CPOX encodes oxygen-dependent coproporphyrinogen-III oxidase (EC 1.3.3.3), the enzyme that catalyzes the sixth step of heme biosynthesis. It carries out the aerobic (O2-dependent) oxidative decarboxylation of the propionate side chains on rings A and B of coproporphyrinogen III to yield the vinyl groups of protoporphyrinogen IX, releasing 2 CO2 and 2 H2O. The enzyme is unusual in being metal- and cofactor-independent and functions as a homodimer. It is a nuclear-encoded mitochondrial protein that, after cleavage of an N-terminal transit peptide, localizes to the mitochondrial intermembrane space in association with the inner membrane. Loss-of-function mutations cause the acute hepatic porphyria hereditary coproporphyria (HCP); a specific set of variants (e.g. K404E, H327R) instead produce the rare erythropoietic variant harderoporphyria (HARPO).
Definition: The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from coproporphyrinogen III, the immediate product of the coproporphyrinogen oxidase reaction in the heme biosynthetic pathway.
Justification: The most direct biological-process term for CPOX's step is the biosynthesis of protoporphyrinogen IX, the immediate product of the coproporphyrinogen oxidase reaction. This is more specific than the broadly-annotated heme biosynthetic process. The term already exists as GO:0006782 (it is listed in the UniProt DR GO section as IDA:UniProt) but is absent from the seeded GOA; adding it would capture the enzyme's direct product-level role.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic (IBA) placement of the enzyme in the cytoplasm. CPOX is a nuclear-encoded mitochondrial enzyme that localizes specifically to the mitochondrial intermembrane space, so "cytoplasm" is imprecise for the human protein. Reason: The enzyme is not a general cytoplasmic protein; it is targeted to the mitochondrion via an N-terminal transit peptide and resides in the mitochondrial intermembrane space. The more accurate compartment (GO:0005758 / GO:0005739) is captured by other, better-supported annotations, so the broad cytoplasm term is an over-annotation for this gene. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000079415 · coproporphyrinogen oxidase family node Family-level cytoplasm assignment is too broad; the human ortholog is specifically mitochondrial intermembrane space. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space PMID:8407975 mammalian coproporphyrinogen oxidase is mitochondrial enzyme |
| GO:0006783 heme biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) assignment to heme biosynthesis, the core biological process for CPOX. CPOX catalyzes the sixth (O2-dependent) step of the heme biosynthetic pathway, converting coproporphyrinogen III to protoporphyrinogen IX. Reason: This is the central, well-established biological role of the enzyme, agreed across IBA, IEA, and experimental/TAS evidence. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway, the oxidation of coproporphyrinogen III to protoporphyrinogen IX |
| GO:0004109 coproporphyrinogen oxidase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) assignment of the diagnostic molecular function, coproporphyrinogen oxidase activity (EC 1.3.3.3). This is the core catalytic activity of CPOX and is directly supported by biochemical experiments. Reason: Core molecular function, concordant with the enzyme's experimentally verified activity and EC number. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway, the oxidation of coproporphyrinogen III to protoporphyrinogen IX |
| GO:0004109 coproporphyrinogen oxidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment of coproporphyrinogen oxidase activity via combined IEA methods (ARBA, InterPro IPR001260/IPR018375/IPR036406, RHEA:18257, EC:1.3.3.3). Consistent with the experimentally established catalytic function. Reason: Correct EC/InterPro/RHEA mapping to the enzyme's core catalytic activity; agrees with experimental evidence. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt Catalyzes the aerobic oxidative decarboxylation of propionate |
| GO:0005758 mitochondrial intermembrane space | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic assignment (UniProtKB Subcellular Location mapping) of localization to the mitochondrial intermembrane space. This is the curated subcellular location of the mature enzyme. Reason: Matches the curated UniProt subcellular location and independent TAS/ISS annotations to the same term. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0006779 porphyrin-containing compound biosynthetic process | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Electronic assignment to porphyrin-containing compound biosynthesis, a broad parent process. CPOX participates in this via the heme branch, but the more specific and better-supported term is heme biosynthetic process (GO:0006783). Reason: Biologically correct but more general than the specific heme biosynthetic role; retained as a non-core, broader-parent annotation rather than the core function. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt protoporphyrinogen-IX from coproporphyrinogen-III (O2 |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from rat/mouse ortholog) of localization to the mitochondrial inner membrane. CPOX is described as residing in the intermembrane space in association with the inner membrane, so this is plausible but not the primary curated compartment. Reason: Consistent with the enzyme being IMS-facing and inner-membrane-associated, but the primary, experimentally/curator-supported location is the intermembrane space (GO:0005758). Retained as a plausible non-core localization. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0006783 heme biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment (ARBA/combined IEA methods) to heme biosynthetic process, the core biological role of CPOX. Concordant with IBA and experimental/TAS annotations to the same term. Reason: Correct assignment of the core biological process, agreeing with all other evidence lines. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway |
