id: P13716
gene_symbol: ALAD
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ALAD encodes delta-aminolevulinic acid dehydratase (ALADH), also known as porphobilinogen
  synthase (PBGS; EC 4.2.1.24). It catalyzes the second step of heme biosynthesis: the
  asymmetric condensation of two molecules of 5-aminolevulinate (ALA) to form the monopyrrole
  porphobilinogen (PBG), releasing two water molecules. This is the first pyrrole-forming
  reaction and commits the pathway toward all tetrapyrroles (heme, and in other organisms
  chlorophyll and cobalamin). The enzyme is a cytosolic, zinc-dependent metalloenzyme that
  assembles as a homo-octamer (the high-activity form), binding up to eight Zn2+ per octamer
  with four required for catalysis; it exists in a morpheein-type equilibrium between the
  active octamer and a low-activity hexamer, with a magnesium ion promoting octamer assembly.
  ALAD activity is potently inhibited by divalent lead, which partially displaces the catalytic
  zinc, making the enzyme the classic biochemical biomarker and principal molecular target of
  lead poisoning. Loss-of-function variants that shift the quaternary equilibrium toward the
  hexamer cause the rare autosomal-recessive ALAD-deficiency porphyria (Doss porphyria / acute
  hepatic porphyria). Independently of its catalytic role, the protein has been characterized
  as an endogenous proteasome inhibitor (CF-2), an ATP-stabilized component associated with the
  26S proteasome, an example of gene sharing/moonlighting.
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:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:human/ALAD/ALAD-uniprot.txt
  title: UniProtKB entry P13716 (HEM2_HUMAN), Delta-aminolevulinic acid dehydratase
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Curated UniProt record documenting catalytic activity (EC 4.2.1.24,
      RHEA:24064), Zn2+ cofactor, octamer/hexamer subunit equilibrium, cytosolic localization,
      lead inhibition, and ALAD-deficiency porphyria variants."
- id: PMID:11032836
  title: The molecular mechanism of lead inhibition of human porphobilinogen synthase.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "PubMed-verified; on human PBGS. Establishes 8 Zn(II)/homo-octamer, 4 required
      for activity, catalytic role of the cysteine-rich ZnB site, and the mechanism of lead
      inhibition (Pb interacts with ZnA and ZnB ligands). Source of the IDA porphobilinogen
      synthase activity, zinc ion binding, heme B/heme biosynthesis, and EXP lead ion binding
      annotations. Abstract-only in cache; full text was read by the curators."
- id: PMID:12897770
  title: Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen
    synthase.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "PubMed-verified; human PBGS crystal structures. Establishes the octamer
      (predominant) vs hexamer (F12L allele) quaternary equilibrium and allosteric Mg2+ site.
      Supports the EXP porphobilinogen synthase activity annotation."
- id: PMID:19812033
  title: Allosteric inhibition of human porphobilinogen synthase.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "PubMed-verified; full text available. Confirms human PBGS catalyzes the first
      common step in tetrapyrrole biosynthesis, the octamer/hexamer/dimer equilibrium, ALAD
      porphyria and lead poisoning as low-activity disease states. Supports EXP porphobilinogen
      synthase activity."
- id: PMID:2063868
  title: 'delta-Aminolevulinate dehydratase deficient porphyria: identification of
    the molecular lesions in a severely affected homozygote.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "PubMed-verified; identifies G133R/V275M lesions causing severe ALAD-deficiency
      porphyria and describes ALAD as the heme biosynthetic enzyme active as a homooctamer.
      Cited (TAS) for catalytic activity; here used to support heme biosynthesis/disease context."
- id: PMID:21630459
  title: Proteomic characterization of the human sperm nucleus.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: "High-throughput sperm-nucleus proteomics; supports only an HDA nucleus
      localization for an abundant cytosolic enzyme. Not indicative of a nuclear function."
- id: PMID:23533145
  title: In-depth proteomic analyses of exosomes isolated from expressed prostatic
    secretions in urine.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: "High-throughput exosome proteomics; supports only an HDA extracellular-exosome
      localization. Bystander detection of an abundant cytosolic protein."
- id: PMID:3463993
  title: 'Human delta-aminolevulinate dehydratase: nucleotide sequence of a full-length
    cDNA clone.'
