CAD

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004070 aspartate carbamoyltransferase activity	IBA GO_REF:0000033	ACCEPT	Summary: Aspartate transcarbamylase (ATCase) is the second of CAD's three catalytic activities, condensing carbamoyl phosphate with L-aspartate to form N-carbamoyl-L-aspartate. This is a well-established core function directly demonstrated for the human protein. Reason: Core molecular function, supported by phylogenetic inference and by direct experimental characterization of the human ATCase activity. Supporting Evidence: PMID:24332717 the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: CAD is predominantly a cytoplasmic/cytosolic enzyme. The more specific term cytosol (GO:0005829) is also annotated and is preferred. Reason: Correct broad localization; consistent with UniProt subcellular location and with the specific cytosol annotations. Cytosol is the more informative term for the pathway. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0006541 L-glutamine metabolic process	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: CAD consumes L-glutamine via its GATase reaction to supply ammonia for carbamoyl phosphate synthesis, so it participates in glutamine metabolism. Reason: True but general: glutamine metabolism is a consequence of the CPS II reaction rather than a standalone core process. The core biological process is de novo pyrimidine/UMP biosynthesis. Supporting Evidence: file:human/CAD/CAD-uniprot.txt amidotransferase activity (GATase) that binds and cleaves glutamine to
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: Cytosol is the primary site where CAD carries out de novo pyrimidine biosynthesis. This is the preferred, most informative localization term and is well supported. Reason: Core localization, supported by phylogenetic inference, immunofluorescence (HPA), and direct cell-fractionation studies showing most CAD is cytosolic. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: CAD initiates and controls de novo pyrimidine biosynthesis, performing the first three of the six reactions of the pathway. This is a core biological process. Reason: Core function, strongly supported by phylogeny and by experimental characterization of the human enzyme. Supporting Evidence: PMID:24332717 initiates and controls the de novo biosynthesis of pyrimidines
GO:0004151 dihydroorotase activity	IBA GO_REF:0000033	ACCEPT	Summary: Dihydroorotase (DHOase) is the third of CAD's catalytic activities, cyclizing N-carbamoyl-L-aspartate to (S)-dihydroorotate. This is a core, experimentally verified Zn2+-dependent activity of human CAD. Reason: Core molecular function, supported by phylogeny and by the crystal structure and functional assays of the human DHOase domain. Supporting Evidence: PMID:24332717 the crystal structure and functional characterization of the dihydroorotase domain of human CAD
GO:0004070 aspartate carbamoyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA duplicate of the ATCase activity (EC 2.1.3.2 / RHEA:20013), consistent with the experimental and IBA annotations. Reason: Correct EC/RHEA-based mapping to a core catalytic activity of CAD. Supporting Evidence: file:human/CAD/CAD-uniprot.txt aspartate transcarbamylase (ATCase;
GO:0004087 carbamoyl-phosphate synthase (ammonia) activity	IEA GO_REF:0000120	ACCEPT	Summary: The ammonia-dependent carbamoyl phosphate synthetase partial reaction (EC 6.3.4.16) of CAD's CPS module. This is the second half of the glutamine-dependent CPS II reaction, using ammonia (from the GATase reaction) plus bicarbonate and ATP. Reason: Correct EC/RHEA mapping to a component activity of the bifunctional CPS II module. Supporting Evidence: file:human/CAD/CAD-uniprot.txt followed by an ammonium-dependent carbamoyl phosphate
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	IEA GO_REF:0000120	ACCEPT	Summary: Glutamine-dependent carbamoyl phosphate synthetase II (CPS II, EC 6.3.5.5): the overall committed first-step activity of CAD that produces carbamoyl phosphate from L-glutamine, bicarbonate and 2 ATP. This is the cytosolic pyrimidine CPS, distinct from urea-cycle CPS1. Reason: Core catalytic activity; correct EC/RHEA mapping, also supported experimentally. Supporting Evidence: file:human/CAD/CAD-uniprot.txt synthetase (CPSase; EC 6.3.5.5)
