id: P08397
gene_symbol: HMBS
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase
  (PBGD) or pre-uroporphyrinogen synthase, is the enzyme that catalyzes the third
  step of heme biosynthesis (EC 2.5.1.61). Acting in the cytosol, it carries out the
  head-to-tail (sequential) polymerization of four molecules of porphobilinogen (PBG)
  into the linear tetrapyrrole hydroxymethylbilane (also called preuroporphyrinogen),
  releasing four molecules of ammonia. The enzyme is a monomer that uses a unique
  self-derived dipyrromethane cofactor, covalently bound at Cys261, which serves as a
  primer onto which the four PBG units are added one at a time; the cofactor is not
  consumed and remains bound as the holoenzyme releases the product. The product
  hydroxymethylbilane is subsequently cyclized by uroporphyrinogen III synthase.
  Alternative transcription/splicing produces a ubiquitously expressed housekeeping
  isoform and an erythroid-specific isoform. Loss-of-function mutations in HMBS cause
  acute intermittent porphyria (AIP), the most common acute hepatic porphyria, and
  biallelic mutations underlie porphyria-related (leuko)encephalopathy.
alternative_products:
- name: 1 (Non-erythropoietic)
  id: P08397-1
- name: 2 (Erythrocyte)
  id: P08397-2
  sequence_note: VSP_002067
- name: '3'
  id: P08397-3
  sequence_note: VSP_047294
- name: '4'
  id: P08397-4
  sequence_note: VSP_002067, VSP_047294
existing_annotations:
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) annotation placing HMBS in the heme biosynthetic process.
      This is a core biological process for HMBS, which catalyzes the third step of
      heme synthesis in the cytosol.
    action: ACCEPT
    reason: >-
      HMBS/PBGD is a canonical heme biosynthesis enzyme; the IBA annotation is
      consistent with experimental and structural literature and with UniProt.
    supported_by:
    - reference_id: PMID:23815679
      supporting_text: "the third enzyme in the haem biosynthesis pathway"
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "As part of the heme biosynthetic pathway, catalyzes the"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) annotation of the diagnostic molecular function,
      hydroxymethylbilane synthase (porphobilinogen deaminase) activity. This is the
      core catalytic function of HMBS.
    action: ACCEPT
    reason: >-
      Well conserved across the HMBS family and strongly supported by experimental
      and structural data in human HMBS.
    supported_by:
    - reference_id: PMID:23815679
      supporting_text: >-
        The enzyme catalyses the assembly of four PBG molecules into the linear
        precursor of uroporphyrinogen III, HMB (hydroxymethylbilane, also called
        preuroporphyrinogen)
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) annotation to cytoplasm. HMBS is a soluble cytosolic
      enzyme; cytoplasm is correct but is a broader parent of the more precise
      cytosol location.
    action: ACCEPT
    reason: >-
      Correct localization, though less specific than the cytosol annotations also
      present. Retained as a valid (parent-level) location.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
    - reference_id: PMID:18004775
      supporting_text: "cytosolic enzymes of heme biosynthesis"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic annotation of hydroxymethylbilane synthase activity via combined
      IEA methods (InterPro/ARBA/RHEA/EC:2.5.1.61). Matches the experimentally
      established function.
    action: ACCEPT
    reason: >-
      The EC 2.5.1.61 / RHEA:13185 mapping is exactly the reaction HMBS catalyzes;
      the electronic call is correct and specific.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "EC=2.5.1.61"
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic annotation to cytosol from the UniProt subcellular-location keyword
      mapping. This is the precise cellular location of HMBS.
    action: ACCEPT
    reason: >-
      Consistent with UniProt SUBCELLULAR LOCATION (Cytoplasm, cytosol) and with the
      Reactome description of cytosolic PBG deaminase. Core location.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0006779
    label: porphyrin-containing compound biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA electronic annotation to porphyrin-containing compound biosynthetic
      process. Correct but more general than the specific heme biosynthetic process.
    action: ACCEPT
    reason: >-
      HMBS participates in porphyrin/tetrapyrrole biosynthesis; the parent-level term
      is accurate. Kept as a broader, still-correct annotation.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "Porphyrin-containing compound metabolism"
- term:
    id: GO:0033014
    label: tetrapyrrole biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO electronic annotation to tetrapyrrole biosynthetic process. HMBS
      builds the linear tetrapyrrole hydroxymethylbilane, so this is correct, though
      broader than heme biosynthesis.
    action: ACCEPT
    reason: >-
      The reaction product is a tetrapyrrole; the parent-level BP term is accurate.