| GO:0010039 response to iron ion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog Q3B7D0) of a "response to iron ion" phenotype. This is a peripheral, ortholog-derived stress/metal response, not a demonstrated function of human CPOX. Reason: Plausible ortholog-transferred physiological response (heme synthesis is iron-linked), but not a core function and not directly demonstrated for the human protein; retained as non-core rather than removed. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0010288 response to lead ion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog) of a "response to lead ion" phenotype. Lead inhibits heme-pathway enzymes, so this is a plausible ortholog-derived toxicological response, but it is not a demonstrated function of human CPOX. Reason: Peripheral ortholog-transferred toxicant response; not core and not shown for the human protein, but not clearly wrong, so retained as non-core. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0016020 membrane | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Electronic transfer (Ensembl Compara, from mouse ortholog P36552) of the uninformative broad location "membrane". The specific, curated compartment is the mitochondrial intermembrane space. Reason: "membrane" is an uninformative high-level CC term; the enzyme's location is captured precisely by GO:0005758 (and plausibly GO:0005743), making this broad term redundant/over-annotated. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0017085 response to insecticide | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog) of a "response to insecticide" phenotype. This is a peripheral, ortholog-derived response with no direct evidence in human CPOX. Reason: Ortholog-transferred toxicant response; peripheral and unverified for the human protein, retained as non-core rather than removed. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0042802 identical protein binding | IEA GO_REF:0000107 | MODIFY | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog) of "identical protein binding". CPOX is indeed a homodimer, so it self-associates, but a more informative and directly experimentally supported term exists: protein homodimerization activity (GO:0042803, IDA from the crystal-structure/AUC study). Reason: The self-association is real, but "identical protein binding" is a weak binding term. It should be represented by the more specific GO:0042803 protein homodimerization activity, which is directly supported for the human enzyme. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:16176984 In the biologically active dimer (K(D) = 5 x 10(-7) M) |
| GO:0046685 response to arsenic-containing substance | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog) of a "response to arsenic-containing substance" phenotype. Peripheral ortholog-derived response with no direct human evidence. Reason: Ortholog-transferred toxicant response; peripheral and unverified for human CPOX, retained as non-core. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0051597 response to methylmercury | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Electronic transfer (Ensembl Compara, from the rat ortholog) of a "response to methylmercury" phenotype. Peripheral ortholog-derived response with no direct human evidence. Reason: Ortholog-transferred toxicant response; peripheral and unverified for human CPOX, retained as non-core. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0006785 heme B biosynthetic process | IDA PMID:7987309 Coproporphyrinogen oxidase: gene organization and descriptio... | KEEP AS NON CORE | Summary: Assignment to heme B biosynthetic process. Heme b is the end product of the protoporphyrin IX / heme branch that CPOX feeds, so the enzyme is genuinely part of heme b biosynthesis. However, CPOX's direct step produces protoporphyrinogen IX, several steps upstream of heme b, and the cited reference (PMID:7987309) is a gene-organization/exon-6-skipping study rather than a heme-b assay. Reason: Biologically correct as a downstream pathway membership, but less direct than the core "heme biosynthetic process" and the immediate protoporphyrinogen IX step; retained as non-core. The essence of the pathway role is sound, so it is not removed. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence-based (HPA, IDA) localization to the mitochondrion. Consistent with CPOX being a nuclear-encoded mitochondrial enzyme. Reason: Directly observed mitochondrial localization, concordant with the intermembrane space annotations and mass-spectrometry evidence. Supporting Evidence: PMID:8407975 mammalian coproporphyrinogen oxidase is mitochondrial enzyme |
