P3H1 (prolyl 3-hydroxylase 1; gene LEPRE1, also known as leprecan-1 and growth suppressor 1) is an endoplasmic-reticulum-lumenal 2-oxoglutarate/Fe(II)-dependent dioxygenase (EC 1.14.11.7) of the leprecan family. It catalyzes the post-translational formation of 3-hydroxyproline at specific -Xaa-Pro-Gly- prolines in procollagen chains, most notably the alpha1(I)Pro986 residue of type I and type II collagen, a modification required for proper collagen triple-helix folding, assembly and stability. P3H1 is the catalytic core of the ER collagen prolyl 3-hydroxylation complex (the "PCP complex"), a 1:1:1 ternary assembly with cartilage-associated protein (CRTAP) and peptidyl-prolyl cis-trans isomerase B (PPIB/cyclophilin B). Within this complex P3H1 contributes prolyl 3-hydroxylase activity while PPIB provides cis-trans isomerase activity and CRTAP stabilizes the assembly and helps recruit collagen substrate; the complex also functions as a collagen chaperone. P3H1 carries a C-terminal KDEL ER-retrieval signal that retains it (and, with it, CRTAP) in the ER lumen. Catalysis requires a non-heme Fe(II) center, the co-substrate 2-oxoglutarate, molecular oxygen, and L-ascorbate (vitamin C) as cofactor. Loss-of-function mutations in LEPRE1 abolish alpha1(I)Pro986 3-hydroxylation, delay collagen folding and cause overmodification of the collagen helix, resulting in autosomal recessive osteogenesis imperfecta type 8 (OI8). A secreted chondroitin sulfate proteoglycan form of leprecan can also be deposited in the extracellular matrix.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: P3H1 acts in the ER lumen, where it 3-hydroxylates procollagen as part of the CRTAP/PPIB complex. The phylogenetic ER localization agrees with direct experimental evidence and the KDEL ER-retention signal. Reason: Correct site of action; corroborated by EXP/IDA ER annotations and the KDEL retention motif retaining isoform 1 in the ER. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0019797 procollagen-proline 3-dioxygenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function of P3H1, conserved across the leprecan/P3H family; it hydroxylates the 3-position of specific procollagen prolines. Reason: Defining core MF; directly demonstrated experimentally (IDA, PMID:39245686, EC 1.14.11.7) and conserved phylogenetically. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Has prolyl 3-hydroxylase activity and catalyzes the post- |
| GO:0032963 collagen metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: P3H1 participates in collagen post-translational modification/biosynthesis, a defining biological process for the gene. Reason: Correct biological process; the enzyme is required for proper collagen biosynthesis, folding and assembly and is conserved across the family. Supporting Evidence: PMID:15044469 The collagen prolyl hydroxylases are enzymes that are required for proper |
| GO:0005506 iron ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: P3H1 coordinates a catalytic non-heme Fe(II)/Fe(3+) ion in its Fe2OG dioxygenase domain (residues His587, Asp589, His659), a structural requirement for hydroxylation. Reason: Accurate cofactor-binding attribute that supports the catalytic MF; structurally demonstrated, but subsidiary to the informative procollagen-proline 3-dioxygenase activity. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Name=Fe cation; Xref=ChEBI:CHEBI:24875; |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic transfer of ER localization from the UniProt subcellular location, consistent with stronger experimental evidence. Reason: Correct compartment; redundant with EXP/IDA ER annotations. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Parent molecular function describing the 2-oxoglutarate/Fe(II) dioxygenase chemistry that incorporates molecular oxygen during proline 3-hydroxylation. Reason: Correct but generic; the specific GO:0019797 procollagen-proline 3-dioxygenase activity better captures the core function. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Reaction=L-prolyl-[collagen] + 2-oxoglutarate + O2 = trans-3-hydroxy-L- |
| GO:0019797 procollagen-proline 3-dioxygenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment of the core dioxygenase activity from the EC/Rhea mapping (EC 1.14.11.7; RHEA:22872), consistent with experimental evidence. Reason: Correct core molecular function; redundant with IDA/IBA/ISS evidence. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Reaction=L-prolyl-[collagen] + 2-oxoglutarate + O2 = trans-3-hydroxy-L- |
| GO:0031418 L-ascorbic acid binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: P3H1, like other collagen hydroxylases, uses L-ascorbate (vitamin C) as a cofactor to maintain the catalytic iron in its reduced state. Reason: Accurate cofactor-binding attribute supporting the catalytic MF; subsidiary to the core dioxygenase activity. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Name=L-ascorbate; Xref=ChEBI:CHEBI:38290; |
| GO:0032963 collagen metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based electronic assignment of the collagen metabolic process, consistent with the experimental and phylogenetic evidence. Reason: Correct biological process; redundant with IBA/ISS. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt in pro-collagen chains, a critical step for the formation of mature |
