id: P27708
gene_symbol: CAD
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  CAD is a large (2225 aa) multifunctional cytosolic enzyme that carries out the first
  three committed steps of de novo pyrimidine (UMP) biosynthesis, combining four catalytic
  activities in a single polypeptide. Its glutamine-dependent carbamoyl-phosphate synthetase
  II (CPS II) module first uses a glutamine amidotransferase (GATase) reaction to release
  ammonia from L-glutamine, which is then combined with bicarbonate and 2 ATP by a
  carbamoyl-phosphate synthetase reaction to form carbamoyl phosphate (this is the cytosolic
  pyrimidine CPS, biochemically and functionally distinct from the mitochondrial urea-cycle
  enzyme CPS1). The carbamoyl phosphate is channeled to the aspartate transcarbamylase
  (ATCase) module, which condenses it with L-aspartate to make N-carbamoyl-L-aspartate, and
  then to the Zn2+-dependent dihydroorotase (DHOase) module, which cyclizes this to
  (S)-dihydroorotate. CAD assembles into a ~1.5 MDa homohexamer and is the rate-controlling
  entry point of the pathway. Its activity is regulated by phosphorylation: MAP kinase
  (Erk1/2) activates it just before S phase and mTOR/S6K1 (RPS6KB1)-dependent
  phosphorylation of Ser-1859 promotes oligomerization and pathway flux, while PKA and
  allosteric feedback by UMP/UTP inhibit it (PRPP activates). Biallelic loss-of-function
  variants cause CAD deficiency (developmental and epileptic encephalopathy 50), a
  uridine-responsive encephalopathy accompanied by anemia and defective glycosylation.
existing_annotations:
- term:
    id: GO:0004070
    label: aspartate carbamoyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Core molecular function, supported by phylogenetic inference and by direct experimental
      characterization of the human ATCase activity.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the multifunctional protein that initiates and controls the
        de novo biosynthesis of pyrimidines in animals
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      CAD is predominantly a cytoplasmic/cytosolic enzyme. The more specific term cytosol
      (GO:0005829) is also annotated and is preferred.
    action: ACCEPT
    reason: >-
      Correct broad localization; consistent with UniProt subcellular location and with the
      specific cytosol annotations. Cytosol is the more informative term for the pathway.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0006541
    label: L-glutamine metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      CAD consumes L-glutamine via its GATase reaction to supply ammonia for carbamoyl
      phosphate synthesis, so it participates in glutamine metabolism.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: amidotransferase activity (GATase) that binds and cleaves glutamine to
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    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.
    action: ACCEPT
    reason: >-
      Core localization, supported by phylogenetic inference, immunofluorescence (HPA), and
      direct cell-fractionation studies showing most CAD is cytosolic.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    reason: >-
      Core function, strongly supported by phylogeny and by experimental characterization of
      the human enzyme.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: initiates and controls the
        de novo biosynthesis of pyrimidines
- term:
    id: GO:0004151
    label: dihydroorotase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Core molecular function, supported by phylogeny and by the crystal structure and
      functional assays of the human DHOase domain.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the crystal structure and functional
        characterization of the dihydroorotase domain of human CAD
- term:
    id: GO:0004070
    label: aspartate carbamoyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      IEA duplicate of the ATCase activity (EC 2.1.3.2 / RHEA:20013), consistent with the
      experimental and IBA annotations.
    action: ACCEPT
    reason: >-
      Correct EC/RHEA-based mapping to a core catalytic activity of CAD.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: aspartate transcarbamylase (ATCase;
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Correct EC/RHEA mapping to a component activity of the bifunctional CPS II module.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: followed by an ammonium-dependent carbamoyl phosphate
- term:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Core catalytic activity; correct EC/RHEA mapping, also supported experimentally.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: synthetase (CPSase; EC 6.3.5.5)
- term:
    id: GO:0004151
    label: dihydroorotase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      IEA duplicate of the DHOase activity (EC 3.5.2.3 / RHEA:24296).
    action: ACCEPT
    reason: >-
      Correct EC/RHEA-based mapping to a core, experimentally verified catalytic activity.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the crystal structure and functional
        characterization of the dihydroorotase domain of human CAD
- term:
    id: GO:0004359
    label: glutaminase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: amidotransferase activity (GATase) that binds and cleaves glutamine to
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Supported by domain architecture (ATP-grasp folds) and by the CPS reaction stoichiometry
      (2 ATP). Ancillary rather than the core catalytic identity.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: hydrogencarbonate and ATP to
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      A subpopulation of CAD (phospho-Thr456) translocates to the nucleus upon EGF
      stimulation. Consistent with UniProt subcellular location.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real but conditional/regulatory localization; catalysis occurs mainly in the cytosol.