GO:0004151 dihydroorotase activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA duplicate of the DHOase activity (EC 3.5.2.3 / RHEA:24296). Reason: Correct EC/RHEA-based mapping to a core, experimentally verified catalytic activity. Supporting Evidence: PMID:24332717 the crystal structure and functional characterization of the dihydroorotase domain of human CAD
GO:0004359 glutaminase activity	IEA GO_REF:0000120	ACCEPT	Summary: The glutamine amidotransferase (GATase, EC 3.5.1.2) partial reaction of CAD hydrolyzes L-glutamine to L-glutamate + ammonia, supplying nitrogen to the CPS reaction. Annotated to the glutaminase term. Reason: Correct EC/RHEA mapping to the GATase component of the CPS II module. This is a component activity feeding CPS II rather than a standalone glutaminase, but the term is appropriate for the partial reaction. Supporting Evidence: file:human/CAD/CAD-uniprot.txt amidotransferase activity (GATase) that binds and cleaves glutamine to
GO:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: The CPS module contains two ATP-grasp folds and hydrolyzes 2 ATP per carbamoyl phosphate produced, so ATP binding is a genuine molecular activity. Reason: Supported by domain architecture (ATP-grasp folds) and by the CPS reaction stoichiometry (2 ATP). Ancillary rather than the core catalytic identity. Supporting Evidence: file:human/CAD/CAD-uniprot.txt hydrogencarbonate and ATP to
GO:0005634 nucleus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: A subpopulation of CAD (phospho-Thr456) translocates to the nucleus upon EGF stimulation. Consistent with UniProt subcellular location. Reason: Real but conditional/regulatory localization; catalysis occurs mainly in the cytosol. Keep as non-core. Supporting Evidence: PMID:15890648 Upon epidermal growth factor stimulation, CAD moved to the nucleus
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Cytoplasm localization from the UniProt subcellular-location mapping; consistent with the cytosol annotations. Reason: Correct broad localization; cytosol (GO:0005829) is the preferred, more specific term. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: IEA duplicate of the core de novo pyrimidine biosynthesis process. Reason: Correct core biological process, consistent with experimental and IBA annotations. Supporting Evidence: PMID:24332717 initiates and controls the de novo biosynthesis of pyrimidines
GO:0006520 amino acid metabolic process	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: An InterPro2GO mapping (from the carbamoyltransferase domains) to amino acid metabolism. CAD does consume/produce amino acids (glutamine -> glutamate; aspartate), but the biological role is pyrimidine biosynthesis, not amino acid metabolism per se. Reason: Over-general domain-based mapping; CAD's amino-acid handling is incidental to pyrimidine synthesis. Not a core process. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0006541 L-glutamine metabolic process	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: InterPro2GO duplicate of glutamine metabolic process (from the CPS small-subunit / GATase domain). Reason: True but general consequence of the GATase reaction; not the core process. Supporting Evidence: file:human/CAD/CAD-uniprot.txt amidotransferase activity (GATase) that binds and cleaves glutamine to
GO:0016597 amino acid binding	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro2GO mapping from the aspartate/ornithine carbamoyltransferase domain. CAD binds L-aspartate as a substrate of the ATCase reaction, so amino acid binding is defensible, though the more specific aspartate binding (GO:0070335) is also annotated. Reason: Generic; substrate binding is captured better by the specific aspartate binding term and by the ATCase activity. Not core. Supporting Evidence: file:human/CAD/CAD-uniprot.txt carbamoyl-L-aspartate from L-aspartate and
GO:0016743 carboxyl- or carbamoyltransferase activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: Parent term of aspartate carbamoyltransferase activity, from the ATCase domain. Reason: Redundant, over-general parent of the specific GO:0004070 (aspartate carbamoyltransferase activity) that is already annotated. Supporting Evidence: file:human/CAD/CAD-uniprot.txt aspartate transcarbamylase (ATCase;
GO:0016787 hydrolase activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: Very general hydrolase parent term from the amidohydrolase (DHOase) domain. Reason: Uninformative top-level parent of the specific dihydroorotase activity (GO:0004151). Supporting Evidence: file:human/CAD/CAD-uniprot.txt dihydroorotase (DHOase; EC 3.5.2.3)