| GO:0005758 mitochondrial intermembrane space | TAS Reactome:R-HSA-189421 | ACCEPT | Summary: Reactome-curated (TAS) localization to the mitochondrial intermembrane space, where CPOX catalyzes conversion of coproporphyrinogen III to protoporphyrinogen IX. This is the primary curated compartment for the enzyme. Reason: Matches the curated UniProt location and independent ISS/IEA annotations to the same term; well supported. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0004109 coproporphyrinogen oxidase activity | EXP PMID:8159699 Molecular cloning, sequencing, and functional expression of ... | ACCEPT | Summary: Experimental (EXP) demonstration of coproporphyrinogen oxidase activity: expression of the human cDNA in E. coli produced a 17-fold increase in coproporphyrinogen oxidase activity, directly establishing the catalytic function. Reason: Directly demonstrated core catalytic function of the enzyme; strongest evidence line for the molecular function. Supporting Evidence: PMID:8159699 17-fold increase in coproporphyrinogen activity over endogenous activity |
| GO:0005758 mitochondrial intermembrane space | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity-based (ISS, from the rat ortholog Q3B7D0) localization to the mitochondrial intermembrane space. Consistent with the curated UniProt location and the Reactome TAS annotation. Reason: Concordant with the curated primary compartment and multiple independent evidence lines for the intermembrane space. Supporting Evidence: file:human/CPOX/CPOX-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion intermembrane space |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: High-throughput (HTP) mass-spectrometry evidence placing CPOX in the human mitochondrial proteome. Consistent with its established mitochondrial localization. Reason: Corroborates mitochondrial localization by an independent proteomic method; concordant with IDA and IMS annotations. Supporting Evidence: PMID:34800366 high-confidence human mitochondrial proteome |
| GO:0004109 coproporphyrinogen oxidase activity | IDA PMID:7987309 Coproporphyrinogen oxidase: gene organization and descriptio... | ACCEPT | Summary: Direct-assay (IDA) assignment of coproporphyrinogen oxidase activity. This is the core, experimentally established catalytic function of CPOX (EC 1.3.3.3), redundant with the EXP/IBA/IEA/TAS annotations to the same term. Reason: Core molecular function; duplicate GO id with additional evidence support is acceptable and reinforces the annotation. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway, the oxidation of coproporphyrinogen III to protoporphyrinogen IX |
| GO:0042803 protein homodimerization activity | IDA PMID:16176984 Structural basis of hereditary coproporphyria. | ACCEPT | Summary: Direct (IDA) evidence that CPOX self-associates into a homodimer, from the 1.58 A crystal structure and analytical ultracentrifugation (KD ~5 x 10^-7 M). The dimer interface, formed in part by exon-6-encoded residues (392-418), is required for the biologically active enzyme. Reason: Well-supported, informative molecular function directly demonstrated for the human enzyme; the homodimer is the functional unit. Non-core relative to catalysis but correct. Supporting Evidence: PMID:16176984 In the biologically active dimer (K(D) = 5 x 10(-7) M) file:human/CPOX/CPOX-uniprot.txt SUBUNIT: Homodimer |
| GO:0004109 coproporphyrinogen oxidase activity | TAS PMID:9888388 Systematic analysis of coproporphyrinogen oxidase gene defec... | ACCEPT | Summary: Author-stated (TAS) coproporphyrinogen oxidase activity in a systematic HCP mutation study; several disease mutations abolished or dramatically reduced CPO activity when expressed in a prokaryotic system, confirming the catalytic function. Reason: Core catalytic function, supported by functional assessment of disease mutations; concordant with the EXP/IDA/IBA evidence. Supporting Evidence: PMID:9888388 These mutations resulted in the absence or a dramatic decrease of CPO activity |
| GO:0005739 mitochondrion | TAS PMID:8407975 Coproporphyrinogen oxidase. Purification, molecular cloning,... | ACCEPT | Summary: Author-stated (TAS) mitochondrial localization: purification/cloning work showed CPO activity is mainly present in mitochondria of transfected cells, establishing that mammalian coproporphyrinogen oxidase is a mitochondrial enzyme. Reason: Directly supports mitochondrial localization; concordant with IDA/HTP/IMS annotations. Supporting Evidence: PMID:8407975 mammalian coproporphyrinogen oxidase is mitochondrial enzyme |
| GO:0006783 heme biosynthetic process | TAS PMID:8159699 Molecular cloning, sequencing, and functional expression of ... | ACCEPT | Summary: Author-stated (TAS) participation in heme biosynthesis: CPO catalyzes the sixth step of the heme biosynthetic pathway. This is the core biological process for CPOX. Reason: Core biological process, directly stated by the primary functional-expression paper and concordant with all other evidence. Supporting Evidence: PMID:8159699 Coproporphyrinogen oxidase (EC 1.3.3.3) catalyzes the sixth step in the heme biosynthetic pathway |
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Download this section (compressed HTML)Q: What is the physiological basis for the mitochondrial intermembrane-space localization, and how is coproporphyrinogen III delivered from the cytosol and protoporphyrinogen IX handed off to the inner-membrane protoporphyrinogen oxidase (PPOX)?
Q: Why do a small subset of CPOX mutations (e.g. K404E, H327R) produce the erythropoietic harderoporphyria phenotype rather than classic hereditary coproporphyria?
Experiment: Steady-state and single-turnover kinetics of purified recombinant human CPOX homodimer to define the two sequential decarboxylation steps and the role of O2 as electron acceptor.
Experiment: Structure-guided mutagenesis of the exon-6-encoded dimer interface (residues 392-418) and active-site residues (Ser-244, His-258, Asn-260, Arg-262, Asp-282, Arg-332) to correlate dimerization/catalysis with HCP vs HARPO disease phenotypes.
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