      Keep as non-core.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: Upon epidermal growth factor stimulation, CAD moved to the nucleus
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Cytoplasm localization from the UniProt subcellular-location mapping; consistent with
      the cytosol annotations.
    action: ACCEPT
    reason: >-
      Correct broad localization; cytosol (GO:0005829) is the preferred, more specific term.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      IEA duplicate of the core de novo pyrimidine biosynthesis process.
    action: ACCEPT
    reason: >-
      Correct core biological process, consistent with experimental and IBA annotations.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: initiates and controls the
        de novo biosynthesis of pyrimidines
- term:
    id: GO:0006520
    label: amino acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general domain-based mapping; CAD's amino-acid handling is incidental to pyrimidine
      synthesis. Not a core process.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0006541
    label: L-glutamine metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO duplicate of glutamine metabolic process (from the CPS small-subunit /
      GATase domain).
    action: KEEP_AS_NON_CORE
    reason: >-
      True but general consequence of the GATase reaction; not the core process.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: amidotransferase activity (GATase) that binds and cleaves glutamine to
- term:
    id: GO:0016597
    label: amino acid binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic; substrate binding is captured better by the specific aspartate binding term and
      by the ATCase activity. Not core.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: carbamoyl-L-aspartate from L-aspartate and
- term:
    id: GO:0016743
    label: carboxyl- or carbamoyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Parent term of aspartate carbamoyltransferase activity, from the ATCase domain.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Redundant, over-general parent of the specific GO:0004070 (aspartate carbamoyltransferase
      activity) that is already annotated.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: aspartate transcarbamylase (ATCase;
- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Very general hydrolase parent term from the amidohydrolase (DHOase) domain.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Uninformative top-level parent of the specific dihydroorotase activity (GO:0004151).
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: dihydroorotase (DHOase; EC 3.5.2.3)
- term:
    id: GO:0016810
    label: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      General hydrolase parent (C-N bonds) from the metal-dependent hydrolase domain.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general parent of the specific dihydroorotase activity (GO:0004151).
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: dihydroorotase (DHOase; EC 3.5.2.3)
- term:
    id: GO:0016812
    label: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds,
      in cyclic amides
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Parent term for cyclic-amide hydrolase activity, close to the dihydroorotase reaction
      (which cyclizes/opens the dihydroorotate ring).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general parent of the specific GO:0004151 dihydroorotase activity already annotated.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: DHOase catalyzes the cyclization
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic parent; zinc ion binding (GO:0008270) is the more informative, experimentally
      supported term.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Binds 3 Zn(2+) ions per subunit (for dihydroorotase activity).
- term:
    id: GO:0055086
    label: nucleobase-containing small molecule metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA-predicted general parent of pyrimidine biosynthesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general parent of the specific de novo pyrimidine/UMP biosynthesis processes.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: de novo pyrimidine pathway
- term:
    id: GO:0072528
    label: pyrimidine-containing compound biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA-predicted parent term for pyrimidine compound biosynthesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      True but over-general parent of the specific de novo pyrimidine/UMP biosynthesis terms.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: de novo pyrimidine pathway
- term:
    id: GO:0090407
    label: organophosphate biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA-predicted very broad process term (carbamoyl phosphate is an organophosphate).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general; the informative process is de novo pyrimidine/UMP biosynthesis.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: form carbamoyl phosphate
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15161933
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare protein binding is uninformative about molecular function. Retain (do not remove
      experimental IPI) but mark as over-annotated per curation policy.