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: General hydrolase parent (C-N bonds) from the metal-dependent hydrolase domain. Reason: Over-general parent of the specific dihydroorotase activity (GO:0004151). Supporting Evidence: file:human/CAD/CAD-uniprot.txt dihydroorotase (DHOase; EC 3.5.2.3)
GO:0016812 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: Parent term for cyclic-amide hydrolase activity, close to the dihydroorotase reaction (which cyclizes/opens the dihydroorotate ring). Reason: Over-general parent of the specific GO:0004151 dihydroorotase activity already annotated. Supporting Evidence: file:human/CAD/CAD-uniprot.txt DHOase catalyzes the cyclization
GO:0046872 metal ion binding	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: CAD binds Zn2+ (DHOase active site) and Mg2+/Mn2+ (CPS). Generic metal ion binding is correct; the more specific zinc ion binding (GO:0008270) is separately annotated (IDA). Reason: Generic parent; zinc ion binding (GO:0008270) is the more informative, experimentally supported term. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Binds 3 Zn(2+) ions per subunit (for dihydroorotase activity).
GO:0055086 nucleobase-containing small molecule metabolic process	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: ARBA-predicted general parent of pyrimidine biosynthesis. Reason: Over-general parent of the specific de novo pyrimidine/UMP biosynthesis processes. Supporting Evidence: file:human/CAD/CAD-uniprot.txt de novo pyrimidine pathway
GO:0072528 pyrimidine-containing compound biosynthetic process	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: ARBA-predicted parent term for pyrimidine compound biosynthesis. Reason: True but over-general parent of the specific de novo pyrimidine/UMP biosynthesis terms. Supporting Evidence: file:human/CAD/CAD-uniprot.txt de novo pyrimidine pathway
GO:0090407 organophosphate biosynthetic process	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: ARBA-predicted very broad process term (carbamoyl phosphate is an organophosphate). Reason: Over-general; the informative process is de novo pyrimidine/UMP biosynthesis. Supporting Evidence: file:human/CAD/CAD-uniprot.txt form carbamoyl phosphate
GO:0005515 protein binding	IPI PMID:15161933 Comprehensive proteomic analysis of interphase and mitotic 1...	MARK AS OVER ANNOTATED	Summary: IntAct IPI capturing a physical interaction with a 14-3-3 protein (YWHAZ, UniProtKB:P63104) from a proteomic screen for 14-3-3-binding proteins. Consistent with CAD being phospho-regulated (14-3-3 binds phosphoproteins), but the bare protein binding term is uninformative. Reason: Bare protein binding is uninformative about molecular function. Retain (do not remove experimental IPI) but mark as over-annotated per curation policy. Supporting Evidence: PMID:15161933 proteins that bind to 14-3-3s during interphase and mitosis
GO:0005515 protein binding	IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce...	MARK AS OVER ANNOTATED	Summary: IntAct IPI (interaction with YWHAZ, UniProtKB:P63104) from the OpenCell endogenous-tagging interactome. Bare protein binding is uninformative. Reason: Uninformative binding term; retain the experimental interaction evidence but mark as over-annotated per policy. Supporting Evidence: PMID:35271311 systematically map the localization and interactions of human proteins
GO:0005515 protein binding	IPI PMID:35709258 Spatial centrosome proteome of human neural cells uncovers d...	MARK AS OVER ANNOTATED	Summary: IntAct IPI (interaction with CNTROB, UniProtKB:Q8N137) from a spatial centrosome proteome of human neural cells. Bare protein binding is uninformative. Reason: Uninformative binding term; retain the experimental interaction but mark as over-annotated per policy. Supporting Evidence: PMID:35709258 protein interaction networks at the centrosome
GO:0042802 identical protein binding	IPI PMID:24332717 Structure, functional characterization, and evolution of the...	KEEP AS NON CORE	Summary: Self-association: CAD assembles into a homohexamer, so it binds identical subunits. This is a genuine structural property from the structural study, but is a general term rather than the core catalytic function. Reason: Real self-interaction (homohexamer) supported by the structural work; keep as non-core. Supporting Evidence: PMID:24332717 it self-assembles into hexamers
