators potassium and magnesium are increased importantly by NAG"]
Location: mitochondrial matrix. [UniProt SUBCELLULAR LOCATION Mitochondrion; PMID:22002106; TRANSIT 1..38 Mitochondrion]
Quaternary: monomer-dimer equilibrium, monomer predominant. [PMID:26592762 "behavior of human CPS1 in solution as a monomer-dimer system in rapid equilibrium in which the monomer predominates"; PMID:6249820 native MW ~190k, monomer ~165k]
Km values: ATP 0.47 mM, HCO3- 4 mM, NH4+ 1 mM (recombinant) PMID:23649895; NAG Km ~0.1 mM PMID:6249820
Tissue: primarily liver and small intestine. [UniProt TISSUE SPECIFICITY]
Disease: CPS1 deficiency (CPS1D), autosomal recessive urea-cycle disorder, severe neonatal
hyperammonemia; >130 private missense mutations. [PMID:21120950; MONDO:0009376; dismech]
Recombinant human CPS1 established EC 6.3.4.16 and kinetics. [PMID:23649895, PMID:24813853]
Regulation by acylation: glutarylation (increases fasting) and succinylation removed by SIRT5
(deacylation activates). [UniProt PTM; PMID:24703693; Reactome R-HSA-9955504]

Over-annotation / dubious annotations

GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity (IBA/IEA): this is the
activity of CPS II (CAD, cytosolic, pyrimidine). CPS1 is ammonia-dependent and lacks a functional
glutaminase (defective GATase, Ser294). MODIFY -> GO:0004087. [PMID:26592762; UniProt DOMAIN comment]
GO:0004175 endopeptidase activity (IEA GO_REF:0000107, Ensembl Compara ortholog transfer): CPS1 is
a ligase, not a protease. Implausible ortholog-transfer artifact. REMOVE.
GO:0005509 calcium ion binding, GO:0005543 phospholipid binding (IEA GO_REF:0000107): no evidence;
CPS1 uses K+/Mg2+ not Ca2+, no lipid-binding role in the matrix. REMOVE (ortholog-transfer).
Bare GO:0005515 protein binding (IPI PMID:12620389 Raf 2-hybrid; PMID:15161933 & PMID:20618440
14-3-3 proteomics): uninformative; the interactions (ARAF/RAF1/YWHAZ in UniProt INTERACTION) are
large-scale-screen hits, not established functional partners. MARK_AS_OVER_ANNOTATED / do not
elevate to core; keep bare term as non-core at most.
GO:0042311 vasodilation (IMP), GO:0046209 nitric oxide metabolic process (IMP), GO:0019240
L-citrulline biosynthetic process (NAS) all from PMID:14718356: a T1405N-polymorphism genotype-
association study of NO metabolites/forearm blood flow. Indirect downstream physiology (CPS1 ->
carbamoyl-P -> citrulline -> arginine -> NO), not a direct CPS1 function. Over-annotation.
PMID:14718356
GO:0050667 homocysteine metabolic process (IDA) and GO:0072341 modified amino acid binding (IDA)
from PMID:20031578: this is a GWAS SNP-plasma-homocysteine association (rs7422339), NOT an IDA of
direct binding or metabolism. The evidence code is misapplied. However GO:0072341 modified amino
acid binding IS actually correct for CPS1 for a different reason: it binds N-acetyl-L-glutamate (a
modified amino acid). PMID:20031578
GO:0019433 triglyceride catabolic process (IMP PMID:9711878): the cited paper is a prenatal
diagnosis of CPS1D by a missense mutation; NO triglyceride content. Misassigned. REMOVE.
GO:0032496 response to LPS (IDA PMID:15897806): CPS1 is released/fragmented into circulation under
septic (LPS) conditions as a biomarker of hepatic mitochondrial injury; CPS1 is not a participant
in the LPS-response process. Over-annotation of a downstream biomarker phenomenon.
PMID:15897806
GO:0042645 mitochondrial nucleoid (IDA PMID:18063578): CPS1 co-purifies with native mtDNA nucleoids
as an abundant matrix protein; the paper explicitly notes several metabolic proteins "were not
observed to cross-link to mtDNA." Likely co-purification, not a genuine nucleoid localization.
GO:0005730 nucleolus (IEA GO_REF:0000044 + IDA GO_REF:0000052) and GO:0005886 plasma membrane
(IEA/ISS): UniProt does list Nucleus/nucleolus (PMID:22002106) and Cell membrane (by similarity to
mouse Q8C196, "cell surface of hepatocytes"). These are unusual moonlighting/secondary localizations
for a matrix enzyme; keep as non-core.
Ensembl-Compara IEA response-to-stimulus terms (GO_REF:0000107): a large block of "response to X"
(glucagon, cAMP, glucocorticoid, LPS, zinc, oleic acid, starvation, food, FGF, GH, dexamethasone,
alcohol, amino acid, amine, steroid hormone, toxic substance, xenobiotic) plus liver/midgut/
hepatocyte development and monoatomic anion homeostasis. These are expression-regulation /
physiological-context transfers from rodent orthologs, not core function; keep as non-core.
GO:0006207 de novo pyrimidine nucleobase biosynthetic process (IEA GO_REF:0000002) and GO:0090407
organophosphate biosynthetic process (IEA GO_REF:0000117 ARBA): pyrimidine biosynthesis is CPS II
(CAD), not CPS1; MODIFY/over-annotation. organophosphate is a broad ARBA mapping.
GO:0006541 L-glutamine metabolic process (IBA/IEA): reflects the glutamine-dependent CPS family
ancestor; human CPS1 does NOT use glutamine. Over-annotation.