    supported_by:
    - reference_id: PMID:15161933
      supporting_text: 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:35271311
  qualifier: enables
  review:
    summary: >-
      IntAct IPI (interaction with YWHAZ, UniProtKB:P63104) from the OpenCell endogenous-tagging
      interactome. Bare protein binding is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Uninformative binding term; retain the experimental interaction evidence but mark as
      over-annotated per policy.
    supported_by:
    - reference_id: PMID:35271311
      supporting_text: systematically map the localization and interactions of human proteins
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:35709258
  qualifier: enables
  review:
    summary: >-
      IntAct IPI (interaction with CNTROB, UniProtKB:Q8N137) from a spatial centrosome
      proteome of human neural cells. Bare protein binding is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Uninformative binding term; retain the experimental interaction but mark as
      over-annotated per policy.
    supported_by:
    - reference_id: PMID:35709258
      supporting_text: protein interaction networks at the centrosome
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:24332717
  qualifier: enables
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real self-interaction (homohexamer) supported by the structural work; keep as non-core.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: it self-assembles into
        hexamers
- term:
    id: GO:0001889
    label: liver development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog (Ensembl Compara). A whole-organism
      physiology association, not a molecular role of CAD.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Pleiotropic developmental association transferred from rodent expression/phenotype data;
      not a core function of the pyrimidine-biosynthesis enzyme.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0006228
    label: UTP biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      True upstream role (CAD feeds UTP synthesis) but downstream of CAD's direct product; the
      core process is de novo UMP biosynthesis.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: CTP, UTP and nearly all UDP-activated sugars
- term:
    id: GO:0006805
    label: xenobiotic metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog. CAD has no role in xenobiotic metabolism; this
      reflects a rodent expression/response association, not enzyme function.
    action: REMOVE
    reason: >-
      Biologically implausible for a cytosolic pyrimidine-biosynthesis enzyme; an over-propagated
      electronic (Ensembl) inference with no mechanistic basis.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0007507
    label: heart development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a whole-organism developmental association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Pleiotropic developmental association transferred electronically; not a core molecular
      role of CAD.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0007565
    label: female pregnancy
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog reflecting expression during pregnancy.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Physiological/expression association transferred electronically; not a core function.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0007595
    label: lactation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog reflecting expression during lactation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Physiological/expression association transferred electronically; not a core function.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0014075
    label: response to amine
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0019240
    label: L-citrulline biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: catalyzes the formation of carbamoyl-L-aspartate from L-aspartate and
- term:
    id: GO:0031000
    label: response to caffeine
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0031100
    label: animal organ regeneration
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog reflecting upregulation during regeneration
      (proliferating tissue demands pyrimidines).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Expression/proliferation-associated physiology transferred electronically; not a core
      function.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0032868
    label: response to insulin
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: part_of
  review:
    summary: >-
      CAD forms a homohexamer, so it is part of a protein-containing complex. Very general term.
    action: KEEP_AS_NON_CORE
    reason: >-
      True (homohexamer) but uninformative parent term; the specific self-assembly is captured
      by identical protein binding.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: it self-assembles into
        hexamers
- term:
    id: GO:0033574
    label: response to testosterone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0042594
    label: response to starvation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Electronic (Ensembl) duplicate of identical protein binding, consistent with the
      experimentally supported homohexamer self-assembly.
    action: KEEP_AS_NON_CORE
    reason: >-
      True self-interaction (homohexamer) but a general term; keep as non-core.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: it self-assembles into
        hexamers
- term:
    id: GO:0043025
    label: neuronal cell body
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Electronic transfer of a neuronal-localization annotation from a rodent ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neuron-specific localization transferred electronically; CAD is a ubiquitous cytosolic
      enzyme and this is not a core localization.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0043195
    label: terminal bouton
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Electronic transfer of a synaptic-terminal localization from a rodent ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neuron-specific localization transferred electronically; not a core localization of the
      cytosolic enzyme.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    reason: >-
      Core biological process; correct UniPathway-based mapping (UPA00070), consistent with
      experimental IDA annotations.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: the first three of six reactions required for de novo
        pyrimidine biosynthesis
- term:
    id: GO:0044210
    label: "'de novo' CTP biosynthetic process"
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      CTP is synthesized downstream of UMP/UTP; CAD acts upstream. Loss of CAD depletes CTP
      (patient studies).