GO:0001889 liver development	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog (Ensembl Compara). A whole-organism physiology association, not a molecular role of CAD. Reason: Pleiotropic developmental association transferred from rodent expression/phenotype data; not a core function of the pyrimidine-biosynthesis enzyme. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0006228 UTP biosynthetic process	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CAD's product (UMP) is the precursor of UTP; CAD acts upstream of UTP synthesis. Loss of CAD depletes UTP (patient studies). A downstream-pathway association. Reason: True upstream role (CAD feeds UTP synthesis) but downstream of CAD's direct product; the core process is de novo UMP biosynthesis. Supporting Evidence: PMID:25678555 CTP, UTP and nearly all UDP-activated sugars
GO:0006805 xenobiotic metabolic process	IEA GO_REF:0000107	REMOVE	Summary: Electronic transfer from a rodent ortholog. CAD has no role in xenobiotic metabolism; this reflects a rodent expression/response association, not enzyme function. Reason: Biologically implausible for a cytosolic pyrimidine-biosynthesis enzyme; an over-propagated electronic (Ensembl) inference with no mechanistic basis. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0007507 heart development	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a whole-organism developmental association. Reason: Pleiotropic developmental association transferred electronically; not a core molecular role of CAD. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0007565 female pregnancy	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog reflecting expression during pregnancy. Reason: Physiological/expression association transferred electronically; not a core function. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0007595 lactation	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog reflecting expression during lactation. Reason: Physiological/expression association transferred electronically; not a core function. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0014075 response to amine	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0019240 L-citrulline biosynthetic process	IEA GO_REF:0000107	REMOVE	Summary: Electronic transfer from a rodent ortholog. Citrulline biosynthesis is a urea-cycle / arginine-pathway process performed by other enzymes; the cytosolic pyrimidine CPS (CAD) does not synthesize citrulline. Reason: Biologically incorrect: citrulline biosynthesis belongs to the ornithine/arginine pathway (e.g. OTC, using the mitochondrial CPS1-derived carbamoyl phosphate), not to CAD's pyrimidine pathway. An over-propagated electronic inference. Supporting Evidence: file:human/CAD/CAD-uniprot.txt catalyzes the formation of carbamoyl-L-aspartate from L-aspartate and
GO:0031000 response to caffeine	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0031100 animal organ regeneration	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog reflecting upregulation during regeneration (proliferating tissue demands pyrimidines). Reason: Expression/proliferation-associated physiology transferred electronically; not a core function. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0032868 response to insulin	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0032991 protein-containing complex	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CAD forms a homohexamer, so it is part of a protein-containing complex. Very general term. Reason: True (homohexamer) but uninformative parent term; the specific self-assembly is captured by identical protein binding. Supporting Evidence: PMID:24332717 it self-assembles into hexamers
GO:0033574 response to testosterone	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0042594 response to starvation	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Nutrient status does regulate pyrimidine synthesis (via mTOR), but this whole-animal term is not core. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0042802 identical protein binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Electronic (Ensembl) duplicate of identical protein binding, consistent with the experimentally supported homohexamer self-assembly. Reason: True self-interaction (homohexamer) but a general term; keep as non-core. Supporting Evidence: PMID:24332717 it self-assembles into hexamers