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: "cDNA cloning of human ALA-D (porphobilinogen synthase, EC 4.2.1.24), the
      second enzyme in the heme biosynthetic pathway; a zinc metalloenzyme with a Cys/His-rich
      zinc site. Cited (TAS) for porphobilinogen synthase activity."
- id: PMID:3758678
  title: Molecular cloning of a cDNA for human delta-aminolevulinate dehydratase.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: "cDNA cloning of human ALA-D (EC 4.2.1.24), the second enzyme in the heme
      biosynthetic pathway. Cited (TAS) for heme biosynthetic process."
- id: PMID:8175643
  title: 240-kDa proteasome inhibitor (CF-2) is identical to delta-aminolevulinic
    acid dehydratase.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "PubMed-verified; identifies the 240-kDa proteasome inhibitor CF-2 as identical
      to ALAD (the second enzyme of heme synthesis), a gene-sharing/moonlighting activity.
      Supports the CAFA IDA porphobilinogen synthase, proteasome inhibition, and homooligomer
      annotations. Abstract-only in cache."
- id: Reactome:R-HSA-189439
  title: ALAD condenses 2 dALAs to form PBG
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Reactome reaction: ALAD catalyzes the asymmetric condensation of two ALA
      molecules to form porphobilinogen; active form is a Zn2+ homo-octamer. Directly describes
      the core catalytic step."
- id: Reactome:R-HSA-189451
  title: Heme biosynthesis
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Reactome pathway: eight-enzyme heme biosynthesis; the cytosolic steps (which
      include the ALAD-catalyzed condensation of 2 ALA to PBG) follow the mitochondrial ALA
      synthase step. Supports heme biosynthetic process and cytosol."
- id: Reactome:R-HSA-190141
  title: ALAD binds to Pb2+
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Reactome reaction: lead binds ALAD, displacing half the essential zinc ions
      and inactivating the enzyme; ALAD is a principal molecular target of lead. Supports lead
      ion binding."
- id: Reactome:R-HSA-6798748
  title: Exocytosis of secretory granule lumen proteins
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: "Reactome neutrophil-degranulation reaction; ALAD is a cargo protein detected
      in granule/secretory proteomes. Supports only bystander extracellular/granule localization,
      not a secreted function."
- id: Reactome:R-HSA-6800434
  title: Exocytosis of ficolin-rich granule lumen proteins
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: "Reactome neutrophil-degranulation reaction; ALAD detected in ficolin-1-rich
      granule proteomes. Supports only bystander extracellular/granule localization."
existing_annotations:
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetically inferred involvement in heme biosynthesis. ALAD catalyzes the second,
      committed pyrrole-forming step of the heme pathway, so this is a core biological process.
    action: ACCEPT
    reason: >-
      Correct and well supported. ALAD is the second enzyme of the heme biosynthetic pathway,
      condensing two ALA molecules into porphobilinogen. This is a core process for the gene.
    supported_by:
    - reference_id: PMID:3463993
      supporting_text: "the second enzyme in the heme"
    - reference_id: Reactome:R-HSA-189451
      supporting_text: "Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG)."
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetically inferred cytosolic localization. The cytosolic steps of heme biosynthesis,
      including the ALAD reaction, occur in the cytosol.
    action: ACCEPT
    reason: >-
      Consistent with the UniProt-curated subcellular location (Cytoplasm, cytosol) and with
      Reactome, which places the ALAD-catalyzed step among the cytosolic heme-synthesis steps.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
    - reference_id: Reactome:R-HSA-189451
      supporting_text: "The next four steps take place in the cytosol."
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetically inferred porphobilinogen synthase (5-aminolevulinate dehydratase)
      activity, the core molecular function of ALAD across the ALAD/PBGS family.
    action: ACCEPT
    reason: >-
      This is the defining molecular function of the gene, congruent with abundant experimental
      evidence (EXP/IDA) and the EC 4.2.1.24 / RHEA:24064 assignment in UniProt.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "Binds two molecules of 5-aminolevulinate per subunit, each at a"
    - reference_id: Reactome:R-HSA-189439
      supporting_text: "catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic annotation (ARBA/InterPro/RHEA/EC) of the core porphobilinogen synthase activity.
    action: ACCEPT
    reason: >-
      Correctly captures the core catalytic function via EC 4.2.1.24 / RHEA:24064 mapping;
      redundant with, and confirmed by, the experimental annotations.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "EC=4.2.1.24"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation from the UniProt subcellular-location vocabulary mapping (cytosol).
    action: ACCEPT
    reason: >-
      Consistent with curated UniProt localization and Reactome; the enzyme acts in the cytosol.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0033014
    label: tetrapyrrole biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro-based electronic annotation to the broader tetrapyrrole biosynthetic process.
    action: ACCEPT
    reason: >-
      Correct parent process: porphobilinogen is the committed precursor of all tetrapyrroles.
