CAD is a multifunctional cytosolic enzyme that catalyzes the first three steps of de novo pyrimidine nucleotide biosynthesis. Its glutamine-dependent carbamoyl-phosphate synthetase II module uses glutamine, bicarbonate and ATP to produce carbamoyl phosphate; its aspartate carbamoyltransferase module forms carbamoylaspartate; and its zinc-dependent dihydroorotase module cyclizes this intermediate to dihydroorotate. Subsequent reactions catalyzed by DHODH and UMPS produce UMP. CAD forms oligomeric assemblies and couples nucleotide supply to growth through allosteric and phosphorylation-dependent regulation, including S6K-mediated phosphorylation. Biallelic loss-of-function variants cause CAD deficiency, a developmental and epileptic encephalopathy associated with impaired pyrimidine production and depleted glycosylation precursors. Clinical studies report uridine responsiveness, and human CAD-knockout complementation distinguishes damaging from functional variants.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004070 aspartate carbamoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: CAD catalyzes aspartate carbamoyl transfer in pyrimidine synthesis. Reason: The exact PTN000150227 IBD and descendant evidence set are present in the cached PAINT export. Human CAD also has independently curated ATCase biochemistry in Reactome. Its appearance among the IBD descendants is legitimate target experimental grounding, not circularity. The complete family tree was not reconstructed. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: Refine the inherited cytoplasmic location to cytosol. Reason: The broad PTN000150222 cytoplasmic IBD is authentic and is not rejected because its descendants include other enzyme architectures. For human CAD, the seeded cytosol annotations and experimental localization provide the more informative compartment. This is a specificity refinement of a correct inherited location. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000150222 SUPPORTS TRANSFER The exact cytoplasmic IBD is present in the cached PAINT export. Human evidence supports the more specific cytosol location; no ancestral placement error is asserted. Proposed replacements: cytosol |
| GO:0006541 L-glutamine metabolic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Glutamine metabolism is a real substrate-level component of CAD function. Reason: The PTN000150223 IBD for glutamine metabolism is present with dictyBase:DDB_G0276335 as its experimental descendant. A single donor does not invalidate this placement. CAD directly hydrolyzes glutamine to supply nitrogen to CPS II, so the annotation is biochemically coherent, although its characteristic pathway is pyrimidine biosynthesis. No claim is made to have read the donor experiment or complete tree. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73577 |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Cytosol is the principal established site of CAD catalysis. Reason: The exact PTN000150227 cytosol IBD is grounded on human P27708. That self-source is appropriate experimental grounding. Independent human localization and cytosolic Reactome reactions support retention; disputes about an additional nuclear pool do not undermine cytosol. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: CAD directly builds the pyrimidine ring through its three catalytic steps. Reason: The exact PTN000150227 process IBD and listed experimental descendants match the local PAINT export. CAD performs pathway chemistry itself, rather than merely being necessary for proliferation. Human enzymology and CAD-deficiency metabolic data independently corroborate the inherited process. |
| GO:0004151 dihydroorotase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Dihydroorotase is a directly established CAD catalytic activity. Reason: The PTN000150227 IBD and descendant set are present in the PAINT export. The human DHO-domain structural and functional study independently establishes the activity on the target, making a loss or erroneous propagation hypothesis unwarranted. |
| GO:0004070 aspartate carbamoyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Retain the specific ATCase catalytic mapping. Reason: The combined source includes the ATCase InterPro signature, RHEA:20013 and EC:2.1.3.2, alongside rodent orthology. These describe the CAD reaction converting carbamoyl phosphate and aspartate into carbamoylaspartate, independently represented in the human Reactome reaction. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IEA GO_REF:0000120 | ACCEPT | Summary: The ammonia-dependent CPS partial reaction is compatible with CAD CPS II. Reason: RHEA:18029 and EC:6.3.4.16 describe the ammonia-dependent reaction of the synthetase module. This does not identify CAD as mitochondrial CPS1. Glutamine hydrolysis supplies ammonia in the coupled physiological reaction, while the synthetase chemistry can be assayed with ammonia supplied externally. |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Glutamine-dependent CPS II is the entry reaction catalyzed by CAD. Reason: The combined InterPro, RHEA:18633, EC:6.3.5.5 and orthology mapping is consistent with the human CAD domain architecture and experimentally assayed CPS activity. CAD catalyzes this step; it is not simply a regulator of another synthetase. |
| GO:0004151 dihydroorotase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The specific DHO mapping agrees with human structural enzymology. Reason: RHEA:24296 and EC:3.5.2.3, combined with ARBA and orthology evidence, map to the DHO module of CAD. Human isolated-domain mutagenesis and activity assays independently verify this chemistry. |
