PPOX

id: P50336
gene_symbol: PPOX
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  Protoporphyrinogen oxidase (PPOX; PPO; EC 1.3.3.4) is the flavoprotein that catalyses
  the seventh (penultimate) step of heme biosynthesis: the FAD-dependent and oxygen-dependent
  six-electron oxidation of protoporphyrinogen IX to protoporphyrin IX (reaction:
  protoporphyrinogen IX + 3 O2 -> protoporphyrin IX + 3 H2O2). The protein is bound to
  the outer (intermembrane-space-facing) surface of the mitochondrial inner membrane, where
  it acts in the terminal, mitochondrial phase of the pathway feeding protoporphyrin IX to
  ferrochelatase for iron insertion. Each subunit binds one non-covalent FAD cofactor. In
  humans, partial loss of PPOX activity causes variegate porphyria (VP), an autosomal
  dominant acute hepatic porphyria with cutaneous photosensitivity; severe deficiency causes
  autosomal recessive childhood-onset variegate porphyria. PPOX is also the molecular target
  of diphenyl-ether herbicides (e.g. acifluorfen).
existing_annotations:
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) assignment of the defining catalytic activity of PPOX, transferred
      across the protoporphyrinogen oxidase orthology group. This is the core molecular
      function and is strongly supported by direct human enzyme assays.
    action: ACCEPT
    reason: >-
      Protoporphyrinogen oxidase (EC 1.3.3.4) is the experimentally established activity of
      the human enzyme, purified and assayed directly, and this IBA sits at the correct level
      of specificity for the whole ortholog group. The current ontology label for this ID is
      "oxygen-dependent protoporphyrinogen oxidase activity".
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) assignment placing PPOX in the heme biosynthetic pathway. This is
      the core biological process for the gene: the PPOX-catalysed step is the penultimate
      reaction of heme synthesis.
    action: ACCEPT
    reason: >-
      PPOX catalyses the seventh of eight steps of heme biosynthesis. The process
      assignment is correct and well supported; deficiency causes the heme-biosynthesis
      disorder variegate porphyria.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) assignment of PPOX to the mitochondrial inner membrane, its
      established site of action. PPOX is a peripheral membrane protein on the
      intermembrane-space-facing (outer) surface of the inner membrane.
    action: ACCEPT
    reason: >-
      The human enzyme is a mitochondrial inner-membrane protein; the crystallographic study
      explicitly describes hPPO as a mitochondrial inner membrane protein, and Reactome
      places it on the outer surface of the inner mitochondrial membrane. Core cellular
      location.
    supported_by:
    - reference_id: PMID:21048046
      supporting_text: >-
        Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane
        protein, converts protoporphyrinogen IX to protoporphyrin IX in the heme
        biosynthetic pathway.
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic assignment (combined IEA methods, tied to EC 1.3.3.4, RHEA:25576 and
      InterPro:IPR004572) of the core catalytic activity. Redundant with the experimental
      and IBA annotations to the same term.
    action: ACCEPT
    reason: >-
      Correct core molecular function, independently supported by direct enzyme assays and
      the mapped EC number/RHEA reaction. Duplicate ID with different evidence is acceptable.
    supported_by:
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: >-
        Reaction=protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2;
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Electronic (combined IEA / SubCell SL-0168) assignment of mitochondrial inner membrane
      localisation, matching the experimentally supported location.
    action: ACCEPT
    reason: >-
      Consistent with the UniProt subcellular location (mitochondrion inner membrane,
      peripheral, intermembrane side) and with the crystallographic characterisation of the
      human enzyme. Core location.
    supported_by:
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion inner membrane"
- term:
    id: GO:0005758
    label: mitochondrial intermembrane space
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    summary: >-
      ARBA electronic assignment to the mitochondrial intermembrane space. PPOX faces the
      intermembrane space (it is a peripheral protein on the outer/IMS-facing surface of the
      inner membrane) but is not a soluble intermembrane-space protein.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PPOX is anchored to the inner membrane with its active site oriented toward the
      intermembrane space; UniProt records the location as "Mitochondrion inner membrane;
      Peripheral membrane protein; Intermembrane side". The more specific and accurate
      component is mitochondrial inner membrane (GO:0005743). Assigning it as an
      intermembrane-space (matrix-of-the-IMS) protein overstates a free-luminal localisation,
      so this is an over-annotation relative to the inner-membrane term.