      Slightly more general than the heme-specific terms but accurate.
    supported_by:
    - reference_id: PMID:19812033
      supporting_text: "catalyzes the first common step in tetrapyrrole"
    - reference_id: Reactome:R-HSA-189439
      supporting_text: "the precursor to all tetrapyrrole pigments such as heme and chlorophyll"
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro-based electronic annotation for metal ion binding. ALAD is a zinc metalloenzyme
      (binds up to 8 Zn2+ per octamer) and also binds inhibitory Pb2+.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but generic parent of the more specific zinc ion binding (IDA) annotation. Zinc
      binding underpins catalysis but is a supporting molecular feature rather than the core
      function; kept as non-core.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "eight Zn(II) per homo-octamer"
- term:
    id: GO:0001666
    label: response to hypoxia
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic (Ensembl Compara) projection from the rat ortholog of a broad stimulus-response
      profile.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Part of a large block of ECO:0000265 "response to X" terms projected from rat P06214. These
      reflect transcriptional/physiological responses in the ortholog, not ALAD's molecular role,
      and over-annotate the gene. No evidence connects ALAD's function specifically to hypoxia.
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Electronic projection of an extracellular-region localization from the rat ortholog.
    action: KEEP_AS_NON_CORE
    reason: >-
      ALAD is a cytosolic enzyme. Extracellular detection reflects bystander presence in
      secretomes/granule proteomes rather than a genuine extracellular function; kept as non-core
      to remain consistent with the Reactome extracellular-region annotations.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Electronic (ARBA) annotation to the core heme biosynthetic process.
    action: ACCEPT
    reason: >-
      Correctly captures the core biological process; redundant with the IBA/IDA/TAS annotations.
    supported_by:
    - reference_id: PMID:3758678
      supporting_text: "the second enzyme in the heme biosynthetic pathway"
- term:
    id: GO:0006979
    label: response to oxidative stress
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a stress-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Part of the broad rat-projected stimulus-response block; not informative of ALAD's molecular
      function and likely over-propagated.
- term:
    id: GO:0007584
    label: response to nutrient
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a nutrient-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term projected from rat P06214; over-annotation.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a xenobiotic-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation not reflecting ALAD's molecular role.
- term:
    id: GO:0009635
    label: response to herbicide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a herbicide-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Highly specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0009636
    label: response to toxic substance
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a toxic-substance-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0009725
    label: response to hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a hormone-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0010038
    label: response to metal ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a metal-ion-response term from the rat ortholog. ALAD activity is
      strongly modulated by metals (Zn2+ cofactor; Pb2+ inhibition).
    action: KEEP_AS_NON_CORE
    reason: >-
      Unlike most terms in the projected block, this one is biologically defensible: ALAD is a
      zinc metalloenzyme whose activity is displaced by lead and other divalent metals. Retained
      as non-core biology rather than removed.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "Inhibited by divalent lead ions."
- term:
    id: GO:0010039
    label: response to iron ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an iron-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Iron is incorporated downstream (ferrochelatase), not by ALAD; this projected term is not
      informative of ALAD's molecular role and is over-annotated.
- term:
    id: GO:0010043
    label: response to zinc ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a zinc-ion-response term from the rat ortholog. ALAD requires Zn2+
      as its catalytic cofactor.
    action: KEEP_AS_NON_CORE
    reason: >-
      Defensible given ALAD's obligate zinc-cofactor dependence; kept as non-core rather than
      removed.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "eight Zn(II) per homo-octamer"
- term:
    id: GO:0010044
    label: response to aluminum ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an aluminum-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0010212
    label: response to ionizing radiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a radiation-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0010266
    label: response to vitamin B1
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a vitamin B1-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0010269
    label: response to selenium ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a selenium-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0010288
    label: response to lead ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a lead-ion-response term from the rat ortholog. ALAD is the
      classic molecular target of lead poisoning.