GO:0043025 neuronal cell body	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer of a neuronal-localization annotation from a rodent ortholog. Reason: Neuron-specific localization transferred electronically; CAD is a ubiquitous cytosolic enzyme and this is not a core localization. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0043195 terminal bouton	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer of a synaptic-terminal localization from a rodent ortholog. Reason: Neuron-specific localization transferred electronically; not a core localization of the cytosolic enzyme. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0044205 'de novo' UMP biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: De novo UMP biosynthesis is the pathway that CAD initiates (first three of six steps). This is the most precise core biological process for CAD. Reason: Core biological process; correct UniPathway-based mapping (UPA00070), consistent with experimental IDA annotations. Supporting Evidence: PMID:25678555 the first three of six reactions required for de novo pyrimidine biosynthesis
GO:0044210 'de novo' CTP biosynthetic process	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CTP is synthesized downstream of UMP/UTP; CAD acts upstream. Loss of CAD depletes CTP (patient studies). Reason: True upstream role but downstream of CAD's direct product (UMP); the core process is de novo UMP biosynthesis. Supporting Evidence: PMID:25678555 CTP, UTP and nearly all UDP-activated sugars
GO:0046134 pyrimidine nucleoside biosynthetic process	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer; a general pyrimidine-nucleoside biosynthesis term related to CAD's pathway. Reason: General/related process; the precise core terms are de novo UMP and de novo pyrimidine nucleobase biosynthesis. Supporting Evidence: file:human/CAD/CAD-uniprot.txt de novo pyrimidine pathway
GO:0051414 response to cortisol	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association. Reason: Non-core stimulus-response association transferred electronically from rodent data. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0071364 cellular response to epidermal growth factor stimulus	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: EGF stimulation triggers MAP-kinase phosphorylation of CAD (Thr-456) and its nuclear translocation, activating pyrimidine synthesis. This response is experimentally supported in human CAD, though the term is a regulatory/physiology association rather than a core catalytic function. Reason: Genuine, experimentally supported regulatory response (EGF -> MAPK -> CAD activation and nuclear import); keep as non-core. Supporting Evidence: PMID:15890648 Upon epidermal growth factor stimulation, CAD moved to the nucleus
GO:0071466 cellular response to xenobiotic stimulus	IEA GO_REF:0000107	REMOVE	Summary: Electronic transfer from a rodent ortholog; a stimulus-response association with no mechanistic basis for CAD. Reason: Biologically unsupported for a pyrimidine-biosynthesis enzyme; over-propagated electronic inference paralleling the xenobiotic metabolism annotation. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Multifunctional protein that encodes the first 3 enzymatic
GO:0006543 L-glutamine catabolic process	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: The GATase reaction hydrolyzes glutamine (catabolizing it to glutamate + ammonia) to feed the CPS reaction. Sequence-similarity transfer from an ortholog (UniProtKB:P08955). Reason: True consequence of the GATase reaction, but glutamine catabolism is incidental to the core pyrimidine-biosynthesis process. Supporting Evidence: file:human/CAD/CAD-uniprot.txt amidotransferase activity (GATase) that binds and cleaves glutamine to
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: Immunofluorescence-based (HPA) cytosol localization. Consistent with the established cytosolic site of de novo pyrimidine biosynthesis. Reason: Core localization, directly supported by imaging and by cell-fractionation studies. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0004070 aspartate carbamoyltransferase activity	EXP PMID:24332717 Structure, functional characterization, and evolution of the...	ACCEPT	Summary: Experimentally characterized ATCase activity of human CAD (EC 2.1.3.2). A core catalytic activity of the multienzyme. Reason: Core molecular function with direct experimental support in the human protein. Supporting Evidence: PMID:24332717 the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals
GO:0004087 carbamoyl-phosphate synthase (ammonia) activity	ISS GO_REF:0000024	ACCEPT	Summary: The ammonia-dependent CPS partial reaction (EC 6.3.4.16), transferred by sequence similarity from an ortholog (UniProtKB:P07259). Part of the CPS II module. Reason: Correct component activity of the CPS module; consistent with the IEA/EC annotation. Supporting Evidence: file:human/CAD/CAD-uniprot.txt followed by an ammonium-dependent carbamoyl phosphate
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	EXP PMID:24332717 Structure, functional characterization, and evolution of the...	ACCEPT	Summary: Experimentally supported glutamine-dependent carbamoyl phosphate synthetase II activity (EC 6.3.5.5) of human CAD, the overall committed first-step reaction of the pathway. Reason: Core molecular function; the overall CPS II reaction that initiates de novo pyrimidine biosynthesis. Supporting Evidence: PMID:24332717 the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals
GO:0004359 glutaminase activity	ISS GO_REF:0000024	ACCEPT	Summary: GATase partial reaction (EC 3.5.1.2) transferred by sequence similarity (UniProtKB:P07259). Hydrolyzes glutamine to supply ammonia to CPS. Reason: Correct component activity of the CPS II module; consistent with the IEA/EC annotation. Supporting Evidence: file:human/CAD/CAD-uniprot.txt amidotransferase activity (GATase) that binds and cleaves glutamine to
GO:0043025 neuronal cell body	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: Neuronal cell body localization transferred by sequence similarity from a rodent ortholog (UniProtKB:A0A8I5ZMM2). Reason: Neuron-specific localization transferred from a rodent ortholog; not a core localization of the ubiquitous cytosolic enzyme. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0043195 terminal bouton	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: Synaptic-terminal localization transferred by sequence similarity from a rodent ortholog. Reason: Neuron-specific localization transferred from a rodent ortholog; not a core localization. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0006225 UDP biosynthetic process	IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn...	KEEP AS NON CORE	Summary: Patient-derived (biallelic CAD mutation) metabolic-flux study showing that CAD is required for de novo synthesis of UDP-activated sugars and pyrimidine nucleotides; CAD acts upstream of UDP synthesis. Reason: Correctly captures CAD as acting upstream of UDP synthesis; downstream of CAD's direct product (UMP). Core process is de novo UMP biosynthesis. Supporting Evidence: PMID:25678555 nearly all UDP-activated sugars that serve as donors for glycosylation were decreased
GO:0044205 'de novo' UMP biosynthetic process	IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn...	ACCEPT	Summary: Patient study demonstrating impaired de novo pyrimidine (UMP) biosynthesis when CAD is mutated, with rescue by uridine. Core biological process. Reason: Directly supports CAD's essential role in de novo UMP biosynthesis; core process. Supporting Evidence: PMID:25678555 impaired aspartate incorporation into RNA and DNA through the de novo synthesis pathway
GO:0006225 UDP biosynthetic process	IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn...	KEEP AS NON CORE	Summary: Duplicate (involved_in) of the UDP biosynthetic process annotation from the same patient study. Reason: True upstream role in UDP-sugar/pyrimidine synthesis; downstream of CAD's direct product. Supporting Evidence: PMID:25678555 nearly all UDP-activated sugars that serve as donors for glycosylation were decreased
GO:0044205 'de novo' UMP biosynthetic process	IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn...	ACCEPT	Summary: Duplicate (involved_in) of the core de novo UMP biosynthetic process from the same patient study. Reason: Core biological process; directly supported by the loss-of-function metabolic phenotype and uridine rescue. Supporting Evidence: PMID:25678555 impaired aspartate incorporation into RNA and DNA through the de novo synthesis pathway
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	MARK AS OVER ANNOTATED	Summary: High-throughput identification of CAD in an NK-cell membrane-proteome preparation. CAD is a soluble cytosolic enzyme; the authors themselves note many identified proteins are only transiently/peripherally associated with membranes. Reason: Proteomic co-purification with a membrane fraction, not a genuine membrane localization for a cytosolic enzyme; the study flags such transient associations. Supporting Evidence: PMID:19946888 predicted to be transiently associated with membranes
