P4HA2 (prolyl 4-hydroxylase subunit alpha-2) is one of three catalytic alpha-subunit isoforms of collagen prolyl 4-hydroxylase (C-P4H), an endoplasmic reticulum-lumenal enzyme. The active enzyme is an alpha2-beta2 heterotetramer in which the beta subunit is P4HB (protein disulfide isomerase, PDI) acting as a structural and ER-retention subunit; the two alpha-2 chains carry the catalytic sites. As a 2-oxoglutarate- and Fe(II)-dependent dioxygenase, P4HA2 catalyzes the post-translational formation of trans-4-hydroxy-L-proline in -Xaa-Pro-Gly- sequences of procollagen (and other proteins), consuming 2-oxoglutarate and O2 and producing succinate and CO2. 4-Hydroxyproline is essential for the folding and thermal stability of the collagen triple helix. The active-site iron is coordinated by a 2-His-1-carboxylate facial triad, and L-ascorbate (vitamin C) is required as a cofactor to maintain the iron in the reduced Fe(II) state. The type II tetramer contributes a substantial fraction of total prolyl 4-hydroxylase activity in human cells, is expressed in heart, placenta, lung and pancreas, and does not co-assemble with the type I (P4HA1) alpha subunit into mixed tetramers. Variants in P4HA2 cause autosomal dominant nonsyndromic high myopia (MYP25), consistent with a role in scleral collagen and extracellular matrix.
Definition: The hydroxylation of peptidyl-proline to peptidyl-4-hydroxy-L-proline catalyzed by P4HA2 as part of collagen biosynthesis (corresponds to the existing term GO:0018401).
Justification: No biological-process annotation is currently present in GOA. The core activity of P4HA2 directly accomplishes peptidyl-proline 4-hydroxylation as part of collagen biosynthesis; existing terms GO:0019471 (peptidyl-proline hydroxylation), GO:0018401 (peptidyl-proline hydroxylation to 4-hydroxy-L-proline) and GO:0032964 (collagen biosynthetic process) would appropriately capture the biological process and should be added rather than newly coined.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004656 procollagen-proline 4-dioxygenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of the core collagen prolyl 4-hydroxylase activity, conserved across the P4HA family (P4HA1/2/3 and orthologs). This is the defining molecular function of P4HA2. Reason: Core molecular function; concordant with direct experimental (IDA, PMID:9211872), TAS and IEA evidence and EC 1.14.11.2. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Catalyzes the post-translational formation of 4-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins. |
| GO:0016222 procollagen-proline 4-dioxygenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: P4HA2 is part of the prolyl 4-hydroxylase complex, the alpha2-beta2 heterotetramer formed with P4HB (PDI). Phylogenetic inference is consistent with the experimentally documented tetramer. Reason: Correct complex; P4HA2 assembles with P4HB into the catalytic C-P4H heterotetramer, the cellular form of the enzyme. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Heterotetramer of two alpha-2 chains and two beta chains (P4HB) |
| GO:0004656 procollagen-proline 4-dioxygenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment of the core dioxygenase activity (RHEA:18945, EC 1.14.11.2), redundant with the experimental IDA annotation. Reason: Correct core molecular function; concordant with experimental evidence. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt EC=1.14.11.2 |
| GO:0005506 iron ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: P4HA2 binds one Fe(2+) ion per subunit via a 2-His-1-carboxylate facial triad (His430, Asp432, His501) in the Fe2OG dioxygenase domain; iron binding is essential for the dioxygenase chemistry. Reason: Accurate cofactor and active-site chemistry directly supported by the UniProt cofactor line and metal-binding residues; integral to the catalytic mechanism. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Binds 1 Fe(2+) ion per subunit. |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment of ER localization, consistent with the documented ER-lumenal residence of the enzyme. Reason: Correct compartment; concordant with the UniProt subcellular location and the HPA IDA ER annotation. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. |
| GO:0005788 endoplasmic reticulum lumen | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location vocabulary mapping to ER lumen, the precise compartment in which the soluble C-P4H tetramer acts on procollagen. Reason: Correct and more specific than ER; matches the UniProt subcellular location. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. |
| GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | IEA GO_REF:0000002 | ACCEPT | Summary: General dioxygenase parent term capturing the O2-incorporating oxidoreductase chemistry of the 2-oxoglutarate/Fe(II)-dependent reaction. Reason: Correct parent of the specific procollagen-proline 4-dioxygenase activity; accurately describes the enzyme oxidoreductase class. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Reaction=L-prolyl-[collagen] + 2-oxoglutarate + O2 = trans-4-hydroxy-L-prolyl-[collagen] + succinate + CO2 |
| GO:0031418 L-ascorbic acid binding | IEA GO_REF:0000002 | ACCEPT | Summary: L-ascorbate (vitamin C) is a required cofactor that maintains the active-site iron in the reduced Fe(2+) state; ascorbate binding is a documented property of the enzyme. Reason: Accurate cofactor binding directly supported by the UniProt cofactor line; mechanistically integral to sustained catalysis. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Name=L-ascorbate |