    action: KEEP_AS_NON_CORE
    reason: >-
      Biologically well supported: divalent lead inhibits ALAD by displacing the catalytic zinc,
      and ALAD is a principal target of lead. Retained as non-core toxicology-relevant biology.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "is a main target in lead poisoning"
    - reference_id: Reactome:R-HSA-190141
      supporting_text: "Lead binds to ALAD enzyme displacing half the zinc ions essential for its catalytic activity"
- term:
    id: GO:0014823
    label: response to activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a "response to activity" term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0031667
    label: response to nutrient levels
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a nutrient-levels-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0032025
    label: response to cobalt ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a cobalt-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0032496
    label: response to lipopolysaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an LPS-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0033197
    label: response to vitamin E
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a vitamin E-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0033273
    label: response to vitamin
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a vitamin-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0043200
    label: response to amino acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an amino-acid-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0045471
    label: response to ethanol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an ethanol-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0046685
    label: response to arsenic-containing substance
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of an arsenic-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0046686
    label: response to cadmium ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a cadmium-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0046689
    label: response to mercury ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a mercury-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0051384
    label: response to glucocorticoid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a glucocorticoid-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0051597
    label: response to methylmercury
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a methylmercury-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0070541
    label: response to platinum ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a platinum-ion-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Specific stimulus-response term projected electronically; over-annotation.
- term:
    id: GO:0070542
    label: response to fatty acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a fatty-acid-response term from the rat ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Generic stimulus-response term; over-annotation.
- term:
    id: GO:0071284
    label: cellular response to lead ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronic projection of a cellular-lead-response term from the rat ortholog. ALAD is
      directly inhibited by lead.
    action: KEEP_AS_NON_CORE
    reason: >-
      Biologically defensible: lead directly targets and inhibits ALAD by displacing its
      catalytic zinc. Retained as non-core toxicology-relevant biology.
    supported_by:
    - reference_id: Reactome:R-HSA-190141
      supporting_text: "Lead is a major environmental toxin and this enzyme is one of its principal molecular targets"
- term:
    id: GO:1904854
    label: proteasome core complex binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      Electronic projection of a proteasome-core-complex-binding term from the rat ortholog,
      matching ALAD's characterized moonlighting role as the proteasome inhibitor CF-2.
    action: KEEP_AS_NON_CORE
    reason: >-
      Corroborates the experimentally documented CF-2/proteasome-inhibitor moonlighting activity
      (PMID:8175643). This is a genuine secondary/moonlighting function, not the core catalytic
      role; kept as non-core.
    supported_by:
    - reference_id: PMID:8175643
      supporting_text: "inhibitory factor is indistinguishable from"
- term:
    id: GO:0006785
    label: heme B biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:11032836
  qualifier: involved_in
  review:
    summary: >-
      Direct-assay involvement in heme B (protoheme) biosynthesis, the specific end-product of
      the pathway ALAD initiates at the pyrrole-forming step.
    action: ACCEPT
    reason: >-
      A valid, more specific child of heme biosynthetic process. ALAD's condensation of ALA to
      porphobilinogen is an essential early step toward heme B. Consistent with the experimental
      characterization of human PBGS.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "porphobilinogen synthase"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189451
  qualifier: involved_in
  review:
    summary: >-
      Traceable (Reactome) involvement in heme biosynthesis; ALAD catalyzes the cytosolic
      condensation of two ALA into porphobilinogen within the eight-enzyme heme pathway.
    action: ACCEPT
    reason: >-
      Core biological process, supported by the curated Reactome heme-biosynthesis pathway.
    supported_by:
    - reference_id: Reactome:R-HSA-189451
      supporting_text: "Eight enzymes are involved in heme biosynthesis"
- term:
    id: GO:0032791
    label: lead ion binding
  evidence_type: EXP
  original_reference_id: PMID:11032836
  qualifier: enables
  review:
    summary: >-
      Experimentally demonstrated lead binding. Pb2+ binds ALAD at a hybrid of the ZnA and ZnB
      metal sites, partially displacing the catalytic zinc and inhibiting activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Well supported experimentally and mechanistically important for lead toxicology, but it
      represents inhibitory metal binding rather than the enzyme's core catalytic function; kept
      as non-core.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "ligands to both ZnA and ZnB interact with Pb(II)"
    - reference_id: Reactome:R-HSA-190141
      supporting_text: "Lead binds to ALAD enzyme displacing half the zinc ions essential for its catalytic activity"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: EXP
  original_reference_id: PMID:12897770
  qualifier: enables
  review:
    summary: >-
      Experimental (crystallographic/biochemical) confirmation of human porphobilinogen synthase
      activity and its octamer/hexamer quaternary regulation.