📄 View Raw YAML

id: P31327
gene_symbol: CPS1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  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.
alternative_products:
- name: '1'
  id: P31327-1
- name: '2'
  id: P31327-2
  sequence_note: VSP_009332
- name: '3'
  id: P31327-3
  sequence_note: VSP_046685
existing_annotations:
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:23649895
      supporting_text: >-
        The kinetic and molecular properties of recombinant CPS1 are essentially
        the same as for natural human CPS1.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic annotation to cytoplasm. CPS1 is a mitochondrial-matrix protein;
      cytoplasm is far too general and does not capture the specific compartment.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0005759
      label: mitochondrial matrix
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        carbamoyl phosphate synthase-1 (CPS-1), an abundant enzyme of the hepatic
        urea cycle, which is normally located in the mitochondrial matrix.
- term:
    id: GO:0006541
    label: L-glutamine metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic annotation to glutamine metabolic process, inherited from the
      glutamine-dependent CPS family ancestor. Human CPS1 does not use glutamine.
    action: REMOVE
    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
      source_entities:
      - source_id: GO_REF:0000033
        source_label: PAN-GO phylogenetic inference (CPS family tree)
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        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
- term:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    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.
    action: MODIFY
    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
      source_entities:
      - source_id: GO_REF:0000033
        source_label: PAN-GO phylogenetic inference (CPS family tree)
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          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_replacement_terms:
    - id: GO:0004087
      label: carbamoyl-phosphate synthase (ammonia) activity
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        Glutamine is utilized as the endogenous source of ammonia by all types of
        CPS31464748 except CPS12
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic annotation of the correct core catalytic activity of CPS1.
    action: ACCEPT
    reason: >-
      Correct core molecular function, consistent with experimental and
      phylogenetic annotations of the same term.
- term:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0004087
      label: carbamoyl-phosphate synthase (ammonia) activity
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        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
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        the adenine ring sandwiched between the central β 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
- term:
    id: GO:0005730
    label: nucleolus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation to mitochondrion, the correct organelle. CPS1 is a
      mitochondrial-matrix protein.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation to plasma membrane. UniProt records a cell-membrane /
      hepatocyte cell-surface location inferred by similarity to the mouse ortholog.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0006207
    label: '''de novo'' pyrimidine nucleobase biosynthetic process'
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain
        enzyme, catalyzes the first step of ammonia detoxification to urea
- term:
    id: GO:0006541
    label: L-glutamine metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO electronic annotation to glutamine metabolic process, inherited
      from the glutamine-dependent CPS family. Human CPS1 does not use glutamine.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        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
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Electronic annotation to metal ion binding. CPS1 uses Mg2+ (coordinated to
      ADP at both phosphorylation sites) and K+ as essential ionic activators.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        CPS1 affinities for its essential ionic activators potassium and magnesium
        are increased importantly by NAG
- term:
    id: GO:0090407
    label: organophosphate biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0070409
      label: carbamoyl phosphate biosynthetic process
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12620389
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:12620389
      supporting_text: >-
        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."
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15161933
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:15161933
      supporting_text: >-
        Here we describe a global proteomics analysis to identify proteins that bind
        to 14-3-3s during interphase and mitosis.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20618440
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a 14-3-3-binding proteomics study during
      ceramide-induced apoptosis. Uninformative screen-derived interaction.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:20618440