| GO:0005515 protein binding | IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma... | KEEP AS NON CORE | Summary: High-throughput crosslinking mass spectrometry (histone interaction landscapes in intact nuclei) capturing P4HA2 interactions with P4HB (the beta subunit of the tetramer) and P4HA1 (the paralogous alpha isoform). The bare protein binding term is uninformative. Reason: Records real IntAct captures (P4HB, P4HA1) but bare protein binding is uninformative per curation guidelines; the meaningful P4HB interaction is better represented by the complex annotation. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt O15460; P07237: P4HB |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | KEEP AS NON CORE | Summary: BioPlex/dual proteome-scale interactome screen capturing P4HA2 interactions with P4HB and KIF7. Bare protein binding term is uninformative. Reason: High-throughput interactome capture; P4HB is the genuine beta subunit but bare protein binding adds no functional specificity, and the KIF7 capture has no established biological meaning for an ER-lumenal enzyme. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt O15460; P07237: P4HB |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | KEEP AS NON CORE | Summary: OpenCell endogenous-tagging interactome capturing a P4HA2-KIF7 (Q2M1P5) interaction. Bare protein binding term is uninformative. Reason: High-throughput capture of an interaction without established functional relevance to the collagen-hydroxylation role of P4HA2; bare protein binding is uninformative. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt O15460; Q2M1P5: KIF7 |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | KEEP AS NON CORE | Summary: Multimodal cell-maps interactome capturing P4HA2 interactions with P4HB, P4HA1 and KIF7. Bare protein binding term is uninformative. Reason: High-throughput interactome capture; the P4HB/P4HA1 captures are consistent with known biology but bare protein binding is uninformative per curation guidelines. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt O15460; P13674: P4HA1 |
| GO:0016222 procollagen-proline 4-dioxygenase complex | IEA GO_REF:0000107 | ACCEPT | Summary: Ortholog-based electronic transfer of membership in the prolyl 4-hydroxylase complex, consistent with the experimentally documented alpha2-beta2 tetramer. Reason: Correct complex membership; redundant with the IBA complex annotation and the UniProt subunit description. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt Heterotetramer of two alpha-2 chains and two beta chains (P4HB) |
| GO:0005783 endoplasmic reticulum | IDA GO_REF:0000052 | ACCEPT | Summary: Direct immunofluorescence (HPA) evidence for ER localization of P4HA2, consistent with its ER-lumenal site of action. Reason: IDA-supported ER localization agrees with the UniProt subcellular location. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. |
| GO:0004656 procollagen-proline 4-dioxygenase activity | IDA PMID:9211872 Cloning of the human prolyl 4-hydroxylase alpha subunit isof... | ACCEPT | Summary: Direct experimental characterization of the purified human type II (P4HA2) enzyme tetramer demonstrating procollagen-proline 4-dioxygenase activity. This is the core molecular function. Reason: Core molecular function with direct experimental (IDA) support; the purified (alpha-II)2-beta2 tetramer hydroxylates collagen prolines. Supporting Evidence: PMID:9211872 Prolyl 4-hydroxylase (proline hydroxylase, EC 1.14.11.2) catalyzes the formation of 4-hydroxyproline in collagens. |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-1650808 | ACCEPT | Summary: Reactome curation placing the prolyl 4-hydroxylase reaction in the ER lumen (collagen biosynthesis pathway). Reason: Correct compartment; redundant with the UniProt subcellular location and the IEA/IDA ER annotations. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-9918779 | ACCEPT | Summary: Reactome curation of proline hydroxylase activity in the ER lumen (here in a viral polyprotein-maturation context); the compartment assignment is correct. Reason: Correct ER-lumenal compartment; redundant with stronger localization evidence. Supporting Evidence: file:human/P4HA2/P4HA2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. |
| GO:0009055 electron transfer activity | TAS PMID:9211872 Cloning of the human prolyl 4-hydroxylase alpha subunit isof... | MARK AS OVER ANNOTATED | Summary: P4HA2 is a 2-oxoglutarate/Fe(II)-dependent dioxygenase; although its chemistry is redox-based and ascorbate-dependent, GO:0009055 (electron transfer activity) denotes electron-carrier function in electron transport chains and is a poor fit. The cited paper characterizes the dioxygenase, not an electron-carrier activity. Reason: Over-interpretation of the redox/ascorbate chemistry of the enzyme; the informative molecular function is the dioxygenase activity (GO:0004656 / GO:0016705), not electron transfer/carrier activity. Supporting Evidence: PMID:9211872 Prolyl 4-hydroxylase (proline hydroxylase, EC 1.14.11.2) catalyzes the formation of 4-hydroxyproline in collagens. |
| GO:0004656 procollagen-proline 4-dioxygenase activity | TAS PMID:9211872 Cloning of the human prolyl 4-hydroxylase alpha subunit isof... | ACCEPT | Summary: Author-asserted procollagen-proline 4-dioxygenase activity for the type II enzyme, redundant with the IDA annotation from the same study. Reason: Correct core molecular function; concordant with the experimental IDA annotation and EC 1.14.11.2. Supporting Evidence: PMID:9211872 Prolyl 4-hydroxylase (proline hydroxylase, EC 1.14.11.2) catalyzes the formation of 4-hydroxyproline in collagens. |
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Download this section (compressed HTML)Q: Do the type I (P4HA1) and type II (P4HA2) collagen prolyl 4-hydroxylases have distinct procollagen substrate or tissue preferences that explain why P4HA2 deficiency manifests primarily as scleral/ocular (high myopia) rather than systemic connective-tissue disease?
Q: Does the high-throughput KIF7 interaction reflect a genuine extra-catalytic role for P4HA2, or is it an incidental interactome capture?
Experiment: Reconstitute the recombinant (alpha-II)2-beta2 tetramer and measure steady-state kinetics on defined procollagen peptide substrates, comparing P4HA2 with P4HA1 to define isoenzyme-specific substrate preferences.
Experiment: Knock out or knock down P4HA2 in scleral fibroblasts and quantify collagen 4-hydroxyproline content, triple-helix thermal stability and ECM deposition to test the mechanistic link to high myopia.
Experiment: Express the MYP25 variants (e.g. E291K) and assay protein abundance, tetramer assembly with P4HB, and residual dioxygenase activity to clarify the loss-of-function mechanism.
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