Affinage

Showing P3H1 — LEPRE1 is a alias.

P3H1

Prolyl 3-hydroxylase 1 · UniProt Q32P28

Length
736 aa
Mass
83.4 kDa
Annotated
2026-06-10
33 papers in source corpus 10 papers cited in narrative 10 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

P3H1 (encoded by LEPRE1) is the catalytic subunit of an endoplasmic reticulum-resident collagen prolyl 3-hydroxylation complex that controls the folding and post-translational modification of fibrillar collagens (PMID:18566967, PMID:19862557). Together with CRTAP and cyclophilin B (PPIB), P3H1 forms a ternary complex that 3-hydroxylates Pro986 in the α1 chains of type I, II, and V collagen and additionally acts as a general collagen chaperone; loss of complex function delays collagen helix folding and causes helical overmodification by lysyl hydroxylase and prolyl 4-hydroxylase, producing osteogenesis imperfecta (PMID:18566967, PMID:19862557). Catalytic activity depends on the 736-amino-acid splice form bearing a C-terminal KDEL sequence, which retains the entire ternary complex in the ER through binding of the P3H1 N-terminal domain to CRTAP; loss of KDEL causes co-secretion of P3H1 and CRTAP and is sufficient to cause disease (PMID:19088120, PMID:22615817, PMID:30993352). Cryo-EM structures show that the P3H1 and PPIB active sites form a face-to-face bifunctional reaction center, coupling prolyl 3-hydroxylation to prolyl cis-trans isomerization across a collagen substrate interaction zone, with the complex adopting both ternary and dimer-of-trimers states (PMID:39245686). In vivo, p3h1 knockout in zebrafish recapitulates intracellular collagen overmodification, partial ER retention, and disorganized extracellular fibrils, establishing the chaperone defect as the primary driver of the skeletal phenotype (PMID:32173581).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1999 Medium

    Established that P3H1 (leprecan) is an ER-associated, KDEL-bearing protein localizing to basement membranes, placing it in the secretory pathway rather than being purely extracellular.

    Evidence cDNA expression screening, chondroitinase digestion and Western blotting, tissue immunostaining and expression in CHO cells

    PMID:10455179

    Open questions at the time
    • No enzymatic activity demonstrated
    • Functional role in collagen biology not yet identified
  2. 2000 Medium

    Initial functional characterization framed P3H1 as a growth suppressor, an interpretation later superseded by its enzymatic role in collagen maturation.

    Evidence Stable sense/antisense transfection with growth and colony-formation assays in NIH3T3 cells

    PMID:10951563

    Open questions at the time
    • Growth-suppressor phenotype not mechanistically linked to collagen function
    • Single cell line, single lab
  3. 2001 Low

    Predicted that P3H1 is a 2-oxoglutarate- and Fe(II)-dependent dioxygenase, providing the first hypothesis that it is a protein hydroxylase.

    Evidence Computational sequence profile analysis / fold recognition

    PMID:11276424

    Open questions at the time
    • Computational prediction only, no biochemical validation
    • Substrate not identified
  4. 2008 High

    Defined the molecular function and disease link by showing P3H1 acts in a complex with CRTAP and PPIB to 3-hydroxylate Pro986 of collagen α1 chains, with loss-of-function abolishing this modification and causing overmodification consistent with delayed helix folding.

    Evidence Biochemical collagen modification assays (SDS-urea-PAGE) and mutation analysis in patient fibroblasts

    PMID:18566967 PMID:19088120

    Open questions at the time
    • Structural basis of catalysis unresolved
    • Mechanism coupling hydroxylation to folding not defined
  5. 2009 High

    Extended the complex's substrate range to types I, II, and V collagen and established a general chaperone role beyond catalysis, linking absent complex function to broad collagen overmodification.

    Evidence Analysis of LEPRE1/CRTAP-null patient cells with collagen modification profiling

    PMID:19862557

    Open questions at the time
    • Chaperone activity not separated from catalytic activity
    • No in vivo validation
  6. 2012 Medium

    Demonstrated that the C-terminal KDEL ER-retention signal is required for P3H1 function, since a KDEL-only mutation causes secretion and disease.