    action: KEEP_AS_NON_CORE
    reason: >-
      True upstream role but downstream of CAD's direct product (UMP); the core process is de
      novo UMP biosynthesis.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: CTP, UTP and nearly all UDP-activated sugars
- term:
    id: GO:0046134
    label: pyrimidine nucleoside biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer; a general pyrimidine-nucleoside biosynthesis term related to CAD's
      pathway.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      General/related process; the precise core terms are de novo UMP and de novo pyrimidine
      nucleobase biosynthesis.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: de novo pyrimidine pathway
- term:
    id: GO:0051414
    label: response to cortisol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-core stimulus-response association transferred electronically from rodent data.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0071364
    label: cellular response to epidermal growth factor stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine, experimentally supported regulatory response (EGF -> MAPK -> CAD activation and
      nuclear import); keep as non-core.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: Upon epidermal growth factor stimulation, CAD moved to the nucleus
- term:
    id: GO:0071466
    label: cellular response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic transfer from a rodent ortholog; a stimulus-response association with no
      mechanistic basis for CAD.
    action: REMOVE
    reason: >-
      Biologically unsupported for a pyrimidine-biosynthesis enzyme; over-propagated electronic
      inference paralleling the xenobiotic metabolism annotation.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Multifunctional protein that encodes the first 3 enzymatic
- term:
    id: GO:0006543
    label: L-glutamine catabolic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The GATase reaction hydrolyzes glutamine (catabolizing it to glutamate + ammonia) to feed
      the CPS reaction. Sequence-similarity transfer from an ortholog (UniProtKB:P08955).
    action: KEEP_AS_NON_CORE
    reason: >-
      True consequence of the GATase reaction, but glutamine catabolism is incidental to the
      core pyrimidine-biosynthesis process.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: amidotransferase activity (GATase) that binds and cleaves glutamine to
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      Immunofluorescence-based (HPA) cytosol localization. Consistent with the established
      cytosolic site of de novo pyrimidine biosynthesis.
    action: ACCEPT
    reason: >-
      Core localization, directly supported by imaging and by cell-fractionation studies.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0004070
    label: aspartate carbamoyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:24332717
  qualifier: enables
  review:
    summary: >-
      Experimentally characterized ATCase activity of human CAD (EC 2.1.3.2). A core catalytic
      activity of the multienzyme.
    action: ACCEPT
    reason: >-
      Core molecular function with direct experimental support in the human protein.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the multifunctional protein that initiates and controls the
        de novo biosynthesis of pyrimidines in animals
- term:
    id: GO:0004087
    label: carbamoyl-phosphate synthase (ammonia) activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Correct component activity of the CPS module; consistent with the IEA/EC annotation.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: followed by an ammonium-dependent carbamoyl phosphate
- term:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  evidence_type: EXP
  original_reference_id: PMID:24332717
  qualifier: enables
  review:
    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.
    action: ACCEPT
    reason: >-
      Core molecular function; the overall CPS II reaction that initiates de novo pyrimidine
      biosynthesis.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the multifunctional protein that initiates and controls the
        de novo biosynthesis of pyrimidines in animals
- term:
    id: GO:0004359
    label: glutaminase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      GATase partial reaction (EC 3.5.1.2) transferred by sequence similarity (UniProtKB:P07259).
      Hydrolyzes glutamine to supply ammonia to CPS.
    action: ACCEPT
    reason: >-
      Correct component activity of the CPS II module; consistent with the IEA/EC annotation.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: amidotransferase activity (GATase) that binds and cleaves glutamine to
- term:
    id: GO:0043025
    label: neuronal cell body
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Neuronal cell body localization transferred by sequence similarity from a rodent ortholog
      (UniProtKB:A0A8I5ZMM2).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neuron-specific localization transferred from a rodent ortholog; not a core localization
      of the ubiquitous cytosolic enzyme.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0043195
    label: terminal bouton
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Synaptic-terminal localization transferred by sequence similarity from a rodent ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Neuron-specific localization transferred from a rodent ortholog; not a core localization.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0006225
    label: UDP biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:25678555
  qualifier: acts_upstream_of_or_within
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correctly captures CAD as acting upstream of UDP synthesis; downstream of CAD's direct
      product (UMP). Core process is de novo UMP biosynthesis.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: nearly all UDP-activated sugars that serve as
        donors for glycosylation were decreased
- term:
    id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  evidence_type: IDA
  original_reference_id: PMID:25678555
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      Patient study demonstrating impaired de novo pyrimidine (UMP) biosynthesis when CAD is
      mutated, with rescue by uridine. Core biological process.