| GO:0004359 glutaminase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Glutaminase is an intrinsic partial activity of the CAD CPS II module. Reason: RHEA:15889 and EC:3.5.1.2 describe conversion of glutamine to glutamate and ammonia. CAD performs this reaction to provide nitrogen for carbamoyl phosphate synthesis. This does not imply that CAD is a general-purpose mitochondrial glutaminase. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73577 |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding supports CAD catalysis but is not a separate defining function. Reason: The InterPro ATP-binding/ATP-grasp signatures agree with the two ATP-consuming CPS reactions and direct ATP-dependent CAD assays. Retain the binding feature as non-core while the chemically specific CPS II activity defines the corresponding core. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | UNDECIDED | Summary: An additional nuclear CAD pool is disputed. Reason: The UniProt location mapping reflects published nuclear-localization evidence, so absence of a classical localization motif is not a refutation. The 2005 study reports conditional nuclear CAD, whereas the separately identified 2020 localization study challenges nuclear translocation. A comparison of exact cell systems, constructs, antibodies and fractionation controls is needed before resolving this mapping. Supporting Evidence: file:human/CAD/CAD-uniprot.txt PMID:31997698 exclusively localized at the cytosol |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MODIFY | Summary: Refine the correct broad cytoplasmic mapping to cytosol. Reason: The UniProt cytoplasmic location is consistent with CAD biology, but the existing experimental cytosol assertions and curated reactions provide a more specific compartment. This is not removal of a valid localization. Proposed replacements: cytosol |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Retain de novo pyrimidine-ring biosynthesis. Reason: ATCase/CPS InterPro mapping and rat orthology are supported independently by the reactions performed by human CAD. The enzyme itself supplies the first three chemical steps, including formation of dihydroorotate. |
| GO:0006520 amino acid metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Amino-acid metabolism is broad but chemically correct for CAD. Reason: CAD consumes glutamine and aspartate in its own catalytic reactions. The ATCase-related InterPro mapping is therefore not false merely because CAD is usually described as a pyrimidine enzyme. Retain this broad metabolic consequence as non-core. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 Reactome:R-HSA-73577 |
| GO:0006541 L-glutamine metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Retain broad glutamine metabolism as a component of CPS II chemistry. Reason: The CPS-family InterPro inference is independently supported by CAD glutamine hydrolysis. Pyrimidine production is the defining pathway, but that does not make glutamine metabolism an erroneous assertion. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73577 |
| GO:0016597 amino acid binding | IEA GO_REF:0000002 | MODIFY | Summary: Specify aspartate binding within the ATCase module. Reason: The mapped InterPro entries are the aspartate/ornithine carbamoyltransferase family and substrate-binding region. For human CAD, the actual substrate is aspartate, supported by the specific ATCase reaction and existing curated aspartate-binding assertion. No ornithine-binding function is inferred from the shared family name. Proposed replacements: aspartate binding Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0016743 carboxyl- or carbamoyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Specify aspartate carbamoyltransferase activity. Reason: The ATCase-family InterPro mapping identifies a true carbamoyltransferase. GO:0004070 is the verified specific child of this broad activity and describes the CAD reaction directly; breadth alone is not over-annotation. Proposed replacements: aspartate carbamoyltransferase activity Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: Specify the CAD dihydroorotase activity. Reason: The amidohydrolase-related IPR006680 mapping is consistent with the experimentally characterized human DHO module. Its reversible cyclic-amide reaction is more informative than the broad hydrolase term. This refinement does not claim that every CAD catalytic module is a hydrolase. Proposed replacements: dihydroorotase activity |
| GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | IEA GO_REF:0000002 | MODIFY | Summary: Specify the CAD dihydroorotase activity. Reason: The metal-dependent hydrolase IPR011059 mapping is consistent with the experimentally characterized human DHO module. Its reversible cyclic-amide reaction is more informative than the broad hydrolase term. This refinement does not claim that every CAD catalytic module is a hydrolase. Proposed replacements: dihydroorotase activity |
| GO:0016812 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides | IEA GO_REF:0000002 | MODIFY | Summary: Specify the CAD dihydroorotase activity. Reason: The DHO conserved-site IPR002195 mapping is consistent with the experimentally characterized human DHO module. Its reversible cyclic-amide reaction is more informative than the broad hydrolase term. This refinement does not claim that every CAD catalytic module is a hydrolase. Proposed replacements: dihydroorotase activity |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Metal binding is a supported cofactor feature. Reason: The electronic source is an ATP-grasp signature, while the complete protein also has directly established DHO zinc sites. CAD has several metal-dependent catalytic contexts; retain broad metal binding without converting every mapped metal site to a zinc-specific assertion. |
| GO:0055086 nucleobase-containing small molecule metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: Refine the broad metabolic classification to de novo UMP biosynthesis. Reason: The ARBA classification of nucleobase-containing small-molecule metabolism is compatible with CAD function. The official GO hierarchy places de novo UMP biosynthesis under this broader scope, and CAD directly catalyzes its first three steps. Replace the broad label with the already-established pathway term rather than treating correct ancestry as a false function. Proposed replacements: 'de novo' UMP biosynthetic process |
| GO:0072528 pyrimidine-containing compound biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: Refine the broad metabolic classification to de novo UMP biosynthesis. Reason: The ARBA classification of pyrimidine-containing compound biosynthesis is compatible with CAD function. The official GO hierarchy places de novo UMP biosynthesis under this broader scope, and CAD directly catalyzes its first three steps. Replace the broad label with the already-established pathway term rather than treating correct ancestry as a false function. Proposed replacements: 'de novo' UMP biosynthetic process |