      Retained as a broader, still-correct annotation.
    supported_by:
    - reference_id: PMID:23815679
      supporting_text: >-
        The enzyme catalyses the assembly of four PBG molecules into the linear
        precursor of uroporphyrinogen III, HMB (hydroxymethylbilane, also called
        preuroporphyrinogen)
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      IPI "protein binding" from a high-throughput human binary-interactome (Y2H)
      screen, recording an interaction with PICK1 (UniProtKB:Q9NRD5). Bare "protein
      binding" is uninformative about HMBS function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction is from a proteome-scale binary-interactome map; the generic
      "protein binding" term conveys no specific molecular function for HMBS and no
      dedicated biological role for this interaction is established. Per curation
      policy the experimental IPI is retained but flagged as over-annotated rather
      than removed.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: "A reference map of the human binary protein interactome."
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  qualifier: enables
  review:
    summary: >-
      IPI "protein binding" from a neurodegenerative-disease interactome mapping
      study, recording an interaction with huntingtin (HTT, UniProtKB:P42858). Bare
      "protein binding" is uninformative about HMBS function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction comes from a large interactome-mapping effort focused on
      neurodegenerative-disease proteins; the generic term does not describe a
      specific HMBS molecular function. Per curation policy the experimental IPI is
      retained but flagged as over-annotated rather than removed.
    supported_by:
    - reference_id: PMID:32814053
      supporting_text: "Network of Neurodegenerative Disease Proteins"
- term:
    id: GO:0006785
    label: heme B biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:18004775
  qualifier: involved_in
  review:
    summary: >-
      IDA annotation to the specific process "heme B biosynthetic process". HMBS
      contributes to heme biosynthesis broadly, but its direct step (producing the
      linear tetrapyrrole hydroxymethylbilane) is several steps upstream of heme b
      formation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      HMBS makes hydroxymethylbilane, a precursor common to all downstream
      tetrapyrroles; attributing specifically "heme B biosynthetic process" is more
      specific than the enzyme's direct chemistry warrants and the generic heme
      biosynthetic process (also annotated) captures its role better. The IDA
      reference is an experimental study of cytosolic heme-biosynthesis enzymes; the
      experimental annotation is retained (not removed) but flagged as
      over-specific/over-annotated.
    supported_by:
    - reference_id: PMID:18004775
      supporting_text: "cytosolic enzymes of heme biosynthesis"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189451
  qualifier: involved_in
  review:
    summary: >-
      Reactome TAS annotation (Heme biosynthesis pathway) to heme biosynthetic
      process. Core biological process for HMBS.
    action: ACCEPT
    reason: >-
      Reactome authoritatively places cytosolic PBG deaminase in the heme
      biosynthesis pathway; consistent with all other evidence.
    supported_by:
    - reference_id: PMID:23815679
      supporting_text: "the third enzyme in the haem biosynthesis pathway"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189406
  qualifier: enables
  review:
    summary: >-
      Reactome TAS annotation (reaction "4 PBGs bind to form HMB") of
      hydroxymethylbilane synthase activity. Core catalytic function.
    action: ACCEPT
    reason: >-
      Directly describes the HMBS-catalyzed reaction (polymerization of four PBG to
      form HMB); fully consistent with experimental data.
    supported_by:
    - reference_id: PMID:18936296
      supporting_text: >-
        which catalyzes the sequential condensation of 4 molecules of
        porphobilinogen to yield preuroporphyrinogen
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: EXP
  original_reference_id: PMID:19138865
  qualifier: enables
  review:
    summary: >-
      Experimental (EXP) annotation of HMBS activity based on recombinant expression
      and enzyme-activity assays of wild-type and AIP-mutant HMBS. Core catalytic
      function.
    action: ACCEPT
    reason: >-
      The study directly measures HMBS enzymatic activity of recombinant human
      protein (e.g., R32P inactive, D178N ~81% of wild-type), confirming the
      molecular function.