    action: ACCEPT
    reason: >-
      Directly supports CAD's essential role in de novo UMP biosynthesis; core process.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: impaired aspartate incorporation into RNA and DNA through the de novo synthesis
        pathway
- term:
    id: GO:0006225
    label: UDP biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:25678555
  qualifier: involved_in
  review:
    summary: >-
      Duplicate (involved_in) of the UDP biosynthetic process annotation from the same patient
      study.
    action: KEEP_AS_NON_CORE
    reason: >-
      True upstream role in UDP-sugar/pyrimidine synthesis; downstream of CAD's direct product.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: nearly all UDP-activated sugars that serve as
        donors for glycosylation were decreased
- term:
    id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  evidence_type: IDA
  original_reference_id: PMID:25678555
  qualifier: involved_in
  review:
    summary: >-
      Duplicate (involved_in) of the core de novo UMP biosynthetic process from the same patient
      study.
    action: ACCEPT
    reason: >-
      Core biological process; directly supported by the loss-of-function metabolic phenotype
      and uridine rescue.
    supported_by:
    - reference_id: PMID:25678555
      supporting_text: impaired aspartate incorporation into RNA and DNA through the de novo synthesis
        pathway
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  qualifier: located_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Proteomic co-purification with a membrane fraction, not a genuine membrane localization for
      a cytosolic enzyme; the study flags such transient associations.
    supported_by:
    - reference_id: PMID:19946888
      supporting_text: predicted to be transiently associated with membranes
- term:
    id: GO:0004151
    label: dihydroorotase activity
  evidence_type: IDA
  original_reference_id: PMID:24332717
  qualifier: enables
  review:
    summary: >-
      Direct experimental (crystal structure + functional assay) demonstration of the
      Zn2+-dependent dihydroorotase activity of the human CAD DHOase domain. Core catalytic
      activity.
    action: ACCEPT
    reason: >-
      Core molecular function with strong direct experimental support in the human protein.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: Site-directed mutagenesis and functional assays prove
        the involvement of the Zn and flexible loop in catalysis
- term:
    id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  evidence_type: IDA
  original_reference_id: PMID:24332717
  qualifier: involved_in
  review:
    summary: >-
      CAD initiates and controls de novo pyrimidine biosynthesis; direct experimental support
      from the structural/functional study of the multienzyme.
    action: ACCEPT
    reason: >-
      Core biological process with direct experimental support.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: initiates and controls the
        de novo biosynthesis of pyrimidines
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IDA
  original_reference_id: PMID:24332717
  qualifier: enables
  review:
    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).
    action: ACCEPT
    reason: >-
      Directly supported cofactor-binding activity essential to the dihydroorotase reaction.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: an active site enclosed by a flexible loop
        with two Zn
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:20458337
  qualifier: located_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Mass-spectrometry co-purification in an exosome preparation; not a genuine functional
      localization for this cytosolic enzyme.
    supported_by:
    - reference_id: PMID:20458337
      supporting_text: total proteome of highly purified B cell-derived exosomes
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-73571
  qualifier: located_in
  review:
    summary: >-
      Reactome (traceable author statement) placing the DHOase step of CAD in the cytosol.
    action: ACCEPT
    reason: >-
      Correct core localization; consistent with all other cytosol evidence.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-73573
  qualifier: located_in
  review:
    summary: >-
      Reactome (traceable author statement) placing the ATCase step of CAD in the cytosol.
    action: ACCEPT
    reason: >-
      Correct core localization; consistent with all other cytosol evidence.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-73577
  qualifier: located_in
  review:
    summary: >-
      Reactome (traceable author statement) placing the CPS (L-Gln -> carbamoyl phosphate) step
      of CAD in the cytosol.
    action: ACCEPT
    reason: >-
      Correct core localization; consistent with all other cytosol evidence.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0004672
    label: protein kinase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: Activated by MAP kinase (Erk1/2) phosphorylation just prior to the
- term:
    id: GO:0070335
    label: aspartate binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Substrate binding supporting the ATCase reaction; ancillary to the core catalytic
      activity (GO:0004070).