    supported_by:
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: "{ECO:0000250|UniProtKB:P51175}; Intermembrane side"
- term:
    id: GO:0006779
    label: porphyrin-containing compound biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Electronic assignment to porphyrin-containing compound biosynthesis. This is a correct
      but more general parent of the specific heme biosynthetic process; PPOX produces the
      porphyrin protoporphyrin IX.
    action: ACCEPT
    reason: >-
      Biologically correct: PPOX generates protoporphyrin IX, a porphyrin. The term is
      broader than the core heme biosynthetic process, but an IEA at this generality is
      acceptable and true.
    supported_by:
    - reference_id: PMID:21048046
      supporting_text: >-
        converts protoporphyrinogen IX to protoporphyrin IX in the heme
        biosynthetic pathway
- term:
    id: GO:0006785
    label: heme B biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA electronic assignment to heme B (protoheme) biosynthesis, the specific branch of
      heme synthesis to which the PPOX-generated protoporphyrin IX is committed (protoporphyrin
      IX + Fe2+ -> heme B).
    action: ACCEPT
    reason: >-
      Heme b (protoheme IX) is the immediate downstream product of the protoporphyrin IX made
      by PPOX (via ferrochelatase). The term is a valid, more specific descendant of heme
      biosynthetic process. Keep as a specific process; the general heme biosynthetic process
      remains the core BP.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro2GO electronic assignment (from the flavin amine-oxidase domain IPR002937) of
      the broad parent activity oxidoreductase.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PPOX is an oxidoreductase, so the term is not wrong, but it is far more general than
      the specific and experimentally established protoporphyrinogen oxidase activity
      (GO:0004729) that is already annotated. The generic parent adds no functional
      information beyond the specific child.
    supported_by:
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: >-
        Reaction=protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2;
- term:
    id: GO:0031966
    label: mitochondrial membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    summary: >-
      ARBA electronic assignment to the generic mitochondrial membrane. Correct but broader
      than the specific mitochondrial inner membrane localisation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PPOX localises specifically to the mitochondrial inner membrane (GO:0005743), which is
      already annotated. The generic mitochondrial membrane parent is true but redundant and
      less informative.
    supported_by:
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Mitochondrion inner membrane"
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl (orthology-based) electronic transfer of the core heme biosynthetic process
      annotation. Redundant with the IBA/ISS/IDA annotations to the same term.
    action: ACCEPT
    reason: >-
      Correct core biological process, supported by direct experimental evidence for the
      human enzyme; the electronic transfer from the rat ortholog is appropriate.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl electronic transfer (from the rat ortholog D3ZVN7) of "response to xenobiotic
      stimulus". PPOX is the molecular target of diphenyl-ether herbicides (e.g. acifluorfen),
      which underlies this annotation, but responding to a xenobiotic is not a core evolved
      function of the enzyme.
    action: KEEP_AS_NON_CORE
    reason: >-
      The annotation reflects that PPOX is inhibited by xenobiotic herbicides (acifluorfen is
      a specific PPO inhibitor), a pharmacologically important but peripheral, non-core
      aspect of the gene. It is retained as non-core rather than removed because the
      xenobiotic-interaction is genuine and experimentally documented for the enzyme.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        this activity was inhibited by
        acifluorfen, a specific inhibitor of PPO
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      Curator sequence-similarity (ISS) transfer of the core catalytic activity from the
      mouse ortholog (MGI:104968). Redundant with the direct experimental and IBA annotations.
    action: ACCEPT
    reason: >-
      Correct core molecular function; sequence-similarity transfer is fully consistent with
      the directly assayed human enzyme activity.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      Curator sequence-similarity (ISS) transfer of the core heme biosynthetic process from
      the mouse ortholog. Redundant with IBA/IEA/IDA annotations to the same term.
    action: ACCEPT
    reason: >-
      Correct core biological process, consistent with all other lines of evidence.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: EXP
  original_reference_id: PMID:23467411
  qualifier: enables
  review:
    summary: >-
      Experimental (EXP) annotation of protoporphyrinogen oxidase activity from the
      quantitative structural/kinetic study of wild-type and VP-mutant human PPO, which
      assayed kcat/Km of the enzyme and characterised the FAD- and O2-dependent oxidation of
      protoporphyrinogen IX to protoporphyrin IX.
    action: ACCEPT
    reason: >-
      Direct experimental determination of the core catalytic activity of the human enzyme,
      including quantitative kinetics; the defining function of the gene.