    Evidence RNA analysis, real-time PCR, and protein localization/secretion studies in compound heterozygous patient fibroblasts

    PMID:22615817

    Open questions at the time
    • Effect on the full ternary complex not yet defined
    • Single lab
  7. 2019 High

    Resolved the assembly mechanism, showing KDEL retains the whole ternary complex via P3H1 N-terminal binding to CRTAP and mapping PPIB interface residues, with a disease PPIB mutation disrupting assembly independent of isomerase activity.

    Evidence KDEL-deletion and co-secretion assays, cysteine modification, chemical crosslinking, and mass spectrometry

    PMID:30993352

    Open questions at the time
    • Atomic-resolution architecture not yet determined
    • Coupling of catalytic and isomerase activities not shown
  8. 2020 High

    Provided in vivo causal evidence that loss of the P3H1/CRTAP complex drives the skeletal phenotype through intracellular collagen overmodification, ER retention, and disorganized extracellular fibrils.

    Evidence CRISPR/Cas9 p3h1 knockout zebrafish with electron microscopy and collagen modification biochemistry

    PMID:32173581

    Open questions at the time
    • Single vertebrate model
    • Direct enzymatic-versus-chaperone contribution not dissected in vivo
  9. 2024 High

    Defined the structural mechanism, showing P3H1 and PPIB active sites form a face-to-face bifunctional reaction center coupling hydroxylation with prolyl isomerization, with a collagen substrate interaction zone and a ternary/dimer-of-trimers equilibrium tunable by active-site mutation and inhibitors.

    Evidence Cryo-EM of ternary and collagen peptide-bound complexes with active-site mutagenesis and PPIB inhibitor treatment

    PMID:39245686

    Open questions at the time
    • Functional significance of the dimer-of-trimers state in vivo unresolved
    • Dynamics of collagen threading through the reaction center not directly observed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the catalytic 3-hydroxylation and chaperone/isomerase activities are individually weighted in collagen folding fidelity, and how the structurally observed complex-state equilibrium is regulated in cells, remain open.
  • No separation of catalytic versus chaperone contributions to disease
  • Regulation of ternary vs dimer-of-trimers state in vivo unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016491 oxidoreductase activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0044183 protein folding chaperone 2
Localization
GO:0005783 endoplasmic reticulum 3
Pathway
R-HSA-1474244 Extracellular matrix organization 3 R-HSA-392499 Metabolism of proteins 2
Partners
CRTAPPPIB
Complex memberships
P3H1/CRTAP/PPIB collagen prolyl 3-hydroxylation complex