| GO:0090407 organophosphate biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: Refine the broad metabolic classification to de novo UMP biosynthesis. Reason: The ARBA classification of organophosphate biosynthesis is compatible with CAD function. The official GO hierarchy places de novo UMP biosynthesis under this broader scope, and CAD directly catalyzes its first three steps. Replace the broad label with the already-established pathway term rather than treating correct ancestry as a false function. Proposed replacements: 'de novo' UMP biosynthetic process |
| GO:0005515 protein binding | IPI PMID:15161933 Comprehensive proteomic analysis of interphase and mitotic 1... | REMOVE | Summary: The CAD interaction is recorded, but a bare protein-binding row describes no CAD activity and is removed. Reason: The exact GOA WITH/FROM partner is P63104/YWHAZ, and the immutable human UniProt interaction block independently lists this pair. The complete cached abstract describes a 14-3-3 affinity/MS screen; the CAD-specific table was not inspected. This supports the collapsed protein-binding assertion with curator deference, without claiming independent reproduction of the source-specific edge or a finer regulatory activity. Per curation policy, GO:0005515 protein binding records only that an interaction was detected and not what CAD does, so the row is removed; removal does not imply the interaction is false, and the cited evidence does not support a more informative molecular-function term for CAD. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | REMOVE | Summary: The CAD interaction is recorded, but a bare protein-binding row describes no CAD activity and is removed. Reason: The exact GOA WITH/FROM partner is P63104/YWHAZ, and the immutable human UniProt interaction block independently lists this pair. The available cache contains the complete abstract and Discussion of the endogenous-tagging/IP-MS resource, not the target interaction table. This supports the collapsed protein-binding assertion with curator deference, without claiming independent reproduction of the source-specific edge or a finer regulatory activity. Per curation policy, GO:0005515 protein binding records only that an interaction was detected and not what CAD does, so the row is removed; removal does not imply the interaction is false, and the cited evidence does not support a more informative molecular-function term for CAD. |
| GO:0005515 protein binding | IPI PMID:35709258 Spatial centrosome proteome of human neural cells uncovers d... | REMOVE | Summary: The CAD interaction is recorded, but a bare protein-binding row describes no CAD activity and is removed. Reason: The exact GOA WITH/FROM partner is Q8N137/CNTROB, and the immutable human UniProt interaction block independently lists this pair. The complete cached abstract describes spatial proteomics of human neural cells; the CAD-specific target assay was not inspected. This supports the collapsed protein-binding assertion with curator deference, without claiming independent reproduction of the source-specific edge or a finer regulatory activity. Per curation policy, GO:0005515 protein binding records only that an interaction was detected and not what CAD does, so the row is removed; removal does not imply the interaction is false, and the cited evidence does not support a more informative molecular-function term for CAD. |
| GO:0042802 identical protein binding | IPI PMID:24332717 Structure, functional characterization, and evolution of the... | KEEP AS NON CORE | Summary: Retain CAD self-association without claiming a whole-protein structure from the DHO study. Reason: The original IPI is self-binding. The primary paper directly characterizes the human DHO domain, while the broader oligomeric CAD context is also curated in UniProt and Reactome. Retain self-association as a non-core assembly feature; the isolated-domain crystal is not direct structural proof of the full human hexamer. |
| GO:0001889 liver development | IEA GO_REF:0000107 | UNDECIDED | Summary: Liver-development participation remains unresolved after a source-specific review. Reason: The historical March 2023 MGI/RGD graph links the rat Cad donor to a historical ATCase tissue-distribution study with IEP evidence. PubMed provides no abstract; the accessible publisher preview describes ATCase tissue distribution but does not expose the developmental experiments. Independently, the cached PMID:7053379 reports increased CPS II activity in differentiating rat liver. Such activity is compatible with biosynthetic work during growth, but neither the preview nor that independent activity comparison establishes the particular developmental contribution represented by this transfer. The final decision is UNDECIDED because that distinction remains unresolved, not because rat orthology or an IEP code is intrinsically inadequate. |
| GO:0006228 UTP biosynthetic process | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain the broader UTP-synthesis context of CAD metabolism. Reason: The rat orthology assertion is consistent with CAD providing the de novo pyrimidine-ring precursor used for UMP, UDP and UTP production. Human CAD-deficiency metabolic evidence independently supports pyrimidine nucleotide supply. CAD releases dihydroorotate, not UMP or UTP, and no terminal nucleotide-kinase activity is assigned. |
| GO:0006805 xenobiotic metabolic process | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain a bounded non-core xenobiotic-metabolism role. Reason: The historical rat donor provenance maps to an experiment in which a DHOase inhibitor reduced conversion of the one-ring-open dexrazoxane metabolites B/C to ADR-925. The paper explicitly assigns the first ring opening to dihydropyrimidinase and the second to DHOase. This positive side-substrate evidence supports the existing orthology-based non-core context. It is not a direct human assay, an assertion that CAD opens the first ring, or a general detoxification function; full experimental controls remain unread. Supporting Evidence: file:human/CAD/CAD-uniprot.txt GO_REF:0000107 PMID:18515330 DHOase directly metabolized B and C |