    supported_by:
    - reference_id: PMID:23467411
      supporting_text: >-
        catalyzes the oxidation of protoporphyrinogen IX (protogen) to protoporphyrin IX
        (porphyrin) in the presence of cofactor FAD and molecular oxygen
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Curator sequence-similarity (ISS) transfer of mitochondrial inner membrane localisation
      from the mouse ortholog (P51175). Consistent with the experimentally supported location.
    action: ACCEPT
    reason: >-
      Correct core location; matches the UniProt subcellular location and the
      crystallographic description of the human enzyme.
    supported_by:
    - reference_id: PMID:21048046
      supporting_text: >-
        Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane
        protein
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      Duplicate GOA line of the curator sequence-similarity (ISS) transfer of mitochondrial
      inner membrane localisation from the mouse ortholog (P51175); differs only in
      annotation date/source. Same conclusion as the other ISS localisation annotation.
    action: ACCEPT
    reason: >-
      Correct core location; matches the UniProt subcellular location and the
      crystallographic description of the human enzyme. Duplicate of the equivalent
      GO:0005743 ISS annotation.
    supported_by:
    - reference_id: PMID:21048046
      supporting_text: >-
        Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane
        protein
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: IDA
  original_reference_id: PMID:21048046
  qualifier: enables
  review:
    summary: >-
      Direct assay (IDA) of protoporphyrinogen oxidase activity from the 1.9 Angstrom crystal
      structure study of human PPO in complex with FAD and the inhibitor acifluorfen, which
      biochemically characterised the wild-type enzyme and 47 VP-causing mutants.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for the core catalytic function of the human enzyme,
      including structural and kinetic characterisation. Defining molecular function.
    supported_by:
    - reference_id: PMID:21048046
      supporting_text: >-
        we report the crystal structure
        of hPPO in complex with the coenzyme flavin adenine dinucleotide (FAD) and the
        inhibitor acifluorfen at a resolution of 1.9
- term:
    id: GO:0006785
    label: heme B biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:7713909
  qualifier: involved_in
  review:
    summary: >-
      Direct assay (IDA) placing PPOX in heme (heme B / protoheme) biosynthesis, from the
      cDNA cloning study that complemented an E. coli hemG (PPO-deficient) mutant and
      demonstrated acifluorfen-inhibitable PPO activity in transfected cells.
    action: ACCEPT
    reason: >-
      Functional complementation of a heme-pathway (hemG) mutant plus demonstration of PPO
      activity directly establishes PPOX's role in producing the protoporphyrin IX committed
      to heme b synthesis. Keep as a specific heme-branch process alongside the general core
      heme biosynthetic process.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        a hemG mutant strain of
        Escherichia coli deficient in PPO is defective in aerobic respiration
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput (HTP) proteomic assignment of PPOX to the mitochondrion, from a
      quantitative high-confidence human mitochondrial proteome (MitoCoP) study. Broader than,
      but consistent with, the specific inner-membrane localisation.
    action: ACCEPT
    reason: >-
      Correct organellar localisation supported by a large-scale, high-confidence
      mitochondrial proteome. The term is more general than mitochondrial inner membrane but
      is accurate; retained as a valid (if less specific) location annotation.
    supported_by:
    - reference_id: PMID:34800366
      supporting_text: >-
        defined a
        mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP)
- term:
    id: GO:0005758
    label: mitochondrial intermembrane space
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-189423
  qualifier: located_in
  review:
    summary: >-
      Reactome traceable-author-statement placing PPO on the outer surface of the inner
      mitochondrial membrane (facing the intermembrane space). As with the IEA IMS
      annotation, the intermembrane-space term overstates a soluble-luminal localisation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Reactome explicitly states the protein resides on the outer surface of the inner
      mitochondrial membrane, i.e. it is inner-membrane-associated with its active site
      facing the intermembrane space, not a free intermembrane-space protein. The specific,
      accurate component is mitochondrial inner membrane (GO:0005743); the IMS assignment is
      an over-annotation.
    supported_by:
    - reference_id: Reactome:R-HSA-189423
      supporting_text: >-
        The protein resides on the outer surface of the inner mitochondrial membrane.