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 Leprecan (P3H1) was identified as a novel chondroitin sulfate proteoglycan core protein (~100 kDa) that localizes to basement membranes and contains a KDEL endoplasmic reticulum retrieval signal, suggesting participation in the secretory pathway in addition to its extracellular matrix role. Expression screening of cDNA library, Western blotting with chondroitinase ABC digestion, immunostaining of tissue sections, expression in CHO K-1 cells The Journal of biological chemistry Medium 10455179
2001 Sequence profile analysis predicted that leprecan (P3H1) belongs to the 2-oxoglutarate- and Fe(II)-dependent dioxygenase superfamily and is a novel protein hydroxylase, potentially involved in generating substrates for protein glycosylation. Computational sequence profile analysis / fold recognition Genome biology Low 11276424
2000 Gros1/leprecan (P3H1) functions as a growth suppressor: stable transfection of the 85-kDa isoform into NIH3T3 cells caused slow growth and reduced colony-forming efficiency, while antisense expression increased colony-forming efficiency. Stable transfection with growth and colony formation assays in NIH3T3 cells Oncogene Medium 10951563
2008 P3H1 (encoded by LEPRE1) forms a complex with CRTAP and cyclophilin B (CypB/PPIB) in the endoplasmic reticulum that catalyzes prolyl 3-hydroxylation of Pro986 in the α1 chains of type I and type II collagen. Loss-of-function mutations in LEPRE1 abolish Pro986 hydroxylation and cause helical overmodification of type I collagen, indicating delayed helix folding. Biochemical analysis of patient fibroblasts (SDS-urea-PAGE, collagen modification assays), genetic mutation identification Human mutation High 18566967
2008 The prolyl 3-hydroxylation activity of P3H1 is restricted to the 736-amino acid splice form that contains the KDEL ER retention signal; a splice-site mutation affecting only this isoform abolishes Pro986 3-hydroxylation and causes overmodification of type I procollagen chains. Western blotting, immunocytochemistry, mass spectrometry, SDS-urea-PAGE of patient fibroblasts, RNA splice-form analysis Journal of medical genetics High 19088120
2009 CRTAP and P3H1, together with cyclophilin B (PPIB), comprise the collagen prolyl 3-hydroxylation complex that catalyzes post-translational hydroxylation of Pro986 in types I, II, and V collagen, and additionally acts as a general collagen chaperone. Absence of complex function delays collagen helix folding, causing overmodification by lysyl hydroxylase and prolyl 4-hydroxylase. Analysis of patient cells with LEPRE1/CRTAP null mutations; collagen biochemical assays (SDS-urea-PAGE, modification profiling) Cell and tissue research High 19862557
2012 The KDEL ER-retrieval sequence at the C-terminus of P3H1 is essential for its functionality; a mutation that eliminates only the KDEL sequence (while leaving other functional domains intact) causes P3H1 to be secreted from the ER and is sufficient for disease onset, demonstrating the KDEL sequence is required for ER retention and prolyl 3-hydroxylase activity. RNA analysis, real-time PCR, protein localization/secretion studies in patient fibroblasts with compound heterozygous LEPRE1 mutations PloS one Medium 22615817
2019 The KDEL sequence of P3H1 is essential for retaining the entire P3H1/CRTAP/PPIB ternary complex in the ER; its removal causes co-secretion of P3H1 and CRTAP mediated by binding of the P3H1 N-terminal domain with CRTAP. PPIB binds with its C-terminus close to both P3H1 and CRTAP in the ternary complex, and PPIB surface residues involved in complex formation were identified. A disease-associated PPIB mutation on the binding interface disrupts ternary complex formation without affecting PPIB prolyl-isomerase activity. KDEL deletion constructs, co-secretion assays, cysteine modification, chemical crosslinking, mass spectrometry Cellular and molecular life sciences : CMLS High 30993352
2020 In zebrafish lacking p3h1 (CRISPR/Cas9 knockout), absence of the P3H1/CRTAP complex causes intracellular overmodification and partial ER retention of type I collagen (enlarged ER cisternae), and extracellular assembly of collagen into disorganized fibers with altered diameter, supporting the defective chaperone role of the 3-hydroxylation complex as the primary cause of the skeletal OI phenotype. CRISPR/Cas9 knockout zebrafish, electron microscopy of ER and collagen fibers, collagen modification biochemistry Matrix biology : journal of the International Society for Matrix Biology High 32173581
2024 Cryo-EM structures of the P3H1/CRTAP/PPIB ternary complex revealed that the active sites of P3H1 and PPIB form a face-to-face bifunctional reaction center, indicating a coupled prolyl hydroxylation and prolyl isomerization mechanism. A P3H1/CRTAP/PPIB/collagen peptide complex structure identified multiple collagen binding sites forming a substrate interaction zone. A dual-ternary (dimer-of-trimers) complex state was observed, and its balance with the ternary state is altered by mutations in the P3H1/PPIB active site and by PPIB inhibitors. Cryo-EM structure determination of ternary and collagen peptide-bound complexes, active-site mutagenesis, PPIB inhibitor treatment Nature communications High 39245686