| GO:0007507 heart development | IEA GO_REF:0000107 | UNDECIDED | Summary: Heart-development participation remains unresolved after a source-specific review. Reason: The historical MGI/RGD graph maps the rat Cad donor to the same historical ATCase tissue-distribution IEP source as liver development. PubMed has no abstract. The publisher preview discusses adult tissue ATCase distribution, including negligible adult-heart activity; it does not disclose the developing-heart measurements or test their functional significance. Adult-heart activity cannot settle a developmental claim. The final UNDECIDED decision preserves this precise gap and does not convert the IEP code into proof that only nonfunctional expression was measured. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0007565 female pregnancy | IEA GO_REF:0000107 | UNDECIDED | Summary: Pregnancy-associated CAD activity does not yet resolve the pregnancy-process assignment. Reason: The historical rat IEP provenance points to a mammary-gland ATCase and nucleic-acid study during pregnancy and hormone treatment. This bibliographic identity is verified, but PubMed supplies no abstract and the publisher body was inaccessible. The uninspected experiment could report a regulated biosynthetic contribution or only an accompanying enzyme-level change. The final decision is UNDECIDED because these alternatives have not been distinguished; the tissue and title alone do not establish either physiological participation or over-annotation. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0007595 lactation | IEA GO_REF:0000107 | UNDECIDED | Summary: The lactation transfer remains unresolved at its actual donor-source boundary. Reason: The historical MGI/RGD graph attaches rat Cad lactation to a historical study with IEP evidence and attaches a pyrimidine-biosynthesis IDA assertion to the same paper. The current primary abstract/body could not be retrieved. Consequently the source code does not establish that the lactation annotation was based only on passive expression, and the assay tissue, substrate flux and connection to milk production remain unverified. UNDECIDED is the final evidence-limited judgment, without assigning CAD a milk-synthesis reaction or dismissing a possible biosynthetic contribution. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0014075 response to amine | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain the rat-supported biochemical response to amine exposure as a non-core context. Reason: The preserved Ensembl transfer identifies rat Cad. Its historical donor source, now available as the complete cached PMID:2864015 abstract, reports a single dimethylnitrosamine exposure in newborn rats and subsequent measurements of CPS I/II, ATCase, dihydroorotase and other activities. Cytosolic enzyme activities increased while mitochondrial urea-cycle activities decreased. This is an experimentally measured metabolic response, so the IEP provenance should not be dismissed as passive expression alone. Retain the curated response as non-core with this rat-assay boundary; the abstract does not establish an amine-metabolizing catalytic activity of CAD or a measured human response. Individual enzyme data and the full protocol remain uninspected. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt PMID:2864015 the activity of enzymes which utilize ornithine and carbamoyl-phosphate was enhanced in the cytosol |
| GO:0019240 L-citrulline biosynthetic process | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: The citrulline-process transfer overextends CAD CPS II assay activity. Reason: CAD supplies cytosolic carbamoyl phosphate that is sequestered and passed to its own ATCase site for pyrimidine synthesis. Physiological ornithine-to-citrulline synthesis instead uses mitochondrial ornithine transcarbamylase and its compartmentalized carbamoyl-phosphate supply. The cached rat CPS II study separates CPS II from CPS I; the inspected indexed Methods excerpt describes added bacterial ornithine carbamoyltransferase used to detect CPS II activity. That coupled citrulline readout does not demonstrate physiological CAD participation in L-citrulline biosynthesis. The electronic transfer is therefore marked as over-annotated on the combined reaction and compartment evidence. This does not deny that CAD-generated carbamoyl phosphate can feed the artificial coupled assay or claim that every possible pathological metabolite exchange has been excluded. |
| GO:0031000 response to caffeine | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain the rat-brain enzyme-activity response to caffeine as a non-core context. Reason: The preserved Ensembl transfer identifies rat Cad. The complete cached PMID:6149265 abstract reports increased rat-brain ATCase and dihydroorotase activities after ingestion of large amounts of caffeine, alongside other nucleotide-metabolism enzymes. This directly supports a biochemical response rather than a transcript-only inference, and justifies non-core retention with curator deference for the ortholog transfer. It does not assign caffeine catabolism to CAD, establish a measured human response or validate the paper's caffeine model as a mechanism of Lesch-Nyhan syndrome; the authors themselves question that model. Exact doses, individual assay data and full Methods remain uninspected. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt PMID:6149265 ingestion of large amounts of caffeine increases the activities in rat brain of adenosine deaminase, purine nucleoside phosphorylase, aspartate carbamoyl-transferase, dihydroorotase, and dihydroorotate oxidase. |
| GO:0031100 animal organ regeneration | IEA GO_REF:0000107 | UNDECIDED | Summary: Regeneration-specific participation remains unresolved despite measured enzyme activity. Reason: The historical rat IEP provenance points to a historical regeneration study; its verified record supplies no abstract, and the regenerative experiment was not inspected. Independently, the complete cached PMID:7053379 abstract reports increased CPS II activity in regenerating rat liver. This is a biochemical measurement rather than proof of expression alone, but it does not establish whether CAD contributes a regeneration-specific metabolic step or merely accompanies proliferating tissue. The final UNDECIDED decision concerns that unresolved process scope; it is not a claim that a metabolic enzyme cannot participate in regeneration. |