    supported_by:
    - reference_id: PMID:19138865
      supporting_text: >-
        Mutations in the hydroxymethylbilane synthase (HMBS) gene are responsible for
        the inherited disorder of acute intermittent porphyria
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: EXP
  original_reference_id: PMID:23815679
  qualifier: enables
  review:
    summary: >-
      Experimental (EXP) annotation of HMBS activity from enzyme-kinetic
      characterization of recombinant wild-type and mutant HMBS. Core catalytic
      function.
    action: ACCEPT
    reason: >-
      Direct kinetic assays of recombinant human HMBS establish the
      hydroxymethylbilane synthase activity and its assembly of four PBG into HMB.
    supported_by:
    - reference_id: PMID:23815679
      supporting_text: >-
        The enzyme catalyses the assembly of four PBG molecules into the linear
        precursor of uroporphyrinogen III, HMB (hydroxymethylbilane, also called
        preuroporphyrinogen)
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: is_active_in
  review:
    summary: >-
      ISS annotation to cytosol by sequence-similarity transfer from mouse (MGI).
      HMBS acts as a soluble cytosolic enzyme.
    action: ACCEPT
    reason: >-
      Consistent with the experimentally supported cytosolic localization of HMBS
      and with UniProt.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: IDA
  original_reference_id: PMID:18936296
  qualifier: enables
  review:
    summary: >-
      IDA annotation of HMBS activity from the crystal structure and functional
      characterization of human PBGD, including the covalently bound dipyrromethane
      cofactor and active-site mutagenesis. Core catalytic function.
    action: ACCEPT
    reason: >-
      Structural and mutagenesis data directly establish the hydroxymethylbilane
      synthase (PBGD) activity of human HMBS and the cofactor-primed mechanism.
    supported_by:
    - reference_id: PMID:18936296
      supporting_text: "covalently linked to C261, sitting in a positively charged"
    - reference_id: PMID:18936296
      supporting_text: "Sequential entry of 4 pyrrole molecules into the active site"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:18936296
  qualifier: involved_in
  review:
    summary: >-
      IDA annotation placing HMBS in the heme biosynthetic process, based on the
      structural/functional study of human PBGD in the context of AIP (a disease of
      heme biosynthesis). Core biological process.
    action: ACCEPT
    reason: >-
      The study characterizes HMBS as the PBGD step of heme biosynthesis; consistent
      with all other BP evidence.
    supported_by:
    - reference_id: PMID:18936296
      supporting_text: >-
        which catalyzes the sequential condensation of 4 molecules of
        porphobilinogen to yield preuroporphyrinogen
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189406
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS annotation to cytosol for the "4 PBGs bind to form HMB" reaction.
      Core location.
    action: ACCEPT
    reason: >-
      Reactome explicitly describes cytosolic porphobilinogen deaminase; consistent
      with UniProt and the ISS/IEA cytosol annotations.
    supported_by:
    - reference_id: file:human/HMBS/HMBS-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IC
  original_reference_id: PMID:18004775
  qualifier: involved_in
  review:
    summary: >-
      IC (inferred by curator) annotation to heme biosynthetic process, based on the
      hydroxymethylbilane synthase activity (with/from GO:0004418). Core biological
      process.
    action: ACCEPT
    reason: >-
      The curator inference from the established MF to the heme-biosynthesis BP is
      sound; HMBS is a cytosolic heme-biosynthesis enzyme.
    supported_by:
    - reference_id: PMID:18004775
      supporting_text: "cytosolic enzymes of heme biosynthesis"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: IDA
  original_reference_id: PMID:18004775
  qualifier: enables
  review:
    summary: >-
      IDA annotation of hydroxymethylbilane synthase activity from a study of the
      cytosolic heme-biosynthesis enzymes (which expressed and characterized human
      HMB-synthase holoenzyme alongside URO-synthase). Core catalytic function.
    action: ACCEPT
    reason: >-
      The study prepared and worked with human HMB-synthase holoenzyme; the
      experimental MF annotation is retained. Although the paper's title foregrounds
      URO-synthase, the full text also involves HMB-synthase, and the function is
      correct for HMBS, so it is accepted (deferring to the curator).
    supported_by:
    - reference_id: PMID:18004775
      supporting_text: "cytosolic enzymes of heme biosynthesis"
- term:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  evidence_type: TAS
  original_reference_id: PMID:2025226
  qualifier: enables
  review:
    summary: >-
      TAS annotation of hydroxymethylbilane synthase activity from a mechanistic
      study of the enzyme (role of conserved arginine residues in substrate binding).