      supporting_text: >-
        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.
- term:
    id: GO:0000050
    label: urea cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara ortholog-transfer annotation to the urea cycle, the core
      biological process of CPS1.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:1840546
      supporting_text: 'Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis.'
- term:
    id: GO:0001889
    label: liver development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara ortholog-transfer annotation to liver development. CPS1 is
      highly expressed in liver but is a metabolic enzyme, not a developmental
      regulator.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0004175
    label: endopeptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:23649895
      supporting_text: >-
        The kinetic and molecular properties of recombinant CPS1 are essentially
        the same as for natural human CPS1.
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Ensembl-Compara ortholog-transfer annotation to calcium ion binding. CPS1's
      catalytically relevant ions are potassium and magnesium, not calcium.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        CPS1 affinities for its essential ionic activators potassium and magnesium
        are increased importantly by NAG
- term:
    id: GO:0005543
    label: phospholipid binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Ensembl-Compara ortholog-transfer annotation to phospholipid binding. No
      evidence that the matrix enzyme CPS1 binds phospholipids as part of its
      function.
    action: REMOVE
    reason: >-
      CPS1 is a soluble mitochondrial-matrix ligase with no phospholipid-binding
      function established in the literature; this is a spurious ortholog-transfer
      artifact.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0005759
      label: mitochondrial matrix
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Ortholog-transfer annotation to cytosol. CPS1 functions in the mitochondrial
      matrix, not the cytosol.
    action: REMOVE
    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.)
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0007494
    label: midgut development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer annotation to midgut development, reflecting intestinal
      expression of CPS1 in model organisms. Not a demonstrated developmental role.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to stimulus" annotation from rodent expression
      studies. Reflects regulation of CPS1 abundance, not a core molecular role.
    action: KEEP_AS_NON_CORE
    reason: >-
      These transferred physiological-context terms describe conditions under which
      CPS1 expression changes rather than the enzyme's molecular function. Keep as
      non-core.
- term:
    id: GO:0009636
    label: response to toxic substance
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to toxic substance" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Physiological-context term transferred from orthologs; describes regulation of
      CPS1 rather than its molecular activity. Keep as non-core.
- term:
    id: GO:0010043
    label: response to zinc ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to zinc ion" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; not a demonstrated molecular role of
      human CPS1. Keep as non-core.
- term:
    id: GO:0014075
    label: response to amine
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to amine" annotation. Context/expression transfer,
      not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; describes conditions affecting CPS1
      rather than its molecular activity. Keep as non-core.
- term:
    id: GO:0016595
    label: glutamate binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Ortholog-transfer annotation to glutamate binding. CPS1's allosteric activator
      is N-acetyl-L-glutamate (a modified amino acid), not free glutamate.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0072341
      label: modified amino acid binding
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        NAG binding to CPS1 as observed in the crystal structure appears to
        genuinely reflect the binding of this effector to the enzyme in vivo.
- term:
    id: GO:0032094
    label: response to food
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to food" annotation. Context/expression transfer,
      not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting dietary regulation of CPS1
      abundance; not a core molecular function. Keep as non-core.
- term:
    id: GO:0032496
    label: response to lipopolysaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to lipopolysaccharide" annotation. Context transfer
      reflecting altered CPS1 levels/release under septic conditions, not a core
      function.
    action: MARK_AS_OVER_ANNOTATED
    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.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: part_of
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        the behavior of human CPS1 in solution as a monomer-dimer system in rapid
        equilibrium in which the monomer predominates
- term:
    id: GO:0033762