| GO:0032868 response to insulin | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain insulin responsiveness as a non-core regulatory context of CAD metabolism. Reason: The historical rat direct-assay source was not reread, but independent primary work directly links insulin to CAD-S1859 phosphorylation and pyrimidine flux in mammalian cells, including human cells. In CAD-deficient CHO-derived cells, WT versus S1859A CAD tests the regulated enzyme contribution. CAD executes the responsive metabolic chemistry; it is not the insulin receptor or S6K protein kinase. This supports the broad response annotation without claiming identical donor assay conditions. Supporting Evidence: file:human/CAD/CAD-uniprot.txt PMID:23429703 S6K1, but not catalytically inactive S6K1, directly phosphorylated CAD |
| GO:0032991 protein-containing complex | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain CAD as part of an oligomeric protein complex. Reason: The rat donor table identifies biochemical complex evidence, and human UniProt/Reactome independently describe CAD oligomerization. The broad complex term is correct but does not specify a distinct catalytic complex beyond the multifunctional CAD assembly. Human hexamer stoichiometry is not claimed to have been newly measured here. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0033574 response to testosterone | IEA GO_REF:0000107 | UNDECIDED | Summary: The testosterone-response transfer remains unresolved at the hormone-assay level. Reason: The historical rat IEP mapping points to a historical ATCase study. Official bibliographic indexing identifies an ATCase study in chemically induced rat mammary tumours and indexes testosterone treatment, but no primary abstract or assay results were available. The direction of the CAD-associated activity change and its relation to the hormone treatment remain unverified. The final decision is UNDECIDED; a tumour-study title and an IEP code do not show that the response was merely passive expression or that no metabolic response occurred. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0042594 response to starvation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain starvation responsiveness as a non-core metabolic adaptation. Reason: The original rat direct-assay experiment remains unread. Independent mammalian-cell work reports suppression of growth-signal-stimulated pyrimidine flux by amino-acid starvation and identifies regulated CAD catalysis as the pathway mechanism. This corroborates nutrient-responsive CAD metabolism, while the exact starvation experiment is described in the main text by reference to supplementary figures that were not inspected. It does not establish that CAD itself senses nutrient availability. |
| GO:0042802 identical protein binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain orthology-supported self-association. Reason: Rat self-association evidence is represented in the historical comparative table and agrees with human CAD assembly evidence. Retain the broad binding feature without interpreting the inherited row as an independent human stoichiometry experiment. |
| GO:0043025 neuronal cell body | IEA GO_REF:0000107 | UNDECIDED | Summary: The fine neuronal cell body localization requires the donor assay. Reason: The exact donor is rat A0A8I5ZMM2. The historical MGI/RGD graph maps this fine localization to PMID:1673139. Its complete abstract reports rat and hamster astrocyte-like staining, GFAP confirmation in rat, and glial subtypes in hamster; it does not expose the neuronal cell body assay. The full article and antibody controls were not inspected, so additional neuronal evidence cannot be excluded. Preserve the original transfer as unresolved rather than rejecting it from the title or assuming that astrocyte observations exhaust the paper. |
| GO:0043195 terminal bouton | IEA GO_REF:0000107 | UNDECIDED | Summary: The fine terminal bouton localization requires the donor assay. Reason: The exact donor is rat A0A8I5ZMM2. The historical MGI/RGD graph maps this fine localization to PMID:1673139. Its complete abstract reports rat and hamster astrocyte-like staining, GFAP confirmation in rat, and glial subtypes in hamster; it does not expose the terminal bouton assay. The full article and antibody controls were not inspected, so additional neuronal evidence cannot be excluded. Preserve the original transfer as unresolved rather than rejecting it from the title or assuming that astrocyte observations exhaust the paper. |
| GO:0044205 'de novo' UMP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: CAD performs the initial steps of de novo UMP biosynthesis. Reason: The mouse B2RQC6 orthology and UniPathway mapping agree with the defined pathway beginning with dihydroorotate synthesis from simple precursors. CAD performs three reactions itself; downstream DHODH and UMPS complete the route. Human metabolic defects independently support this assignment. |
| GO:0044210 'de novo' CTP biosynthetic process | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain the broader de novo CTP-synthesis context. Reason: The mouse B2RQC6 transfer concerns the complete de novo pathway, to which CAD supplies pyrimidine-ring synthesis. Reduced CTP in human CAD deficiency corroborates the pathway context. CAD does not directly aminate UTP or produce CTP, and no CTP synthase molecular activity is inferred. |
| GO:0046134 pyrimidine nucleoside biosynthetic process | IEA GO_REF:0000107 | MODIFY | Summary: Use the directly supported de novo UMP pathway instead of the nucleoside branch. Reason: CAD catalyzes the initial reactions yielding dihydroorotate in de novo UMP biosynthesis. Downstream DHODH and UMPS proceed through orotate and OMP to the phosphorylated nucleotide UMP, rather than through a free pyrimidine nucleoside intermediate. GO:0046134 describes nucleoside formation and is not the appropriate branch for this established CAD pathway. Refine the inherited metabolic assertion to GO:0044205, already present among the source annotations and consistent with the other pathway refinements. The rat donor assay for the nucleoside term is not claimed to have been recovered; the replacement rests on the independently established CAD reactions, not on an assumption that CAD performs the terminal UMPS reaction. Proposed replacements: 'de novo' UMP biosynthetic process |