    action: ACCEPT
    reason: >-
      Directly supports the core molecular function with experimental evidence on the human enzyme.
    supported_by:
    - reference_id: PMID:12897770
      supporting_text: "catalyzes the first common step in the"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: EXP
  original_reference_id: PMID:19812033
  qualifier: enables
  review:
    summary: >-
      Experimental confirmation of human porphobilinogen synthase activity as an allosterically
      regulated enzyme (octamer/hexamer/dimer equilibrium).
    action: ACCEPT
    reason: >-
      Directly supports the core molecular function with experimental evidence on the human enzyme.
    supported_by:
    - reference_id: PMID:19812033
      supporting_text: "catalyzes the first common step in tetrapyrrole"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: is_active_in
  review:
    summary: >-
      Sequence-similarity-based transfer of cytosolic localization from the mouse ortholog.
    action: ACCEPT
    reason: >-
      Consistent with the curated cytosolic location and the cytosolic phase of heme synthesis.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798748
  qualifier: located_in
  review:
    summary: >-
      Reactome annotation placing ALAD in the extracellular region via neutrophil
      secretory-granule exocytosis.
    action: KEEP_AS_NON_CORE
    reason: >-
      ALAD is a cytosolic enzyme detected as cargo in neutrophil granule/secretome datasets. This
      is a bystander localization, not a core function; kept as non-core rather than removed.
    supported_by:
    - reference_id: Reactome:R-HSA-6798748
      supporting_text: "Secretory vesicles provide a reservoir of secreted proteins"
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6800434
  qualifier: located_in
  review:
    summary: >-
      Reactome annotation placing ALAD in the extracellular region via ficolin-1-rich granule
      exocytosis.
    action: KEEP_AS_NON_CORE
    reason: >-
      Bystander granule/secretome localization of a cytosolic enzyme; not a core function.
    supported_by:
    - reference_id: Reactome:R-HSA-6800434
      supporting_text: "rapid release of pattern recognition molecules"
- term:
    id: GO:0034774
    label: secretory granule lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798748
  qualifier: located_in
  review:
    summary: >-
      Reactome annotation to the secretory granule lumen (neutrophil degranulation).
    action: KEEP_AS_NON_CORE
    reason: >-
      Reflects detection of the abundant cytosolic protein in neutrophil granule proteomes; a
      bystander localization, not the core cytosolic catalytic compartment.
    supported_by:
    - reference_id: Reactome:R-HSA-6798748
      supporting_text: "Secretory vesicles provide a reservoir of secreted proteins"
- term:
    id: GO:1904813
    label: ficolin-1-rich granule lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6800434
  qualifier: located_in
  review:
    summary: >-
      Reactome annotation to the ficolin-1-rich granule lumen (neutrophil degranulation).
    action: KEEP_AS_NON_CORE
    reason: >-
      Bystander granule-proteome localization of a cytosolic enzyme; not a core function.
    supported_by:
    - reference_id: Reactome:R-HSA-6800434
      supporting_text: "ficolin-1 rich granules"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: IDA
  original_reference_id: PMID:8175643
  qualifier: enables
  review:
    summary: >-
      Direct-assay porphobilinogen synthase (dehydratase) activity; the CF-2/proteasome-inhibitor
      protein retained ALA-dehydratase activity, confirming its identity as ALAD.
    action: ACCEPT
    reason: >-
      Supports the core catalytic function; the study showed similar dehydratase specific
      activities in CF-2 and ALAD and dehydratase activity in recombinant ALAD.
    supported_by:
    - reference_id: PMID:8175643
      supporting_text: "similar dehydratase and proteasome"
- term:
    id: GO:1901799
    label: negative regulation of proteasomal protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:8175643
  qualifier: involved_in
  review:
    summary: >-
      Direct-assay evidence that ALAD (as CF-2) inhibits the proteasome, a moonlighting function
      distinct from its heme-synthesis role.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine gene-sharing/moonlighting activity: the 240-kDa proteasome inhibitor CF-2 is
      identical to ALAD and inhibits the ATP/ubiquitin-dependent proteasome pathway. Not the core
      catalytic function; retained as non-core.