| GO:0005515 protein binding | IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma... | KEEP AS NON CORE | Summary: High-throughput crosslinking mass-spectrometry interactome capturing P3H1 with CRTAP (O75718). CRTAP is a genuine PCP complex partner, but the bare protein binding term is uninformative. Reason: Records a real interaction with the complex partner CRTAP, but bare protein binding is uninformative; complex membership is better captured by GO:0032991 and the core catalytic MF. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Q32P28; O75718: CRTAP; |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | KEEP AS NON CORE | Summary: Proteome-scale (BioPlex) affinity-purification interactome capturing the P3H1-CRTAP (O75718) interaction. The partner is biologically real; the bare term is uninformative. Reason: Real interaction with the complex partner CRTAP, but bare protein binding is uninformative and not elevated to core. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Q32P28; O75718: CRTAP; |
| GO:0005515 protein binding | IPI PMID:39245686 The structural basis for the collagen processing by human P3... | KEEP AS NON CORE | Summary: Structural study establishing P3H1's direct interactions with CRTAP (O75718) and PPIB (P23284) within the PCP ternary complex. These are the genuine, biologically central complex partners, but the bare protein binding term is uninformative. Reason: Partners CRTAP and PPIB are the real PCP complex components (demonstrated structurally), but bare protein binding does not convey the core function; captured better by GO:0032991 and GO:0019797. Supporting Evidence: PMID:39245686 P3H1 and PPIB were identified as components of an ER-associated ternary complex consisting of P3H1/CRTAP/PPIB |
| GO:0019797 procollagen-proline 3-dioxygenase activity | IDA PMID:39245686 The structural basis for the collagen processing by human P3... | ACCEPT | Summary: Direct biochemical/structural demonstration that P3H1 is the core prolyl 3-hydroxylase of the PCP complex, hydroxylating Pro986 of collagen alpha1(I); active-site mutants (H587A, D589A, H659A, R669) lose catalytic activity. Reason: Core molecular function with direct experimental (IDA) support, EC 1.14.11.7 assigned, and mutagenesis confirming the catalytic residues. Supporting Evidence: PMID:39245686 P3H1 is the core prolyl 3-hydroxylase, specially hydroxylating Pro986 |
| GO:0005783 endoplasmic reticulum | EXP PMID:19088120 Recessive osteogenesis imperfecta caused by LEPRE1 mutations... | ACCEPT | Summary: Experimental localization of the KDEL-bearing splice form (isoform 1) of P3H1 to the ER, the catalytically relevant compartment. Reason: Experimentally supported ER localization consistent with the site of action. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0050821 protein stabilization | IMP PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | ACCEPT | Summary: P3H1 and CRTAP are mutually stabilizing within the ER prolyl 3-hydroxylation complex; loss of either leads to proteasomal degradation of the other. P3H1 thus stabilizes its partner CRTAP (and the complex stabilizes/chaperones collagen). Reason: Directly supported by mutational analysis (null cells deplete both proteins; proteasome inhibitors partially rescue); reflects a genuine stabilization function of the complex. Supporting Evidence: PMID:19846465 CRTAP and P3H1 are mutually stabilized in the collagen prolyl 3-hydroxylation |
| GO:0050821 protein stabilization | IMP PMID:22615817 A novel mutation in LEPRE1 that eliminates only the KDEL ER-... | ACCEPT | Summary: A KDEL-only mutation that prevents ER retention of P3H1 impairs its function, consistent with P3H1's role in maintaining the ER collagen-modifying complex and stabilizing its components/substrate. Reason: Supported by patient mutation analysis; consistent with the genuine stabilization role of P3H1 within the ER collagen prolyl 3-hydroxylation complex. Supporting Evidence: PMID:22615817 the KDEL ER- retrieval sequence is essential for P3H1 functionality |
| GO:0031012 extracellular matrix | HDA PMID:28327460 Comprehensive proteomic characterization of stem cell-derive... | KEEP AS NON CORE | Summary: High-throughput proteomic detection of P3H1 in stem-cell-derived extracellular matrix. Consistent with the secreted chondroitin-sulfate proteoglycan (leprecan) form, but not the catalytic ER site of action. Reason: Plausible given the documented secreted ECM proteoglycan form, but a weak colocalizes_with proteomics annotation peripheral to the core ER enzymatic role. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Secreted, extracellular space, extracellular |
| GO:0005518 collagen binding | ISS PMID:15044469 Prolyl 3-hydroxylase 1, enzyme characterization and identifi... | ACCEPT | Summary: P3H1 specifically interacts with denatured/unfolded collagen, contributing to the PCP complex's substrate-binding (collagen recruitment) function. Reason: Supported by enzyme characterization (specific interaction with denatured collagen) and the structurally demonstrated collagen-binding of the complex; an informative MF. Supporting Evidence: PMID:15044469 specifically interact with denatured collagen |