| GO:0051414 response to cortisol | IEA GO_REF:0000107 | UNDECIDED | Summary: The cortisol-response transfer remains unresolved because its target assay is inaccessible. Reason: The historical MGI/RGD graph maps rat Cad to a historical cortisol study with IEP evidence. Primary access attempts did not recover its abstract or body, so the exact hormone treatment, tissue and CAD readout remain unknown. The current evidence therefore cannot distinguish hormone-responsive CAD metabolism from an incidental abundance correlation. UNDECIDED is the final decision on this specific source gap, without assuming CPS I confusion or treating IEP as a measurement of transcript abundance alone. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0071364 cellular response to epidermal growth factor stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Retain conditional EGF responsiveness as a non-core regulatory context. Reason: The rat transfer has a historical expression-based EGF source. Independently, the human-review reference reports EGF-related changes in CAD localization/phosphorylation and metabolic measurements. Retain the broad cellular-response context without asserting that CAD is an EGF receptor or that MAPK phosphorylation causes nuclear entry. |
| GO:0071466 cellular response to xenobiotic stimulus | IEA GO_REF:0000107 | UNDECIDED | Summary: CAD gene amplification does not by itself settle the protein-level xenobiotic response. Reason: The historical rat IEP source is a cyclin D1/CAD-amplification study. Its complete official indexed abstract reports that cyclin D1 overexpression in rat liver epithelial cells increases recovery of cells with amplified CAD gene copies and altered checkpoint control. This establishes a genomic-selection phenomenon, while the accessible abstract does not expose the xenobiotic-selection protocol or test how CAD protein activity contributes to the response. The final decision remains UNDECIDED because functional dosage-mediated adaptation and a selected genomic marker cannot be distinguished from the inspected evidence. Neither an adaptive CAD role nor a purely passive expression effect is asserted. Supporting Evidence: GO_REF:0000107 file:human/CAD/CAD-uniprot.txt |
| GO:0006543 L-glutamine catabolic process | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Glutamine catabolism describes a genuine CAD partial reaction. Reason: The exact ISS donor P08955 is golden-hamster CAD, as recorded in the local PANTHER entry table. Human CAD hydrolyzes glutamine within CPS II. This partial chemistry is real but does not make bulk glutamine degradation its defining physiological function. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73577 |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Retain experimentally curated cytosol localization. Reason: The HPA immunofluorescence annotation is consistent with independent human CAD localization and the cytosolic reactions. The original HPA images were not independently rescored; there is no conflicting evidence against the broad cytosolic pool. |
| GO:0004070 aspartate carbamoyltransferase activity | EXP PMID:24332717 Structure, functional characterization, and evolution of the... | ACCEPT | Summary: Retain ATCase activity with independent reaction support. Reason: The cited study focuses on the human DHO domain, so its abstract is not described as a direct isolated-ATCase assay. Nonetheless the specific ATCase activity is independently established for CAD and curated in the human Reactome reaction. Preserve the original EXP source and accept the correct molecular function with that explicit source boundary. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | ISS GO_REF:0000024 | ACCEPT | Summary: Retain the ammonia-dependent CPS partial activity. Reason: The exact ISS donor P07259 is budding-yeast URA2, not mammalian CPS1. Its CPS chemistry is compatible with human CAD, whose curated reaction record and CPS assay context support use of externally supplied ammonia. This does not transfer the urea-cycle role or mitochondrial localization of CPS1. |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | EXP PMID:24332717 Structure, functional characterization, and evolution of the... | ACCEPT | Summary: Retain glutamine-dependent CPS II activity. Reason: The original EXP source is a human DHO-domain study, not a newly verified CPS assay in this review. Independent CAD/Rad9 kinetic experiments and the curated human CPS reaction establish the activity, so the source citation remains immutable while the supporting evidence is broadened honestly. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73577 |
| GO:0004359 glutaminase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Retain glutaminase chemistry within CAD CPS II. Reason: The yeast URA2 ISS donor is a related multifunctional pyrimidine enzyme. Human CAD has the glutamine amidotransferase module and corresponding curated reaction, supporting the partial activity without assigning a separate glutaminase-driven physiological pathway. |
| GO:0043025 neuronal cell body | ISS GO_REF:0000024 | UNDECIDED | Summary: The fine neuronal cell body localization requires the donor assay. Reason: The exact donor is rat A0A8I5ZMM2. The historical MGI/RGD graph maps this fine localization to PMID:1673139. Its complete abstract reports rat and hamster astrocyte-like staining, GFAP confirmation in rat, and glial subtypes in hamster; it does not expose the neuronal cell body assay. The full article and antibody controls were not inspected, so additional neuronal evidence cannot be excluded. Preserve the original transfer as unresolved rather than rejecting it from the title or assuming that astrocyte observations exhaust the paper. |
| GO:0043195 terminal bouton | ISS GO_REF:0000024 | UNDECIDED | Summary: The fine terminal bouton localization requires the donor assay. Reason: The exact donor is rat A0A8I5ZMM2. The historical MGI/RGD graph maps this fine localization to PMID:1673139. Its complete abstract reports rat and hamster astrocyte-like staining, GFAP confirmation in rat, and glial subtypes in hamster; it does not expose the terminal bouton assay. The full article and antibody controls were not inspected, so additional neuronal evidence cannot be excluded. Preserve the original transfer as unresolved rather than rejecting it from the title or assuming that astrocyte observations exhaust the paper. |