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: carbamoyl-L-aspartate from L-aspartate and
- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: IPI
  original_reference_id: PMID:15326225
  qualifier: enables
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine, functionally characterized interaction (Rad9 stimulates CAD CPSase), but a
      regulatory binding activity rather than CAD's core catalytic function.
    supported_by:
    - reference_id: PMID:15326225
      supporting_text: Rad9 binds to the
        CPSase domain, and, moreover, this binding results in a 2-fold stimulation of
        the CPSase activity of CAD
- term:
    id: GO:0004070
    label: aspartate carbamoyltransferase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      ISS duplicate of the ATCase activity (from UniProtKB:P08955).
    action: ACCEPT
    reason: >-
      Correct core catalytic activity, consistent with the experimental and IBA annotations.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: aspartate transcarbamylase (ATCase;
- term:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      ISS duplicate of the CPS II activity (from UniProtKB:P08955).
    action: ACCEPT
    reason: >-
      Correct core catalytic activity, consistent with the experimental and IBA annotations.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: synthetase (CPSase; EC 6.3.5.5)
- term:
    id: GO:0004151
    label: dihydroorotase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      ISS duplicate of the DHOase activity (from UniProtKB:P08955).
    action: ACCEPT
    reason: >-
      Correct core catalytic activity, consistent with experimental and IBA annotations.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: the crystal structure and functional
        characterization of the dihydroorotase domain of human CAD
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      ISS duplicate of ATP binding (from UniProtKB:P08955); consistent with the ATP-grasp folds
      of the CPS module.
    action: ACCEPT
    reason: >-
      Correct ancillary molecular function supporting the CPS reaction.
    supported_by:
    - reference_id: file:human/CAD/CAD-uniprot.txt
      supporting_text: hydrogencarbonate and ATP to
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:15890648
  qualifier: located_in
  review:
    summary: >-
      Direct cell-fractionation/microscopy showing a phospho-Thr456 CAD subpopulation in the
      nucleus following EGF stimulation; nuclear import promotes optimal cell growth.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real, experimentally supported conditional localization; catalysis is chiefly cytosolic, so
      keep as non-core.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: Thr(P)-456
        CAD was primarily localized within the nucleus
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:15890648
  qualifier: located_in
  review:
    summary: >-
      Direct demonstration that most CAD is cytosolic. Core localization.
    action: ACCEPT
    reason: >-
      Core localization with direct experimental support.
    supported_by:
    - reference_id: PMID:15890648
      supporting_text: most of the CAD in the cell was cytosolic
- term:
    id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      ISS duplicate of the core de novo pyrimidine biosynthesis process (from UniProtKB:P08955).
    action: ACCEPT
    reason: >-
      Core biological process, consistent with experimental and IBA annotations.
    supported_by:
    - reference_id: PMID:24332717
      supporting_text: initiates and controls the
        de novo biosynthesis of pyrimidines
- term:
    id: GO:0016363
    label: nuclear matrix
  evidence_type: IDA
  original_reference_id: PMID:9525610
  qualifier: located_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real but conditional/subpopulation localization; the core catalytic location is the cytosol.
    supported_by:
    - reference_id: PMID:9525610
      supporting_text: pTP binds to a multifunctional pyrimidine biosynthesis enzyme found at replication domains on the NM
core_functions:
- description: >-
    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.
  molecular_function:
    id: GO:0004088
    label: carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
  directly_involved_in:
  - id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  - id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:24332717
    supporting_text: the multifunctional protein that initiates and controls the
      de novo biosynthesis of pyrimidines in animals
- description: >-
    Aspartate transcarbamylase (ATCase): condenses carbamoyl phosphate with L-aspartate to form
    N-carbamoyl-L-aspartate, the second committed step of de novo pyrimidine biosynthesis.