- term:
    id: GO:0004729
    label: protoporphyrinogen oxidase activity, oxygen as acceptor
  evidence_type: IDA
  original_reference_id: PMID:7713909
  qualifier: enables
  review:
    summary: >-
      Direct assay (IDA) of protoporphyrinogen oxidase activity from the original human cDNA
      cloning: COS-1 cells transfected with the cDNA showed markedly higher, acifluorfen-
      inhibitable PPO activity than controls.
    action: ACCEPT
    reason: >-
      Direct experimental demonstration of the core catalytic activity of the human gene
      product. Defining molecular function.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        A homogenate of the monkey kidney
        COS-1 cells that had been transfected with the cDNA had much higher PPO activity
        than an extract of control cells, and this activity was inhibited by
        acifluorfen, a specific inhibitor of PPO.
- term:
    id: GO:0006779
    label: porphyrin-containing compound biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:7713909
  qualifier: involved_in
  review:
    summary: >-
      Direct assay (IDA) placing PPOX in porphyrin-containing compound biosynthesis, from the
      cloning/complementation study. PPOX generates the porphyrin protoporphyrin IX.
    action: ACCEPT
    reason: >-
      Correct but general process; PPOX produces protoporphyrin IX, a porphyrin. The specific
      heme biosynthetic process is the core BP, with this as a valid broader annotation.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:7713909
  qualifier: involved_in
  review:
    summary: >-
      Direct assay (IDA) of PPOX's role in heme biosynthesis, from functional complementation
      of an E. coli hemG (PPO-deficient) mutant with the human cDNA. This is the core
      biological process for the gene.
    action: ACCEPT
    reason: >-
      Functional complementation of a heme-pathway mutant and restoration of PPO activity
      directly establishes the role of PPOX in heme biosynthesis. Core BP.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
        penultimate step in the heme biosynthetic pathway.
- term:
    id: GO:0031966
    label: mitochondrial membrane
  evidence_type: IMP
  original_reference_id: PMID:7713909
  qualifier: located_in
  review:
    summary: >-
      Mutant-phenotype-based (IMP) localisation to the mitochondrial membrane, from the
      cloning study showing the in vitro-translated protein associates with isolated
      mitochondria without size change, indicating no cleaved targeting presequence.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The evidence supports mitochondrial (membrane) localisation, but the generic
      mitochondrial membrane term is broader than the experimentally and structurally
      supported mitochondrial inner membrane (GO:0005743), which is already annotated. Kept
      but flagged as an over-general component. (Deferring to the curator, this is not a
      removal — the localisation is genuine.)
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        after incubation with isolated mitochondria
        the protein was found to be located in the mitochondria, having just the same
        size as before, an indication that PPO is a mitochondrial enzyme and has no
        apparent transport-specific leader sequence.
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: TAS
  original_reference_id: PMID:7713909
  qualifier: enables
  review:
    summary: >-
      Traceable author statement that PPOX binds FAD. The N-terminal sequence contains a
      classic dinucleotide-binding motif, and the crystal structure resolves one FAD bound
      per subunit; FAD is the essential redox cofactor for the oxidation reaction.
    action: ACCEPT
    reason: >-
      PPOX is a flavoprotein that binds one FAD per subunit as its catalytic cofactor,
      confirmed both by sequence motif and by crystal structures. This is a genuine, though
      secondary/enabling, molecular function supporting the core oxidase activity.
    supported_by:
    - reference_id: PMID:7713909
      supporting_text: >-
        The NH2-terminal amino acid sequence of the deduced
        PPO contains a conserved amino acid sequence that forms the dinucleotide-binding
        site in many flavin-containing proteins.
    - reference_id: file:human/PPOX/PPOX-uniprot.txt
      supporting_text: "Note=Binds 1 FAD per subunit."
core_functions:
- description: >-
    FAD- and oxygen-dependent six-electron oxidation of protoporphyrinogen IX to
    protoporphyrin IX, the seventh (penultimate) step of heme biosynthesis, catalysed at the
    mitochondrial inner membrane.
  molecular_function:
    id: GO:0004729
    label: oxygen-dependent protoporphyrinogen oxidase activity
  directly_involved_in:
  - id: GO:0006783
    label: heme biosynthetic process
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  supported_by:
  - reference_id: PMID:23467411
    supporting_text: >-
      catalyzes the oxidation of protoporphyrinogen IX (protogen) to protoporphyrin IX
      (porphyrin) in the presence of cofactor FAD and molecular oxygen
  - reference_id: PMID:21048046
    supporting_text: >-
      Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane
      protein, converts protoporphyrinogen IX to protoporphyrin IX in the heme
      biosynthetic pathway.