    label: response to glucagon
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to glucagon" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Reflects hormonal regulation of CPS1 expression transferred from rodent
      orthologs; not a core molecular function. Keep as non-core.
- term:
    id: GO:0034201
    label: response to oleic acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to oleic acid" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; not a demonstrated molecular function
      of human CPS1. Keep as non-core.
- term:
    id: GO:0042594
    label: response to starvation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Reflects fasting/starvation regulation of ureagenesis and CPS1 acylation
      rather than a distinct molecular function. Keep as non-core.
- term:
    id: GO:0043200
    label: response to amino acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to amino acid" annotation. Context/expression
      transfer reflecting dietary-protein regulation of ureagenesis.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting protein/amino-acid-load
      regulation of the urea cycle; not a core molecular function. Keep as non-core.
- term:
    id: GO:0044344
    label: cellular response to fibroblast growth factor stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "cellular response to FGF" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; not a demonstrated molecular role of
      human CPS1. Keep as non-core.
- term:
    id: GO:0044877
    label: protein-containing complex binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Ortholog-transfer annotation to protein-containing complex binding. Generic
      and uninformative for CPS1, a predominantly monomeric enzyme.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0048545
    label: response to steroid hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to steroid hormone" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting hormonal regulation of CPS1
      expression; not a core molecular function. Keep as non-core.
- term:
    id: GO:0051384
    label: response to glucocorticoid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to glucocorticoid" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Reflects glucocorticoid regulation of CPS1 expression transferred from rodent
      orthologs; not a core molecular function. Keep as non-core.
- term:
    id: GO:0051591
    label: response to cAMP
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to cAMP" annotation. Context/expression transfer,
      not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting cAMP-mediated regulation of
      CPS1; not a core molecular function. Keep as non-core.
- term:
    id: GO:0055081
    label: monoatomic anion homeostasis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer annotation to monoatomic anion homeostasis. Not a
      recognized function of CPS1.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0060416
    label: response to growth hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to growth hormone" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting hormonal regulation of CPS1
      expression; not a core molecular function. Keep as non-core.
- term:
    id: GO:0070365
    label: hepatocyte differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      CPS1 is a marker of differentiated hepatocytes rather than a demonstrated
      regulator of hepatocyte differentiation; this reflects expression context.
      Keep as non-core.
- term:
    id: GO:0071320
    label: cellular response to cAMP
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "cellular response to cAMP" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting cAMP-mediated regulation of
      CPS1; not a core molecular function. Keep as non-core.
- term:
    id: GO:0071377
    label: cellular response to glucagon stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "cellular response to glucagon stimulus" annotation.
      Context/expression transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting glucagon regulation of
      ureagenesis/CPS1; not a core molecular function. Keep as non-core.
- term:
    id: GO:0071400
    label: cellular response to oleic acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "cellular response to oleic acid" annotation.
      Context/expression transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; not a demonstrated molecular function
      of human CPS1. Keep as non-core.
- term:
    id: GO:0071548
    label: response to dexamethasone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to dexamethasone" annotation. Context/expression
      transfer reflecting glucocorticoid induction of CPS1.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term reflecting glucocorticoid (dexamethasone)
      induction of CPS1 expression; not a core molecular function. Keep as non-core.
- term:
    id: GO:0097305
    label: response to alcohol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer "response to alcohol" annotation. Context/expression
      transfer, not a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Transferred physiological-context term; not a demonstrated molecular function
      of human CPS1. Keep as non-core.
- term:
    id: GO:0000050
    label: urea cycle
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70635