      Core catalytic function.
    action: ACCEPT
    reason: >-
      A classical mechanistic study of hydroxymethylbilane synthase supporting the
      molecular function (substrate/cofactor binding via conserved arginines). The
      work was done in E. coli enzyme by site-directed mutagenesis but establishes
      the conserved HMBS/PBGD activity; retained as TAS support for the MF.
    supported_by:
    - reference_id: PMID:2025226
      supporting_text: >-
        The role of conserved arginine residues in hydroxymethylbilane synthase
core_functions:
- description: >-
    Catalyzes the third step of heme biosynthesis: the sequential (head-to-tail)
    polymerization of four molecules of porphobilinogen into the linear tetrapyrrole
    hydroxymethylbilane (preuroporphyrinogen), using a covalently bound, self-derived
    dipyrromethane cofactor as a primer, in the cytosol.
  molecular_function:
    id: GO:0004418
    label: hydroxymethylbilane synthase activity
  directly_involved_in:
  - id: GO:0006783
    label: heme biosynthetic process
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:18936296
    supporting_text: >-
      porphobilinogen deaminase (PBGD), which catalyzes the sequential condensation
      of 4 molecules of porphobilinogen to yield preuroporphyrinogen
  - reference_id: PMID:23815679
    supporting_text: "the third enzyme in the haem biosynthesis pathway"
  - reference_id: file:human/HMBS/HMBS-uniprot.txt
    supporting_text: "SUBCELLULAR LOCATION: Cytoplasm, cytosol"
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:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:18004775
  title: 'Human uroporphyrinogen III synthase: NMR-based mapping of the active site.'
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Title foregrounds URO-synthase (UROS), but the study developed expression and
      purification of the cytosolic heme-biosynthesis enzymes including human
      HMB-synthase holoenzyme; used to support HMBS MF/BP annotations. PubMed-verified.
- id: PMID:18936296
  title: Structural insight into acute intermittent porphyria.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Crystal structure and functional analysis of human PBGD/HMBS; establishes the
      dipyrromethane cofactor at C261 and the sequential-condensation mechanism.
- id: PMID:19138865
  title: Correlation between biochemical findings, structural and enzymatic abnormalities
    in mutated HMBS identified in six Israeli families with acute intermittent porphyria.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Recombinant expression and activity assays of wild-type and AIP-mutant human
      HMBS directly support the enzymatic function.
- id: PMID:2025226
  title: Studies on the mechanism of hydroxymethylbilane synthase concerning the role
    of arginine residues in substrate binding.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Mechanistic (E. coli enzyme) study of conserved arginine residues in
      substrate/cofactor binding; supports the conserved HMBS molecular function.
- id: PMID:23815679
  title: Conformational stability and activity analysis of two hydroxymethylbilane
    synthase mutants, K132N and V215E, with different phenotypic association with
    acute intermittent porphyria.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text available; kinetic characterization of recombinant human HMBS and
      explicit description of the reaction (assembly of four PBG into HMB) and the
      enzyme as the third step of heme biosynthesis.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput binary interactome (Y2H) map; source of a bare "protein
      binding" IPI (HMBS-PICK1). Uninformative about HMBS's specific function.
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
    and Uncovers Widespread Protein Aggregation in Affected Brains.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale neurodegenerative-disease interactome mapping; source of a bare
      "protein binding" IPI (HMBS-HTT). Uninformative about HMBS's specific function.
- id: Reactome:R-HSA-189406
  title: 4 PBGs bind to form HMB
  findings: []
- id: Reactome:R-HSA-189451
  title: Heme biosynthesis
  findings: []
- id: file:human/HMBS/HMBS-uniprot.txt
  title: UniProtKB entry P08397 (HEM3_HUMAN) - HMBS / porphobilinogen deaminase
  findings: []