| GO:0006225 UDP biosynthetic process | IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn... | KEEP AS NON CORE | Summary: Retain UDP biosynthesis as a broader CAD-dependent metabolic context. Reason: The human CAD-deficiency study demonstrates impaired de novo nucleotide production and depleted downstream UDP-sugar precursors, with cellular rescue by uridine. CAD catalyzes initial pyrimidine-ring synthesis and releases dihydroorotate; it does not directly phosphorylate UMP to UDP. Preserve this sourced pathway context as non-core and retain the two distinct original source assertions. |
| GO:0044205 'de novo' UMP biosynthetic process | IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn... | ACCEPT | Summary: Retain direct participation in de novo UMP biosynthesis. Reason: CAD itself catalyzes the first three pathway reactions. Human CAD-deficiency cells show reduced precursor incorporation into nucleic acids and nucleotide-pool defects, rescued by uridine. This supports the established enzymatic pathway role, not merely a generic necessity inference. The two original assertions are preserved separately. |
| GO:0006225 UDP biosynthetic process | IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn... | KEEP AS NON CORE | Summary: Retain UDP biosynthesis as a broader CAD-dependent metabolic context. Reason: The human CAD-deficiency study demonstrates impaired de novo nucleotide production and depleted downstream UDP-sugar precursors, with cellular rescue by uridine. CAD catalyzes initial pyrimidine-ring synthesis and releases dihydroorotate; it does not directly phosphorylate UMP to UDP. Preserve this sourced pathway context as non-core and retain the two distinct original source assertions. |
| GO:0044205 'de novo' UMP biosynthetic process | IDA PMID:25678555 Biallelic mutations in CAD, impair de novo pyrimidine biosyn... | ACCEPT | Summary: Retain direct participation in de novo UMP biosynthesis. Reason: CAD itself catalyzes the first three pathway reactions. Human CAD-deficiency cells show reduced precursor incorporation into nucleic acids and nucleotide-pool defects, rescued by uridine. This supports the established enzymatic pathway role, not merely a generic necessity inference. The two original assertions are preserved separately. |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: Recovered in a membrane-fraction proteome without protein-specific evidence that it associates with membranes. Reason: UniProt: cytoplasm and nucleus (ECO:0000269); soluble pyrimidine-synthesis enzyme. (Manual re-review for OMICS_EVIDENCE, 2026-10-10; previous action: UNDECIDED.) |
| GO:0004151 dihydroorotase activity | IDA PMID:24332717 Structure, functional characterization, and evolution of the... | ACCEPT | Summary: Retain the directly assayed human DHO activity. Reason: The human DHO-domain study combines structure, site-directed mutagenesis and functional assays to establish the zinc-dependent catalytic mechanism. This is direct target evidence for the third CAD reaction. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IDA PMID:24332717 Structure, functional characterization, and evolution of the... | ACCEPT | Summary: DHO catalysis directly contributes to pyrimidine-ring biosynthesis. Reason: The human CAD DHO domain performs the cyclization step generating dihydroorotate. That is chemical participation in the biosynthetic pathway, independently supported by the other CAD reaction assignments and human deficiency data. |
| GO:0008270 zinc ion binding | IDA PMID:24332717 Structure, functional characterization, and evolution of the... | KEEP AS NON CORE | Summary: Zinc binding is a directly supported catalytic cofactor feature. Reason: The human DHO-domain structure identifies zinc sites and mutational/functional experiments test their catalytic importance. Retain this feature as non-core because the DHO catalytic activity captures the defining molecular work; do not generalize the DHO zinc sites to the CPS module. |
| GO:0070062 extracellular exosome | HDA PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... | KEEP AS NON CORE | Summary: Detected in an extracellular-vesicle proteome. The protein is plausible EV content, but this is not where it functions. Reason: Cytoplasmic pyrimidine-synthesis enzyme. Cytosolic protein (UniProt); cytosolic proteins, including abundant enzymes and cytoskeletal proteins, are expected and often promiscuous EV contents (MISEV2018 (PMID:30637094) category 2b). True, but not its core location. (Manual re-review for OMICS_EVIDENCE, 2026-10-10; previous action: UNDECIDED.) |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73571 | ACCEPT | Summary: Retain the cytosolic CAD reaction location. Reason: The complete cached Reactome reaction R-HSA-73571 explicitly assigns CAD catalysis to the cytosol. This agrees with independent experimental localization. The historical reaction notes distinguish direct human evidence from hamster-based oligomeric inference; a specific whole-human-hexamer structure is not claimed. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73573 | ACCEPT | Summary: Retain the cytosolic CAD reaction location. Reason: The complete cached Reactome reaction R-HSA-73573 explicitly assigns CAD catalysis to the cytosol. This agrees with independent experimental localization. The historical reaction notes distinguish direct human evidence from hamster-based oligomeric inference; a specific whole-human-hexamer structure is not claimed. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73577 | ACCEPT | Summary: Retain the cytosolic CAD reaction location. Reason: The complete cached Reactome reaction R-HSA-73577 explicitly assigns CAD catalysis to the cytosol. This agrees with independent experimental localization. The historical reaction notes distinguish direct human evidence from hamster-based oligomeric inference; a specific whole-human-hexamer structure is not claimed. |