- description: >-
    Binds one non-covalent FAD cofactor per subunit, the flavin redox centre required for
    the oxidase activity.
  molecular_function:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  supported_by:
  - reference_id: PMID:21048046
    supporting_text: >-
      in complex with the coenzyme flavin adenine dinucleotide (FAD)
  - reference_id: file:human/PPOX/PPOX-uniprot.txt
    supporting_text: "Note=Binds 1 FAD per subunit."
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: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: PMID:21048046
  title: Structural insight into human variegate porphyria disease.
  findings:
  - statement: >-
      1.9 Angstrom crystal structure of human PPO in complex with FAD and the inhibitor
      acifluorfen; hPPO converts protoporphyrinogen IX to protoporphyrin IX and is a
      mitochondrial inner membrane protein. Also characterised 47 VP-causing mutants.
    supporting_text: >-
      Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane
      protein, converts protoporphyrinogen IX to protoporphyrin IX in the heme
      biosynthetic pathway.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; provides direct structural and biochemical evidence for the catalytic
      activity, FAD binding, and mitochondrial inner membrane localisation of human PPOX.
- id: PMID:23467411
  title: Quantitative structural insight into human variegate porphyria disease.
  findings:
  - statement: >-
      PPO (EC 1.3.3.4) is the penultimate enzyme of heme biosynthesis, oxidising
      protoporphyrinogen IX to protoporphyrin IX using FAD and molecular oxygen; ~50%
      decreased activity causes dominantly inherited variegate porphyria (an acute hepatic
      porphyria).
    supporting_text: >-
      catalyzes the oxidation of protoporphyrinogen IX (protogen) to protoporphyrin IX
      (porphyrin) in the presence of cofactor FAD and molecular oxygen
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified full-text; quantitative kinetic/structural study of wild-type and
      VP-mutant hPPO. Source of the EXP catalytic-activity annotation.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
  - statement: >-
      Large-scale proteomic study defining a high-confidence human mitochondrial proteome
      (MitoCoP) of >1,100 proteins, supporting mitochondrial localisation of PPOX.
    supporting_text: >-
      defined a
      mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP)
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; high-throughput evidence for mitochondrial localisation (GO:0005739),
      broader than the specific inner-membrane location.
- id: PMID:7713909
  title: Cloning of a human cDNA for protoporphyrinogen oxidase by complementation
    in vivo of a hemG mutant of Escherichia coli.
  findings:
  - statement: >-
      Cloning of the human PPOX cDNA by complementation of an E. coli hemG (PPO-deficient)
      mutant; PPO is the penultimate heme-pathway enzyme, a mitochondrial flavoprotein whose
      activity is inhibited by acifluorfen.
    supporting_text: >-
      Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the enzyme that catalyzes in the
      penultimate step in the heme biosynthetic pathway.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; original human PPOX cDNA cloning and functional characterisation.
      Anchors the IDA activity, heme/porphyrin process, mitochondrial localisation, and FAD
      binding annotations.
- id: Reactome:R-HSA-189423
  title: PPO oxidises PPGEN9 to PRIN9
  findings:
  - statement: >-
      Reactome reaction: six-electron oxidation of protoporphyrinogen IX to protoporphyrin
      IX by PPO, a FAD-containing enzyme on the outer surface of the inner mitochondrial
      membrane; PPO deficiency causes variegate porphyria.
    supporting_text: >-
      The protein resides on the outer surface of the inner mitochondrial membrane.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Reactome curated reaction for the PPOX-catalysed step; source of the TAS intermembrane
      space annotation. Title left exactly as fetched.
- id: file:human/PPOX/PPOX-uniprot.txt
  title: UniProtKB entry P50336 (PPOX_HUMAN)
  findings:
  - statement: >-
      UniProt records the catalytic reaction (protoporphyrinogen IX + 3 O2 = protoporphyrin
      IX + 3 H2O2; EC 1.3.3.4), FAD cofactor (one per subunit), mitochondrial inner membrane
      peripheral (intermembrane-side) localisation, and the disease associations variegate
      porphyria and childhood-onset variegate porphyria.
    supporting_text: >-
      Reaction=protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2;
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary UniProt record for PPOX; source of the catalytic reaction, FAD cofactor,
      subcellular location, and disease annotations used above.