  qualifier: involved_in
  review:
    summary: >-
      Reactome traceable-author-statement annotation of CPS1 in the urea cycle,
      the core biological process.
    action: ACCEPT
    reason: >-
      CPS1 catalyzes the first committed step of the urea cycle; this is a core,
      well-supported biological-process annotation.
    supported_by:
    - reference_id: PMID:1840546
      supporting_text: 'Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis.'
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: EXP
  original_reference_id: PMID:6249820
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for the core catalytic function using the
      purified human enzyme. This is the central molecular function of CPS1.
    supported_by:
    - reference_id: PMID:6249820
      supporting_text: >-
        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.
- term:
    id: GO:0005730
    label: nucleolus
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9955543
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS annotation to the mitochondrial matrix, the correct functional
      location of CPS1.
    action: ACCEPT
    reason: >-
      The mitochondrial matrix is the established site of CPS1 catalysis and is the
      correct, specific cellular location. Core localization.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9955504
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS annotation (SIRT5 deglutarylation of CPS1) to the mitochondrial
      matrix, the correct functional location.
    action: ACCEPT
    reason: >-
      Correct, specific core cellular location; consistent with all other matrix
      annotations.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: EXP
  original_reference_id: PMID:23649895
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for the ammonia-dependent carbamoyl-phosphate
      synthase activity of recombinant human CPS1. Core molecular function.
    supported_by:
    - reference_id: PMID:23649895
      supporting_text: >-
        The kinetic and molecular properties of recombinant CPS1 are essentially
        the same as for natural human CPS1.
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: EXP
  original_reference_id: PMID:24813853
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for the core catalytic function of human CPS1.
      Core molecular function.
    supported_by:
    - reference_id: PMID:24813853
      supporting_text: >-
        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)
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Sequence-similarity (ISS) annotation to plasma membrane, consistent with the
      UniProt cell-surface location inferred from the mouse ortholog.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput mitochondrial-proteome evidence localizing CPS1 to the
      mitochondrion, the correct organelle.
    action: ACCEPT
    reason: >-
      Consistent with the established mitochondrial-matrix localization; a valid
      (organelle-level) location annotation.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0030955
    label: potassium ion binding
  evidence_type: EXP
  original_reference_id: PMID:26592762
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        being fully structured, having at its center a coordinated potassium ion
        (thus the name K-loop)
- term:
    id: GO:0036094
    label: small molecule binding
  evidence_type: EXP
  original_reference_id: PMID:26592762
  qualifier: enables
  review:
    summary: >-
      Experimental annotation to the very broad "small molecule binding" from the
      structural study, which resolved ADP, NAG, potassium and magnesium binding.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0072341
      label: modified amino acid binding
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        One NAG molecule was found sitting with full occupancy in each subunit of
        ligand-bound CPS1
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: EXP
  original_reference_id: PMID:26592762
  qualifier: enables
  review:
    summary: >-
      Experimental/structural evidence for metal ion binding (magnesium coordinating
      ADP; potassium in the K-loop) in the active enzyme.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        besides having also two bound magnesium ions, hosted a potassium ion
        coordinated to its K-loop
- term:
    id: GO:0042311
    label: vasodilation
  evidence_type: IMP
  original_reference_id: PMID:14718356
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:14718356
      supporting_text: >-
        a polymorphism in the gene encoding carbamoyl-phosphate synthetase 1
        influences nitric oxide production as well as vascular smooth muscle
        reactivity.
- term:
    id: GO:0070409
    label: carbamoyl phosphate biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:21120950
  qualifier: involved_in
  review:
    summary: >-
      Mutant-phenotype evidence that CPS1 is required for carbamoyl phosphate
      biosynthesis, from the large CPS1D mutational-spectrum study.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:21120950
      supporting_text: >-
        Deficiency of carbamoyl phosphate synthetase I (CPSI) results in
        hyperammonemia ranging from neonatally lethal to environmentally induced