GO:0004151 dihydroorotase activity	IDA PMID:24332717 Structure, functional characterization, and evolution of the...	ACCEPT	Summary: Direct experimental (crystal structure + functional assay) demonstration of the Zn2+-dependent dihydroorotase activity of the human CAD DHOase domain. Core catalytic activity. Reason: Core molecular function with strong direct experimental support in the human protein. Supporting Evidence: PMID:24332717 Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process	IDA PMID:24332717 Structure, functional characterization, and evolution of the...	ACCEPT	Summary: CAD initiates and controls de novo pyrimidine biosynthesis; direct experimental support from the structural/functional study of the multienzyme. Reason: Core biological process with direct experimental support. Supporting Evidence: PMID:24332717 initiates and controls the de novo biosynthesis of pyrimidines
GO:0008270 zinc ion binding	IDA PMID:24332717 Structure, functional characterization, and evolution of the...	ACCEPT	Summary: The DHOase domain binds Zn2+ ions essential for catalysis, shown directly by the crystal structure (two Zn2+ bridged by a carboxylated lysine plus a third Zn coordinating a histidinate). Reason: Directly supported cofactor-binding activity essential to the dihydroorotase reaction. Supporting Evidence: PMID:24332717 an active site enclosed by a flexible loop with two Zn
GO:0070062 extracellular exosome	HDA PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote...	MARK AS OVER ANNOTATED	Summary: High-throughput identification of CAD in the proteome of B-cell exosomes. CAD is a cytosolic enzyme; presence in an exosome proteome does not establish a functional extracellular localization. Reason: Mass-spectrometry co-purification in an exosome preparation; not a genuine functional localization for this cytosolic enzyme. Supporting Evidence: PMID:20458337 total proteome of highly purified B cell-derived exosomes
GO:0005829 cytosol	TAS Reactome:R-HSA-73571	ACCEPT	Summary: Reactome (traceable author statement) placing the DHOase step of CAD in the cytosol. Reason: Correct core localization; consistent with all other cytosol evidence. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0005829 cytosol	TAS Reactome:R-HSA-73573	ACCEPT	Summary: Reactome (traceable author statement) placing the ATCase step of CAD in the cytosol. Reason: Correct core localization; consistent with all other cytosol evidence. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0005829 cytosol	TAS Reactome:R-HSA-73577	ACCEPT	Summary: Reactome (traceable author statement) placing the CPS (L-Gln -> carbamoyl phosphate) step of CAD in the cytosol. Reason: Correct core localization; consistent with all other cytosol evidence. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0004672 protein kinase activity	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: Protein kinase activity transferred by sequence similarity from UniProtKB:P08955. CAD has no protein-kinase domain; its four domains are GATase, CPS (ATP-grasp), DHOase (metallohydrolase) and ATCase. CAD is a substrate of kinases (MAPK, PKA, mTOR/S6K1), not a kinase. This is a spurious ISS transfer. Reason: Biologically unsupported self-annotation: no kinase domain and no evidence CAD phosphorylates other proteins. Flagged as over-annotated (ISS transfer, not experimental); the phosphorylation biology is CAD being phosphorylated by other kinases. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Activated by MAP kinase (Erk1/2) phosphorylation just prior to the
GO:0070335 aspartate binding	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Aspartate binding transferred by sequence similarity (UniProtKB:P08955). CAD binds L-aspartate as the substrate of its ATCase reaction, so this is a defensible substrate- binding activity. Reason: Substrate binding supporting the ATCase reaction; ancillary to the core catalytic activity (GO:0004070). Supporting Evidence: file:human/CAD/CAD-uniprot.txt carbamoyl-L-aspartate from L-aspartate and