| GO:0004672 protein kinase activity | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Retain the reported autophosphorylation-related kinase activity as non-core. Reason: The exact ISS donor P08955 is golden-hamster CAD, not Dictyostelium. The primary mammalian CAD study reports MgATP-dependent Thr1037 autophosphorylation, SDS purification/renaturation controls and a concentration-dependent component compatible with intermolecular phosphorylation. The GO definition does not require a canonical kinase-domain fold. Retain the conserved activity with curator deference as non-core: no direct human assay or general phosphorylation of signaling substrates is asserted, and phosphorylation of CAD by S6K is separate evidence about CAD as a substrate. Supporting Evidence: file:human/CAD/CAD-uniprot.txt GO_REF:0000024 PMID:11986331 in the absence of exogenous kinases |
| GO:0070335 aspartate binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Aspartate binding is a substrate-recognition feature of ATCase. Reason: The golden-hamster CAD ISS source is consistent with the human CAD ATCase reaction. Retain substrate binding as non-core while the more informative carbamoyltransferase activity defines the catalytic core. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0019899 enzyme binding | IPI PMID:15326225 The human Rad9 checkpoint protein stimulates the carbamoyl p... | KEEP AS NON CORE | Summary: Retain the curated CAD–RAD9A enzyme-binding annotation with a directional caveat. Reason: The original abstract and inspected primary Results establish CAD association with RAD9A/Q99638 and stimulation of CAD CPS activity. They do not themselves assay a catalytic activity of RAD9A. Retain the existing enzyme-binding classification with curator deference; its enzyme-side premise is the separately reported RAD9A nuclease characterization documented with external-source access limits in the notes, not CAD itself being an enzyme. Purified-protein mixing did not reproduce the stable coexpression-derived complex, and no CAD-mediated activation of RAD9A is inferred. |
| GO:0004070 aspartate carbamoyltransferase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Retain orthology-supported ATCase catalysis. Reason: The exact ISS source P08955 is golden-hamster CAD, a multifunctional pyrimidine enzyme. Its ATCase activity agrees with independent target biochemistry. The conserved activity is accepted without claiming that an uninspected donor assay was newly repeated in human protein. Supporting Evidence: file:human/CAD/CAD-uniprot.txt Reactome:R-HSA-73573 |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | ISS GO_REF:0000024 | ACCEPT | Summary: Retain orthology-supported glutamine-dependent CPS II catalysis. Reason: The exact ISS source P08955 is golden-hamster CAD, a multifunctional pyrimidine enzyme. Its glutamine-dependent CPS II activity agrees with independent target biochemistry. The conserved activity is accepted without claiming that an uninspected donor assay was newly repeated in human protein. |
| GO:0004151 dihydroorotase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Retain orthology-supported DHO catalysis. Reason: The exact ISS source P08955 is golden-hamster CAD, a multifunctional pyrimidine enzyme. Its DHO activity agrees with independent target biochemistry. The conserved activity is accepted without claiming that an uninspected donor assay was newly repeated in human protein. |
| GO:0005524 ATP binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ATP binding is a supported non-core feature of CAD chemistry. Reason: The golden-hamster CAD ISS source is consistent with the two ATP-consuming reactions within human CPS II and ATP-dependent kinetic measurements. Specific catalytic terms, rather than a separate ATP-binding core, describe the principal work. |
| GO:0005634 nucleus | IDA PMID:15890648 Nuclear localization and mitogen-activated protein kinase ph... | UNDECIDED | Summary: The experimentally reported nuclear pool conflicts with a later localization study. Reason: The 2005 abstract reports nuclear/nuclear-matrix CAD and conditional EGF-associated changes; it also states that MAPK phosphorylation did not itself mediate import. A later primary study challenges nuclear translocation. The older IDA cannot be rejected from motif reasoning, and a complete comparison of the conflicting assay systems remains necessary. |
| GO:0005829 cytosol | IDA PMID:15890648 Nuclear localization and mitogen-activated protein kinase ph... | ACCEPT | Summary: Retain the cytosolic CAD pool. Reason: The original localization study explicitly reports that most CAD is cytosolic. The later disagreement concerns an additional nuclear pool, not loss of the major cytosolic population. Independent pathway curation agrees. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | ISS GO_REF:0000024 | ACCEPT | Summary: Retain the conserved de novo pyrimidine pathway role. Reason: The golden-hamster CAD ISS donor is appropriate for the three catalytic steps independently established for human CAD. The enzyme performs pathway chemistry directly; this assignment does not extend to every proliferation-dependent process. |
| GO:0016363 nuclear matrix | IDA PMID:9525610 Adenovirus preterminal protein binds to the CAD enzyme at ac... | KEEP AS NON CORE | Summary: Retain the reported nuclear-matrix association in the viral-replication context. Reason: The complete abstract reports CAD/pTP interaction, a tagged CAD complex and confocal colocalization with active adenoviral DNA replication on the nuclear matrix. This is a specific infection-associated observation, not a constitutive nuclear CAD claim. A later general nuclear-localization challenge warrants comparison of context and antibody controls but does not by itself refute this conditional experiment. |
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Download this section (compressed HTML)Q: Which experimental conditions reconcile the reported nuclear or infection-associated nuclear-matrix pools of CAD with the later cytoplasm-only localization study?
Q: Does human CAD show the autophosphorylation behavior reported for mammalian CAD preparations, and what is its physiological contribution relative to phosphorylation by other kinases?
Q: Does the rat citrulline-biosynthesis annotation represent physiological CAD participation or a coupled CPS II assay using added ornithine carbamoyltransferase?
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