        adult-onset disease.
- term:
    id: GO:0071242
    label: cellular response to ammonium ion
  evidence_type: IMP
  original_reference_id: PMID:21120950
  qualifier: involved_in
  review:
    summary: >-
      Annotation to cellular response to ammonium ion from the CPS1D mutational
      study. CPS1 consumes ammonia as a substrate for detoxification.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:21120950
      supporting_text: >-
        Deficiency of carbamoyl phosphate synthetase I (CPSI) results in
        hyperammonemia
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70555
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS annotation to the mitochondrial matrix (the CPS1 reaction event),
      the correct functional location.
    action: ACCEPT
    reason: >-
      Correct, specific core cellular location for the site of the CPS1-catalyzed
      reaction.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9959874
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS annotation to the mitochondrial matrix (CPS1 gene-expression
      event context), the correct functional location.
    action: ACCEPT
    reason: >-
      Correct, specific core cellular location; consistent with all other matrix
      annotations.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        an abundant enzyme of the hepatic urea cycle, which is normally located in
        the mitochondrial matrix.
- term:
    id: GO:0050667
    label: homocysteine metabolic process
  evidence_type: IDA
  original_reference_id: PMID:20031578
  qualifier: involved_in
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: PMID:20031578
      supporting_text: >-
        we found novel associations with CPS1 (2q34; rs7422339; P=1.9 x 10(-11))
- term:
    id: GO:0072341
    label: modified amino acid binding
  evidence_type: IDA
  original_reference_id: PMID:20031578
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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).
    supported_by:
    - reference_id: PMID:26592762
      supporting_text: >-
        One NAG molecule was found sitting with full occupancy in each subunit of
        ligand-bound CPS1
- term:
    id: GO:0070409
    label: carbamoyl phosphate biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:7416778
  qualifier: involved_in
  review:
    summary: >-
      Mutant/deficiency-phenotype evidence (reduced CPS1 activity in duodenal biopsy
      of a hyperammonemic patient) that CPS1 is required for carbamoyl phosphate
      biosynthesis.
    action: ACCEPT
    reason: >-
      Reduced CPS1 activity in patient tissue with hyperammonemia supports CPS1's
      required role in carbamoyl phosphate biosynthesis. Core biological process.
    supported_by:
    - reference_id: PMID:7416778
      supporting_text: >-
        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.
- term:
    id: GO:0000050
    label: urea cycle
  evidence_type: NAS
  original_reference_id: PMID:1840546
  qualifier: involved_in
  review:
    summary: >-
      Non-traceable author statement that CPS1 is the first enzyme of urea
      synthesis, from the human CPS1 cDNA cloning paper.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:1840546
      supporting_text: 'Carbamyl phosphate synthetase I (CPSI) is the first enzyme involved in urea synthesis.'
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: IMP
  original_reference_id: PMID:8486760
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      A disease-causing CPS1 mutation abolishing normal CPS1 supports the enzyme's
      core carbamoyl-phosphate synthase (ammonia) activity. Core molecular function.
    supported_by:
    - reference_id: PMID:8486760
      supporting_text: >-
        Northern and Western blots revealed a marked decrease in CPS I mRNA and
        enzyme protein
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: IMP
  original_reference_id: PMID:9711878
  qualifier: enables
  review:
    summary: >-
      Mutant-phenotype evidence: a homozygous Thr544Met missense mutation causing
      severe (lethal) CPS1 deficiency, supporting CPS1's core synthetase function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:9711878
      supporting_text: >-
        Direct sequencing of the complete CPS1 coding region revealed a
        disease-associated homozygous Thr544Met mutation in CPS1.
- term:
    id: GO:0019240
    label: L-citrulline biosynthetic process
  evidence_type: NAS
  original_reference_id: PMID:14718356
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:14718356
      supporting_text: >-
        the enzyme catalyzing the rate-limiting step in l-citrulline formation
- term:
    id: GO:0019433
    label: triglyceride catabolic process
  evidence_type: IMP
  original_reference_id: PMID:9711878
  qualifier: involved_in
  review:
    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.
    action: UNDECIDED
    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.
    supported_by:
    - reference_id: PMID:9711878
      supporting_text: >-
        Carbamoyl phosphate synthetase I (CPS1) deficiency is an autosomal recessive
        metabolic disorder affecting the first enzymatic step of urea cycle.
- term:
    id: GO:0032496
    label: response to lipopolysaccharide
  evidence_type: IDA
  original_reference_id: PMID:15897806