  molecular_function:
    id: GO:0004070
    label: aspartate carbamoyltransferase activity
  directly_involved_in:
  - id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  - id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:24332717
    supporting_text: the multifunctional protein that initiates and controls the
      de novo biosynthesis of pyrimidines in animals
- description: >-
    Dihydroorotase (DHOase): Zn2+-dependent cyclization of N-carbamoyl-L-aspartate to
    (S)-dihydroorotate, the third committed step of de novo pyrimidine biosynthesis.
  molecular_function:
    id: GO:0004151
    label: dihydroorotase activity
  directly_involved_in:
  - id: GO:0044205
    label: "'de novo' UMP biosynthetic process"
  - id: GO:0006207
    label: "'de novo' pyrimidine nucleobase biosynthetic process"
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:24332717
    supporting_text: Site-directed mutagenesis and functional assays prove
      the involvement of the Zn and flexible loop in catalysis
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: file:human/CAD/CAD-uniprot.txt
  title: UniProtKB entry P27708 (PYR1_HUMAN), Multifunctional protein CAD
  findings: []
- 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: >-
      PubMed-verified proteomic screen; supports a 14-3-3 (YWHAZ) interaction but only a bare
      protein binding annotation, uninformative about CAD's molecular function.
- id: PMID:15326225
  title: The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase
    activity of the multifunctional protein CAD.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; directly demonstrates the CAD-Rad9 interaction and Rad9-mediated ~2-fold
      stimulation of CAD CPSase activity, supporting the enzyme binding annotation.
- id: PMID:15890648
  title: Nuclear localization and mitogen-activated protein kinase phosphorylation
    of the multifunctional protein CAD.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; establishes CAD is mainly cytosolic, MAPK-phosphorylated (Thr-456), and
      EGF-induced nuclear/nuclear-matrix translocation that promotes cell growth.
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified high-throughput membrane-proteome study; the membrane localization for CAD is
      a transient co-purification, flagged by the authors, not a genuine location.
- id: PMID:20458337
  title: MHC class II-associated proteins in B-cell exosomes and potential functional
    implications for exosome biogenesis.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified exosome proteome study; CAD's presence is mass-spec co-purification, not a
      functional extracellular localization.
- id: PMID:24332717
  title: Structure, functional characterization, and evolution of the dihydroorotase
    domain of human CAD.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; primary structural/functional study of human CAD - defines the multienzyme,
      the Zn2+-dependent DHOase mechanism, and homohexamer assembly. Anchor for core catalytic MFs.
- id: PMID:25678555
  title: Biallelic mutations in CAD, impair de novo pyrimidine biosynthesis and decrease
    glycosylation precursors.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; defines human CAD deficiency (DEE50/CAD-CDG), shows impaired de novo
      pyrimidine synthesis and depleted UDP-sugars, rescued by uridine.
- id: PMID:35271311
  title: 'OpenCell: Endogenous tagging for the cartography of human cellular organization.'
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified interactome/localization resource; supports a YWHAZ interaction but only a
      bare protein binding annotation for CAD.
- id: PMID:35709258
  title: Spatial centrosome proteome of human neural cells uncovers disease-relevant
    heterogeneity.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified spatial-proteome study; supports a CNTROB interaction but only a bare protein
      binding annotation for CAD.
- id: PMID:9525610
  title: Adenovirus preterminal protein binds to the CAD enzyme at active sites of
    viral DNA replication on the nuclear matrix.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; shows CAD at the nuclear matrix at adenoviral replication foci, supporting
      the nuclear-matrix localization of the conditional nuclear CAD population.
- id: Reactome:R-HSA-73571
  title: CAD hexamer dehydrates N-carb-L-Asp to (S)-DHO
  findings: []
- id: Reactome:R-HSA-73573
  title: CAD hexamer transforms CAP to N-carb-L-Asp
  findings: []
- id: Reactome:R-HSA-73577
  title: CAD hexamer transforms L-Gln to CAP
  findings: []