GO:0019899 enzyme binding	IPI PMID:15326225 The human Rad9 checkpoint protein stimulates the carbamoyl p...	KEEP AS NON CORE	Summary: CAD physically interacts with the Rad9 checkpoint protein (UniProtKB:Q99638); free Rad9 binds the CPSase domain of CAD and stimulates its CPSase activity ~2-fold. A specific, functionally meaningful protein-protein interaction. Reason: Genuine, functionally characterized interaction (Rad9 stimulates CAD CPSase), but a regulatory binding activity rather than CAD's core catalytic function. Supporting Evidence: PMID:15326225 Rad9 binds to the CPSase domain, and, moreover, this binding results in a 2-fold stimulation of the CPSase activity of CAD
GO:0004070 aspartate carbamoyltransferase activity	ISS GO_REF:0000024	ACCEPT	Summary: ISS duplicate of the ATCase activity (from UniProtKB:P08955). Reason: Correct core catalytic activity, consistent with the experimental and IBA annotations. Supporting Evidence: file:human/CAD/CAD-uniprot.txt aspartate transcarbamylase (ATCase;
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	ISS GO_REF:0000024	ACCEPT	Summary: ISS duplicate of the CPS II activity (from UniProtKB:P08955). Reason: Correct core catalytic activity, consistent with the experimental and IBA annotations. Supporting Evidence: file:human/CAD/CAD-uniprot.txt synthetase (CPSase; EC 6.3.5.5)
GO:0004151 dihydroorotase activity	ISS GO_REF:0000024	ACCEPT	Summary: ISS duplicate of the DHOase activity (from UniProtKB:P08955). Reason: Correct core catalytic activity, consistent with experimental and IBA annotations. Supporting Evidence: PMID:24332717 the crystal structure and functional characterization of the dihydroorotase domain of human CAD
GO:0005524 ATP binding	ISS GO_REF:0000024	ACCEPT	Summary: ISS duplicate of ATP binding (from UniProtKB:P08955); consistent with the ATP-grasp folds of the CPS module. Reason: Correct ancillary molecular function supporting the CPS reaction. Supporting Evidence: file:human/CAD/CAD-uniprot.txt hydrogencarbonate and ATP to
GO:0005634 nucleus	IDA PMID:15890648 Nuclear localization and mitogen-activated protein kinase ph...	KEEP AS NON CORE	Summary: Direct cell-fractionation/microscopy showing a phospho-Thr456 CAD subpopulation in the nucleus following EGF stimulation; nuclear import promotes optimal cell growth. Reason: Real, experimentally supported conditional localization; catalysis is chiefly cytosolic, so keep as non-core. Supporting Evidence: PMID:15890648 Thr(P)-456 CAD was primarily localized within the nucleus
GO:0005829 cytosol	IDA PMID:15890648 Nuclear localization and mitogen-activated protein kinase ph...	ACCEPT	Summary: Direct demonstration that most CAD is cytosolic. Core localization. Reason: Core localization with direct experimental support. Supporting Evidence: PMID:15890648 most of the CAD in the cell was cytosolic
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process	ISS GO_REF:0000024	ACCEPT	Summary: ISS duplicate of the core de novo pyrimidine biosynthesis process (from UniProtKB:P08955). Reason: Core biological process, consistent with experimental and IBA annotations. Supporting Evidence: PMID:24332717 initiates and controls the de novo biosynthesis of pyrimidines
GO:0016363 nuclear matrix	IDA PMID:9525610 Adenovirus preterminal protein binds to the CAD enzyme at ac...	KEEP AS NON CORE	Summary: CAD was found associated with the nuclear matrix, where adenovirus preterminal protein (pTP) binds CAD at active sites of viral DNA replication (colocalization by confocal microscopy). Consistent with the MAPK-phosphorylated nuclear CAD population that associates with insoluble nuclear substructures including the nuclear matrix. Reason: Real but conditional/subpopulation localization; the core catalytic location is the cytosol. Supporting Evidence: PMID:9525610 pTP binds to a multifunctional pyrimidine biosynthesis enzyme found at replication domains on the NM

Gene Description

Existing Annotations Review

Core Functions

Glutamine-dependent carbamoyl phosphate synthetase II (CPS II): the committed first step of de novo pyrimidine biosynthesis, producing carbamoyl phosphate from L-glutamine, bicarbonate and 2 ATP. This is the cytosolic pyrimidine CPS, distinct from the mitochondrial urea-cycle CPS1.

Aspartate transcarbamylase (ATCase): condenses carbamoyl phosphate with L-aspartate to form N-carbamoyl-L-aspartate, the second committed step of de novo pyrimidine biosynthesis.

Dihydroorotase (DHOase): Zn2+-dependent cyclization of N-carbamoyl-L-aspartate to (S)-dihydroorotate, the third committed step of de novo pyrimidine biosynthesis.

References

📚 Additional Documentation

Notes

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