    supported_by:
    - reference_id: PMID:8175643
      supporting_text: "The dual role of this protein as CF-2 in the"
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:23533145
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomic detection of ALAD in urinary/prostatic exosome preparations.
    action: KEEP_AS_NON_CORE
    reason: >-
      Bystander localization of an abundant cytosolic protein in exosome proteomes; not a core
      function. Retained per curation policy for experimental HDA localizations.
    supported_by:
    - reference_id: PMID:23533145
      supporting_text: "exosome preparations were characterized by a shotgun proteomics procedure"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: HDA
  original_reference_id: PMID:21630459
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomic detection of ALAD in isolated human sperm nuclei.
    action: KEEP_AS_NON_CORE
    reason: >-
      Bystander localization of an abundant cytosolic protein in a sperm-nucleus proteome; there
      is no functional evidence for a nuclear role. Retained (not removed) per policy for
      experimental HDA localizations.
    supported_by:
    - reference_id: PMID:21630459
      supporting_text: "403 different proteins have been identified from the isolated sperm nuclei"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189439
  qualifier: located_in
  review:
    summary: >-
      Reactome traceable annotation placing the ALAD-catalyzed ALA-condensation reaction in the
      cytosol.
    action: ACCEPT
    reason: >-
      Core localization; the enzyme acts in the cytosol.
    supported_by:
    - reference_id: Reactome:R-HSA-189439
      supporting_text: "catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-190141
  qualifier: located_in
  review:
    summary: >-
      Reactome traceable annotation of cytosolic localization (ALAD-Pb2+ binding reaction).
    action: ACCEPT
    reason: >-
      Core localization; consistent with UniProt and the other cytosol annotations.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: IDA
  original_reference_id: PMID:11032836
  qualifier: enables
  review:
    summary: >-
      Direct-assay porphobilinogen synthase activity of purified/recombinant human PBGS, with
      kinetic characterization and cysteine mutagenesis defining the catalytic zinc site.
    action: ACCEPT
    reason: >-
      Strong experimental support for the core molecular function on the human enzyme.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "is a main target in lead poisoning"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:11032836
  qualifier: involved_in
  review:
    summary: >-
      Direct-assay involvement in heme biosynthesis via characterization of human PBGS as the
      pyrrole-forming enzyme of the heme pathway.
    action: ACCEPT
    reason: >-
      Core biological process, experimentally supported on the human enzyme.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "porphobilinogen synthase"
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IDA
  original_reference_id: PMID:11032836
  qualifier: enables
  review:
    summary: >-
      Direct-assay zinc binding: human PBGS purifies with eight Zn2+ per homo-octamer, four of
      which are required for activity; cysteine mutagenesis maps the catalytic ZnB site.
    action: KEEP_AS_NON_CORE
    reason: >-
      Well-supported and mechanistically essential (the catalytic metal), but it is a supporting
      molecular feature underpinning the porphobilinogen synthase activity rather than the core
      function term itself; kept as non-core.
    supported_by:
    - reference_id: PMID:11032836
      supporting_text: "eight Zn(II) per homo-octamer"
    - reference_id: PMID:11032836
      supporting_text: "are required for activity"
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:11032836
  qualifier: enables
  review:
    summary: >-
      Self-interaction (ALAD binds ALAD), reflecting its assembly into a homo-octamer/homohexamer.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Identical protein binding" is an uninformative binding term; the biologically meaningful
      fact (self-assembly into the active octamer) is better captured by protein
      homooligomerization. Per curation policy this bare protein-binding IPI is marked as
      over-annotated rather than removed.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "Homooctamer; active form. Homohexamer; low activity form."
- term:
    id: GO:0051260
    label: protein homooligomerization
  evidence_type: IPI
  original_reference_id: PMID:11032836
  qualifier: involved_in
  review:
    summary: >-
      Homo-oligomerization into the catalytically active octamer (and low-activity hexamer),
      central to ALAD's morpheein-type allosteric regulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Functionally meaningful: the octamer is the active oligomeric form and the octamer/hexamer
      equilibrium governs activity and disease. Retained as non-core biology that supports, but is
      not itself, the catalytic function.
    supported_by:
    - reference_id: file:human/ALAD/ALAD-uniprot.txt
      supporting_text: "Homooctamer; active form. Homohexamer; low activity form."