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:15897806
      supporting_text: >-
        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.
- term:
    id: GO:0042645
    label: mitochondrial nucleoid
  evidence_type: IDA
  original_reference_id: PMID:18063578
  qualifier: located_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:18063578
      supporting_text: >-
        Several other metabolic proteins and chaperones identified in native
        nucleoids, including ATAD3, were not observed to cross-link to mtDNA.
- term:
    id: GO:0046209
    label: nitric oxide metabolic process
  evidence_type: IMP
  original_reference_id: PMID:14718356
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:14718356
      supporting_text: >-
        a polymorphism in the gene encoding carbamoyl-phosphate synthetase 1
        influences nitric oxide production as well as vascular smooth muscle
        reactivity.
core_functions:
- description: >-
    CPS1 catalyzes the first, committed and rate-limiting step of the urea cycle:
    the ATP-dependent, ammonia-utilizing synthesis of carbamoyl phosphate from
    ammonia and bicarbonate, using 2 ATP. This ammonia detoxification reaction
    occurs in the hepatic (and intestinal) mitochondrial matrix and has an absolute
    allosteric requirement for the activator N-acetyl-L-glutamate.
  molecular_function:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  directly_involved_in:
  - id: GO:0000050
    label: urea cycle
  - id: GO:0070409
    label: carbamoyl phosphate biosynthetic process
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  substrates:
  - id: CHEBI:28938
    label: ammonium
  - id: CHEBI:17544
    label: hydrogencarbonate
  - id: CHEBI:30616
    label: ATP
  supported_by:
  - reference_id: PMID:23649895
    supporting_text: >-
      The kinetic and molecular properties of recombinant CPS1 are essentially the
      same as for natural human CPS1.
  - reference_id: PMID:26592762
    supporting_text: >-
      Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain
      enzyme, catalyzes the first step of ammonia detoxification to urea requiring
      N-acetyl-L-glutamate (NAG) as essential activator
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  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:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12620389
  title: Novel raf kinase protein-protein interactions found by an exhaustive yeast
    two-hybrid analysis.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput yeast two-hybrid screen for Raf kinase interactors; CPS1 is
      one of many hits. Supports only a bare, low-value protein-binding annotation
      with no established functional consequence for ureagenesis.
- id: PMID:14718356
  title: Relationship between carbamoyl-phosphate synthetase genotype and systemic
    vascular function.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Genotype-phenotype association of a CPS1 coding polymorphism (T1405N) with NO
      metabolites and vasodilation. Supports only indirect, downstream physiological
      links (vasodilation, NO metabolism, citrulline), which are over-annotations of
      CPS1's actual molecular function.
- id: PMID:15161933
  title: Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding
    proteins.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Global 14-3-3 affinity proteomics screen. Supports only a bare protein-binding
      annotation.
- id: PMID:15897806
  title: Release of the mitochondrial enzyme carbamoyl phosphate synthase under septic
    conditions.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Confirms CPS1 is normally a mitochondrial-matrix enzyme of the hepatic urea
      cycle and shows it is fragmented/released as a serum biomarker under septic
      (LPS) conditions. Supports matrix localization; the response-to-LPS annotation
      is a biomarker phenomenon, not a functional role.
- id: PMID:18063578
  title: The layered structure of human mitochondrial DNA nucleoids.
  findings: []
  reference_review:
    relevance: LOW
    correctness: MISCITED
    review_notes: >-
      Nucleoid co-purification study. CPS1 co-purifies as an abundant matrix protein,
      but the paper notes several metabolic proteins in native nucleoids do not
      cross-link to mtDNA; supports co-purification rather than genuine nucleoid
      localization.
- id: PMID:1840546
  title: 'Cloning and sequence of a cDNA encoding human carbamyl phosphate synthetase
    I: molecular analysis of hyperammonemia.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Cloning/sequence of human CPS1 cDNA (1500-aa precursor with N-terminal
      presequence); establishes CPS1 as the first enzyme of urea synthesis.
- id: PMID:20031578
  title: 'Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine
    in a healthy population: a genome-wide evaluation of 13 974 participants in the
    Women''s Genome Health Study.'
  findings: []
  reference_review:
    relevance: LOW
    correctness: MISCITED
    review_notes: >-
      GWAS association of a common CPS1 SNP with plasma homocysteine; does not
      demonstrate that CPS1 acts in homocysteine metabolism or directly binds a
      modified amino acid. The IDA annotations attributed to it (homocysteine
      metabolic process; modified amino acid binding) are misapplied to this
