Affinage

P3H3

Prolyl 3-hydroxylase 3 · UniProt Q8IVL6

Length
736 aa
Mass
81.8 kDa
Annotated
2026-06-10
19 papers in source corpus 12 papers cited in narrative 12 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/6 claims corpus-supported (83%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

P3H3 is an endoplasmic reticulum-resident member of the prolyl 3-hydroxylase family that, despite its sequence-predicted prolyl 3-hydroxylase identity (PMID:15044469), functions principally as a regulator of collagen lysyl hydroxylation at helical cross-linking sites rather than as a canonical 3Hyp-forming enzyme (PMID:28115524). P3h3-null mice show collagen lysine under-hydroxylation specifically at helical-domain cross-linking sites across skin, bone, tendon, aorta, and cornea — phenocopying EDS type VIA — with abnormal cross-link chemistry and a reversed bone HP/LP cross-link ratio, but no detectable defect at known prolyl 3-hydroxylation sites (PMID:28115524). This activity is exerted through a stable ER complex with SC65 and lysyl hydroxylase 1 (LH1), whose loss produces defective collagen lysyl hydroxylation, low bone mass, and skin fragility (PMID:30417103). P3H3 and LH1 act through distinct mechanisms: P3H3 selectively controls cross-link-site hydroxylation in type I collagen and additional sites in type V collagen, where LH1 is dispensable (PMID:33631195). P3H3 also participates in a feedback network of collagen biosynthesis, being upregulated when P3H1 activity is lost (PMID:41932442). Independently, P3H3 acts as a tumor suppressor: its endogenous silencing in breast, melanoma, and lung cancers is reversed by ectopic expression, which suppresses proliferation, colony formation, migration, and invasion and induces G2/M arrest and apoptosis (PMID:19436308, PMID:30452903, PMID:29277505), and it functions downstream of the transcription factor ZNF334 to suppress epithelial-to-mesenchymal transition in cervical cancer (PMID:38954116).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2004 Low

    Established P3H3's molecular identity by placing it in the prolyl 3-hydroxylase family, framing the initial expectation that it is a collagen prolyl 3-hydroxylase enzyme.

    Evidence Primary sequence analysis comparing conserved active-site residues with P3H1/P4H/LH enzymes

    PMID:15044469

    Open questions at the time
    • No enzymatic assay performed on P3H3 itself
    • Predicted activity not confirmed; later work shows it does not act at 3Hyp sites
  2. 2014 Low

    Began linking P3H3 to a defined functional partner by showing co-expression with SC65 in the ER of collagen-rich tissues, setting up a complex hypothesis.

    Evidence Immunolocalization and co-expression analysis in Sc65-KO and wild-type tissues

    PMID:23959653

    Open questions at the time
    • P3H3-specific localization inferred from related protein SC65
    • Direct complex formation not demonstrated here
  3. 2017 High

    Overturned the assumption that P3H3 is a prolyl 3-hydroxylase by demonstrating in vivo that it instead controls collagen lysyl hydroxylation at helical cross-linking sites, with loss phenocopying EDS type VIA.

    Evidence P3h3 knockout mouse with tandem MS of collagen PTMs, SDS-PAGE chain analysis, and cross-link chemistry across multiple tissues

    PMID:28115524

    Open questions at the time
    • Molecular mechanism by which P3H3 directs LH activity to cross-link sites not resolved
    • Whether P3H3 has any direct catalytic role unclear
  4. 2018 Medium

    Identified the protein assembly underlying P3H3 function — a stable ER complex with SC65 and LH1 whose disruption causes defective lysyl hydroxylation, low bone mass, and skin fragility.

    Evidence Co-complex biochemical characterization and KO mouse phenotyping with collagen PTM readouts

    PMID:30417103

    Open questions at the time
    • Single lab with limited methodological detail
    • Stoichiometry and structural basis of the complex not defined
  5. 2021 High

    Resolved how P3H3 and LH1 divide labor, showing P3H3 specifically governs cross-link-site hydroxylation and type V collagen sites that LH1 does not require.

    Evidence Site-resolved tandem MS comparing hydroxylysine in type I and V collagen from P3H3-null, LH1-null, and wild-type mice

    PMID:33631195

    Open questions at the time
    • Biochemical basis for differential collagen-type and site recognition not defined
    • Direct enzymatic contribution of P3H3 vs partner enzymes unresolved
  6. 2026 Medium

    Placed P3H3 within a regulatory feedback network of collagen biosynthesis by showing its protein levels rise compensatorily when P3H1 is lost.