Source papers

Stage 0 corpus · 33 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2001 The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome biology 361 11276424
2008 CRTAP and LEPRE1 mutations in recessive osteogenesis imperfecta. Human mutation 173 18566967
2009 Null mutations in LEPRE1 and CRTAP cause severe recessive osteogenesis imperfecta. Cell and tissue research 85 19862557
2008 Recessive osteogenesis imperfecta caused by LEPRE1 mutations: clinical documentation and identification of the splice form responsible for prolyl 3-hydroxylation. Journal of medical genetics 68 19088120
2011 The identification of novel mutations in COL1A1, COL1A2, and LEPRE1 genes in Chinese patients with osteogenesis imperfecta. Journal of bone and mineral metabolism 59 21667357
1999 Molecular characterization of a novel basement membrane-associated proteoglycan, leprecan. The Journal of biological chemistry 51 10455179
2012 A founder mutation in LEPRE1 carried by 1.5% of West Africans and 0.4% of African Americans causes lethal recessive osteogenesis imperfecta. Genetics in medicine : official journal of the American College of Medical Genetics 41 22281939
2020 Crtap and p3h1 knock out zebrafish support defective collagen chaperoning as the cause of their osteogenesis imperfecta phenotype. Matrix biology : journal of the International Society for Matrix Biology 34 32173581
2009 The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Developmental biology 32 19217895
2004 LEPREL1, a novel ER and Golgi resident member of the Leprecan family. Biochemical and biophysical research communications 31 15063763
2000 Gros1, a potential growth suppressor on chromosome 1: its identity to basement membrane-associated proteoglycan, leprecan. Oncogene 30 10951563
2012 A novel mutation in LEPRE1 that eliminates only the KDEL ER- retrieval sequence causes non-lethal osteogenesis imperfecta. PloS one 28 22615817
2013 Allelic background of LEPRE1 mutations that cause recessive forms of osteogenesis imperfecta in different populations. Molecular genetics & genomic medicine 20 24498616
2015 Mutational characterization of the P3H1/CRTAP/CypB complex in recessive osteogenesis imperfecta. Genetics and molecular research : GMR 16 26634552
2010 Lethal/severe osteogenesis imperfecta in a large family: a novel homozygous LEPRE1 mutation and bone histological findings. Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society 14 20946018
2013 Osteogenesis imperfecta due to compound heterozygosity for the LEPRE1 gene. Fetal and pediatric pathology 13 23301918
2019 Characterization of PPIB interaction in the P3H1 ternary complex and implications for its pathological mutations. Cellular and molecular life sciences : CMLS 12 30993352
2024 The structural basis for the collagen processing by human P3H1/CRTAP/PPIB ternary complex. Nature communications 11 39245686
2022 Biomarker LEPRE1 induces pelitinib-specific drug responsiveness by regulating ABCG2 expression and tumor transition states in human leukemia and lung cancer. Scientific reports 9 35190588
2007 Leprecan distribution in the developing and adult kidney. Kidney international 8 17495866
2021 A novel P3H1 mutation is associated with osteogenesis imperfecta type VIII and dental anomalies. Oral surgery, oral medicine, oral pathology and oral radiology 7 33737016
2016 Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII. Clinica chimica acta; international journal of clinical chemistry 7 27864101
2020 Upregulated LEPRE1 correlates with poor outcome and its knockdown attenuates cells proliferation, migration and invasion in osteosarcoma. Anti-cancer drugs 6 32197005
2022 Phenotypic Variation in Vietnamese Osteogenesis Imperfecta Patients Sharing a Recessive P3H1 Pathogenic Variant. Genes 5 35327962
2021 Severe cases of osteogenesis imperfecta type VIII due to a homozygous mutation in P3H1 (LEPRE1) and review of the literature. Advances in clinical and experimental medicine : official organ Wroclaw Medical University 5 34637196
2018 Expression characterization and functional implication of the collagen-modifying Leprecan proteins in mouse gonadal tissue and mature sperm. AIMS genetics 5 30417103
2024 Pan-Cancer Analysis of P3H1 and Experimental Validation in Renal Clear Cell Carcinoma. Applied biochemistry and biotechnology 4 38175417
2023 A Founder Intronic Variant in P3H1 Likely Results in Aberrant Splicing and Protein Truncation in Patients of Karen Descent with Osteogenesis Imperfecta Type VIII. Genes 3 36833249
2023 Milder presentation of osteogenesis imperfecta type VIII due to compound heterozygosity for a predicted loss-of-function variant and novel missense variant in P3H1-further expansion of the phenotypic spectrum. Cold Spring Harbor molecular case studies 3 36963805
2025 P3H1 promotes malignant progression of esophageal squamous cell carcinoma (ESCC) and modulates the immune microenvironment. Journal of thoracic disease 1 41229743
2026 Prolyl 3-hydroxylase 1 (P3H1) deficient osteogenesis imperfecta with vascular malformations: a rare disorder with atypical features. JBMR plus 0 42170682
2025 Rare Variants in the P3H1 Gene in Patients With Osteogenesis Imperfecta of Bashkir Origin From Russia. Clinical genetics 0 41499654
2024 A non-lethal presentation of osteogenesis imperfecta type VIII due to homozygous mutation in P3H1 gene. BMJ case reports 0 39455078

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