      reference, though modified amino acid binding is independently correct (NAG).
- id: PMID:20618440
  title: Proteomic and biochemical analysis of 14-3-3-binding proteins during C2-ceramide-induced
    apoptosis.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      14-3-3-binding proteomics/apoptosis study. Supports only a bare protein-binding
      annotation.
- id: PMID:21120950
  title: 'Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum,
    diagnostic and protein structure considerations.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Comprehensive CPS1D mutational spectrum (222 changes); loss-of-function
      mutations abolish carbamoyl phosphate biosynthesis and cause hyperammonemia.
      Strong support for the core biological process.
- id: PMID:23649895
  title: Molecular characterization of carbamoyl-phosphate synthetase (CPS1) deficiency
    using human recombinant CPS1 as a key tool.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Recombinant human CPS1 expression/purification with full kinetic
      characterization; one of the two UniProt references anchoring EC 6.3.4.16.
      Directly supports the core ammonia-dependent synthetase activity.
- id: PMID:24813853
  title: 'Understanding carbamoyl phosphate synthetase (CPS1) deficiency by using
    the recombinantly purified human enzyme: effects of CPS1 mutations that concentrate
    in a central domain of unknown function.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Recombinant human CPS1 mutational analysis (effects on Vmax/Km/stability);
      second UniProt reference anchoring EC 6.3.4.16. Supports the core catalytic
      function.
- id: PMID:26592762
  title: 'Structure of human carbamoyl phosphate synthetase: deciphering the on/off
    switch of human ureagenesis.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Crystal structures of human CPS1 (apo and NAG/ADP-bound). Establishes the NAG
      allosteric on/off switch, the two ATP-grasp phosphorylation sites, the
      carbamate tunnel, coordinated potassium and magnesium, and the molecular basis
      for CPS1's inability to use glutamine (Cys->Ser294). Anchors most core-function
      and cofactor claims.
- 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-throughput mitochondrial-proteome study confirming CPS1's mitochondrial
      localization.
- id: PMID:6249820
  title: Human carbamylphosphate synthetase I. Stabilization, purification, and partial
    characterization of the enzyme from human liver.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Purification and partial characterization of CPS1 from human liver, including
      Km values for NH4+, HCO3-, MgATP and the activator NAG; native MW ~190 kDa,
      monomeric ~165 kDa. Directly supports the core catalytic activity and NAG
      dependence.
- id: PMID:7416778
  title: Detection of carbamyl phosphate synthetase 1 deficiency using duodenal biopsy
    samples.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Demonstrates reduced NAG-dependent CPS1 activity in duodenal biopsy of a
      hyperammonemic patient; supports the requirement of CPS1 for carbamoyl
      phosphate biosynthesis and its NAG dependence.
- id: PMID:8486760
  title: Carbamyl phosphate synthetase I deficiency. One base substitution in an exon
    of the CPS I gene causes a 9-basepair deletion due to aberrant splicing.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Molecular characterization of a splicing mutation causing CPS1 deficiency;
      supports the loss-of-function-to-phenotype link for the core synthetase
      function.
- id: PMID:9711878
  title: Prenatal diagnosis of carbamoyl phosphate synthetase I deficiency by identification
    of a missense mutation in CPS1.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Prenatal diagnosis of severe CPS1D via a homozygous Thr544Met mutation.
      Supports the core synthetase function; the triglyceride-catabolism annotation
      attributed to this paper is unsupported and should be removed.
- id: Reactome:R-HSA-70555
  title: 2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
  findings: []
- id: Reactome:R-HSA-70635
  title: Urea cycle
  findings: []
- id: Reactome:R-HSA-9955504
  title: SIRT5 deglutarylates CPS1
  findings: []
- id: Reactome:R-HSA-9955543
  title: CPS1 variants don't synthesize carbamoyl phosphate
  findings: []
- id: Reactome:R-HSA-9959874
  title: CPS1 gene expression
  findings: []

CPS1

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

Comprehensive Functional Annotation of Human CPS1 (Carbamoyl-Phosphate Synthase 1, Mitochondrial)

Gene and Protein Identity

Enzymatic Reaction and Catalytic Mechanism

Domain Architecture and Structural Biology

Subcellular Localization and Supramolecular Organization

Metabolic Pathway Context

The Urea Cycle

Connection to Pyrimidine Biosynthesis

Regulation of CPS1 Activity

Allosteric Activation by N-Acetylglutamate (NAG)

Post-Translational Regulation by SIRT5

Post-Translational Regulation by O-GlcNAcylation

Additional Post-Translational Modifications

Disease Associations

CPS1 Deficiency (OMIM 237300)

CPS1 in Cancer

Conclusions

Artifacts

Citations

📚 Additional Documentation

Notes

CPS1 (human, P31327) review notes

Core biology (verified)

Over-annotation / dubious annotations

📄 View Raw YAML