| GO:0006457 protein folding | ISS PMID:15044469 Prolyl 3-hydroxylase 1, enzyme characterization and identifi... | ACCEPT | Summary: P3H1 (within the PCP complex) is required for proper collagen folding and assembly, and the complex has molecular chaperone activity. Reason: Supported by enzyme characterization and the complex's documented chaperone role; loss of P3H1 delays collagen helix folding. Supporting Evidence: PMID:15044469 required for proper |
| GO:0010976 positive regulation of neuron projection development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Electronic ISS transfer of a neuronal role from the rat leprecan ortholog (Q9R1J8). No human/primary evidence supports a neuron-projection function for P3H1, and it is tangential to its established collagen-modifying role. Reason: Ortholog-based ISS with no supporting primary evidence in the P3H1 literature reviewed; peripheral and not corroborated, so retained only as non-core. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Leucine- and proline-enriched proteoglycan 1 |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: High-throughput NK-cell membrane proteome detection. P3H1 is an ER-lumenal/secreted protein; the generic "membrane" assignment most likely reflects co-fractionation rather than a genuine integral-membrane localization. Reason: Generic, low-resolution proteomics localization inconsistent with the soluble ER-lumenal/secreted nature of P3H1; likely a contaminant/co-fractionation capture. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0005783 endoplasmic reticulum | IDA PMID:20089953 Lack of cyclophilin B in osteogenesis imperfecta with normal... | ACCEPT | Summary: Direct experimental ER localization of P3H1 from the cyclophilin B osteogenesis imperfecta study, consistent with the catalytic site of action. Reason: IDA-supported ER localization agrees with the site of collagen hydroxylation. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0019797 procollagen-proline 3-dioxygenase activity | ISS PMID:15044469 Prolyl 3-hydroxylase 1, enzyme characterization and identifi... | ACCEPT | Summary: Sequence-similarity assignment of the core prolyl 3-hydroxylase activity, transferred from the chick P3H1 ortholog and consistent with the direct human evidence. Reason: Correct core molecular function; redundant with IDA/IBA/IEA support. Supporting Evidence: PMID:15044469 required for proper |
| GO:0032963 collagen metabolic process | ISS PMID:15044469 Prolyl 3-hydroxylase 1, enzyme characterization and identifi... | ACCEPT | Summary: Sequence-similarity assignment of the collagen metabolic process, consistent with the enzyme's documented role in collagen biosynthesis and modification. Reason: Correct biological process; redundant with IBA/IEA support. Supporting Evidence: PMID:15044469 required for proper |
| GO:0032991 protein-containing complex | ISS PMID:15044469 Prolyl 3-hydroxylase 1, enzyme characterization and identifi... | ACCEPT | Summary: P3H1 exists in a tight ER-resident complex (the PCP complex with CRTAP and PPIB). This captures complex membership, now established structurally. Reason: Genuine and central complex membership; the generic parent term is the available CC capturing the PCP ternary complex. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Forms a ternary complex with PPIB (CYPB) and CRTAP, known as |
| GO:0060348 bone development | IMP PMID:22615817 A novel mutation in LEPRE1 that eliminates only the KDEL ER-... | KEEP AS NON CORE | Summary: Loss-of-function LEPRE1 mutations cause recessive osteogenesis imperfecta, reflecting P3H1's requirement for normal skeletal collagen and bone development. Reason: Bone development is a downstream physiological consequence of the core collagen 3-hydroxylation function; experimentally grounded in OI phenotype but not the core MF/BP. Supporting Evidence: PMID:17277775 crucial for bone development and collagen helix formation |
| GO:1901874 negative regulation of post-translational protein modification | IMP PMID:22615817 A novel mutation in LEPRE1 that eliminates only the KDEL ER-... | KEEP AS NON CORE | Summary: Loss of P3H1 delays collagen folding, leading to overmodification (excess lysyl hydroxylation/glycosylation) of the helix; functional P3H1 thereby limits this overmodification. Reason: An indirect, downstream description (overmodification follows delayed folding); a defensible IMP but secondary to the core hydroxylation function. Supporting Evidence: PMID:17277775 excess lysyl hydroxylation and |
| GO:0005783 endoplasmic reticulum | IDA PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | ACCEPT | Summary: Direct immunofluorescence/biochemical ER localization of P3H1 from the mutual stabilization study, consistent with its catalytic site. Reason: IDA-supported ER localization agrees with the documented compartment. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0006457 protein folding | IMP PMID:17277775 Prolyl 3-hydroxylase 1 deficiency causes a recessive metabol... | ACCEPT | Summary: P3H1 deficiency delays collagen helix folding; P3H1 (within the PCP complex) is required for proper, timely collagen folding. Reason: Supported by patient/mutation analysis showing delayed collagen folding in P3H1-null cells; reflects the complex's chaperone/folding role. Supporting Evidence: PMID:17277775 crucial for bone development and collagen helix formation |