- term:
    id: GO:0003824
    label: catalytic activity
  evidence_type: TAS
  original_reference_id: PMID:2063868
  qualifier: enables
  review:
    summary: >-
      Traceable annotation to generic catalytic activity; ALAD's specific catalytic function is
      porphobilinogen synthase activity.
    action: MODIFY
    reason: >-
      The root-level "catalytic activity" term is uninformative for a well-characterized enzyme.
      It should be replaced by the specific molecular function porphobilinogen synthase activity
      (GO:0004655).
    proposed_replacement_terms:
    - id: GO:0004655
      label: porphobilinogen synthase activity
    supported_by:
    - reference_id: PMID:2063868
      supporting_text: "the heme biosynthetic enzyme, delta-aminolevulinate dehydratase"
- term:
    id: GO:0004655
    label: porphobilinogen synthase activity
  evidence_type: TAS
  original_reference_id: PMID:3463993
  qualifier: enables
  review:
    summary: >-
      Traceable annotation of porphobilinogen synthase activity from the cDNA-cloning paper that
      identified ALA-D (PBGS, EC 4.2.1.24).
    action: ACCEPT
    reason: >-
      Supports the core molecular function; consistent with all other MF evidence.
    supported_by:
    - reference_id: PMID:3463993
      supporting_text: "porphobilinogen synthase; EC 4.2.1.24"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: TAS
  original_reference_id: PMID:3758678
  qualifier: involved_in
  review:
    summary: >-
      Traceable annotation of involvement in heme biosynthesis from the cDNA-cloning paper that
      identified ALA-D as the second enzyme of the heme pathway.
    action: ACCEPT
    reason: >-
      Supports the core biological process.
    supported_by:
    - reference_id: PMID:3758678
      supporting_text: "the second enzyme in the heme biosynthetic pathway"
core_functions:
- description: >-
    Porphobilinogen synthase (5-aminolevulinate dehydratase, EC 4.2.1.24): catalyzes the second
    step of heme biosynthesis, the zinc-dependent asymmetric condensation of two molecules of
    5-aminolevulinate into the monopyrrole porphobilinogen, acting as a cytosolic homo-octamer.
  molecular_function:
    id: GO:0004655
    label: porphobilinogen synthase activity
  directly_involved_in:
  - id: GO:0006783
    label: heme biosynthetic process
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: file:human/ALAD/ALAD-uniprot.txt
    supporting_text: "Binds two molecules of 5-aminolevulinate per subunit, each at a"
  - reference_id: Reactome:R-HSA-189439
    supporting_text: "catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen"
- description: >-
    Zinc-dependent metallo-catalysis: ALAD binds zinc ions (up to eight per octamer, four required
    for activity) at its catalytic site; this metal-ion binding is essential for the porphobilinogen
    synthase reaction and is the site displaced by inhibitory lead.
  molecular_function:
    id: GO:0008270
    label: zinc ion binding
  supported_by:
  - reference_id: PMID:11032836
    supporting_text: "eight Zn(II) per homo-octamer"
  - reference_id: PMID:11032836
    supporting_text: "are required for activity"
proposed_new_terms: []
suggested_questions:
- question: >-
    Beyond the well-characterized CF-2/proteasome-inhibitor moonlighting activity, is there a
    physiological context (e.g. specific tissues or stress states) in which ALAD's proteasome
    regulation is functionally significant in vivo?
- question: >-
    Do the ALAD*1/ALAD*2 (K59N) allele differences alter any function beyond susceptibility to
    lead accumulation?
suggested_experiments:
- description: >-
    Quantitative structure-function analysis of the octamer/hexamer equilibrium for each
    ALAD-deficiency porphyria variant, correlating hexamer propensity with residual PBGS activity
    and clinical severity.
  experiment_type: biophysical/enzyme kinetics
- description: >-
    Interactome and proximity-labeling studies in erythroid and hepatic cells to test whether the
    CF-2/proteasome-inhibitory role is physiologically engaged or is an in vitro property of an
    abundant enzyme.
  experiment_type: proximity labeling / interactome