| GO:0050708 regulation of protein secretion | IMP PMID:17277775 Prolyl 3-hydroxylase 1 deficiency causes a recessive metabol... | KEEP AS NON CORE | Summary: P3H1-null proband cells show altered collagen secretion (moderately delayed secretion but increased total collagen secretion), indicating an influence on collagen secretion. Reason: A downstream/indirect effect on collagen secretion observed in null cells; secondary to the core hydroxylation/folding function. Supporting Evidence: PMID:17277775 moderately delayed, but total collagen secretion was increased |
| GO:0060348 bone development | IMP PMID:17277775 Prolyl 3-hydroxylase 1 deficiency causes a recessive metabol... | KEEP AS NON CORE | Summary: LEPRE1 null alleles cause a recessive metabolic bone disorder resembling severe/lethal osteogenesis imperfecta, establishing P3H1 as crucial for bone development. Reason: Downstream physiological role; experimentally grounded in the OI phenotype but not the core molecular function. Supporting Evidence: PMID:17277775 crucial for bone development and collagen helix formation |
| GO:1901874 negative regulation of post-translational protein modification | IMP PMID:17277775 Prolyl 3-hydroxylase 1 deficiency causes a recessive metabol... | KEEP AS NON CORE | Summary: P3H1 deficiency leads to excess lysyl hydroxylation and glycosylation of the collagen helix; functional P3H1 limits this overmodification by enabling normal-rate folding. Reason: Indirect downstream consequence of delayed folding; a defensible IMP but secondary to the core function. Supporting Evidence: PMID:17277775 excess lysyl hydroxylation and |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: High-throughput detection of P3H1 in urinary exosomes. Consistent with the secreted proteoglycan form, but not the functional ER compartment. Reason: Proteomics localization peripheral to the core ER catalytic role; plausible given the documented secreted form but non-core. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt Secreted, extracellular space, extracellular |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-1980233 | ACCEPT | Summary: Reactome curation of P3H1 in the ER lumen, the soluble compartment where it catalyzes collagen prolyl 3-hydroxylation. Reason: Correct, specific compartment for this soluble KDEL-bearing enzyme; consistent with experimental ER evidence. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-2022073 | ACCEPT | Summary: Reactome curation of P3H1 in the ER lumen during procollagen triple-helix formation. Reason: Correct, specific compartment; redundant with experimental ER evidence. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-8948226 | ACCEPT | Summary: Reactome curation of P3H1 in the ER lumen (prolyl 3-hydroxylase complex reaction). Reason: Correct, specific compartment; redundant with experimental ER evidence. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-8948230 | ACCEPT | Summary: Reactome curation of P3H1 in the ER lumen (binding of 4-Hyp collagen propeptides). Reason: Correct, specific compartment; redundant with experimental ER evidence. Supporting Evidence: file:human/P3H1/P3H1-uniprot.txt SUBCELLULAR LOCATION: [Isoform 1]: Endoplasmic reticulum |
| GO:0008285 negative regulation of cell population proliferation | NAS PMID:10951563 Gros1, a potential growth suppressor on chromosome 1: its id... | MARK AS OVER ANNOTATED | Summary: Historical "growth suppressor 1" (Gros1) annotation from the original cloning paper, based on slowed growth of NIH3T3 cells overexpressing the cDNA. This predates and is not part of the established collagen prolyl 3-hydroxylase function. Reason: NAS, historical assertion superseded by enzymatic characterization; no mechanistic link to P3H1's established function and not corroborated by later work. Supporting Evidence: PMID:10951563 85-kDa protein into NIH3T3 cells resulted in their slow growth and reduced |
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Download this section (compressed HTML)Q: Does P3H1 have any biologically meaningful function (e.g., growth suppression) outside the PCP collagen-modifying complex, or are the historical "growth suppressor 1" and secreted proteoglycan observations independent of its enzymatic role?
Q: What determines the strict substrate specificity of P3H1 for alpha1(I)Pro986 among the many Pro-containing triplets in collagen, and how is this encoded by the collagen-binding sites of the PCP complex?
Experiment: Reconstitute the purified P3H1/CRTAP/PPIB complex with a full-length procollagen substrate and use mass spectrometry to map the complete set of 3-hydroxyproline sites and the kinetics conferred by each complex component.
Experiment: Generate catalytically dead (e.g., H587A/H659A) versus complex-assembly-deficient P3H1 knock-in cells and compare collagen 3-hydroxylation, folding kinetics, overmodification and secretion to separate the enzymatic from the chaperone/stabilization contributions.
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