    Evidence P3H1 KO mouse tendon and P3H1 siRNA knockdown in human lung fibroblasts with proteomics and expression analysis

    PMID:41932442

    Open questions at the time
    • Mechanism of compensatory upregulation unknown
    • Functional sufficiency of compensation not tested
  7. 2009 Medium

    Opened a second functional axis by establishing P3H3 as a tumor suppressor whose ectopic re-expression suppresses colony growth in epigenetically silenced breast cancer cells.

    Evidence Ectopic expression in silenced breast cancer cell lines with colony formation assay

    PMID:19436308

    Open questions at the time
    • Single method, single lab
    • Molecular mechanism of growth suppression not defined
  8. 2017 Medium

    Extended the tumor-suppressor role to lung cancer with mechanistic readouts, linking P3H3 to G2/M arrest and apoptosis via p21, cyclin A1, and caspase changes.

    Evidence Bidirectional ectopic expression and knockdown in lung cancer cells with proliferation, migration/invasion, cell cycle, caspase, and western blot assays

    PMID:29277505

    Open questions at the time
    • Connection between collagen-modifying ER role and cell cycle control unexplained
    • Single lab
  9. 2018 Medium

    Generalized the tumor-suppressor function to a third cancer type, showing P3H3 re-expression inhibits melanoma proliferation where the gene is methylation-silenced.

    Evidence Ectopic expression in melanoma cell lines with proliferation assays

    PMID:30452903

    Open questions at the time
    • Mechanism not dissected
    • No in vivo tumor model
  10. 2024 Medium

    Identified an upstream transcriptional regulator, placing P3H3 downstream of ZNF334 in an EMT-suppressive pathway in cervical cancer.

    Evidence Dual-luciferase reporter and ChIP showing direct regulation; P3H3 siRNA with EMT phenotype readout

    PMID:38954116

    Open questions at the time
    • Effector mechanism by which P3H3 suppresses EMT unknown
    • Whether enzymatic/collagen function underlies the tumor phenotype untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Whether the ER collagen-cross-link function and the tumor-suppressor/EMT function of P3H3 are mechanistically connected, and what direct biochemical activity P3H3 itself contributes within the SC65–LH1 complex, remains unresolved.
  • No structural model of the SC65–P3H3–LH1 complex
  • Direct catalytic activity of P3H3 not demonstrated
  • Mechanistic link between collagen role and cancer phenotype unestablished

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 2
Localization
GO:0005783 endoplasmic reticulum 2
Pathway
R-HSA-1474244 Extracellular matrix organization 2
Partners
P3H1PLOD1SC65
Complex memberships
SC65–P3H3–LH1 ER complex

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 P3H3 (then called GRCB) was identified as a member of the prolyl 3-hydroxylase family, sharing conserved active-site residues with prolyl 4-hydroxylase and lysyl hydroxylase, and predicted to function as a collagen prolyl 3-hydroxylase enzyme residing in the endoplasmic reticulum. Primary sequence analysis, conserved active-site residue comparison with characterized P3H1/P4H/LH enzymes The Journal of biological chemistry Low 15044469
2013 P3H3 is a member of the prolyl 3-hydroxylase family (together with P3H1 and P3H2) that has evolved different collagen substrate site and tissue specificities; the family is responsible for converting proline to 3-hydroxyproline in various collagen types. Mass spectrometry-based post-translational modification fingerprinting of collagens from null mouse models of related family members Connective tissue research Low 23772978
2017 P3h3 knockout mice show collagen lysine under-hydroxylation at helical domain cross-linking sites in skin, bone, tendon, aorta, and cornea — phenocopying EDS type VIA — without detectable effect on prolyl 3-hydroxylation at any known 3Hyp site. SDS-PAGE of P3h3-/- skin collagen type I showed an abnormal chain pattern with overabundance of a γ112 cross-linked trimer from intramolecular aldol cross-links, and altered divalent aldimine cross-link chemistry. The ratio of mature HP/LP cross-links in bone was reversed relative to wild type. Targeted knockout mouse model; tandem mass spectrometry of collagen PTMs; SDS-PAGE cross-link analysis The Journal of biological chemistry High 28115524
2018 SC65 forms a stable complex in the endoplasmic reticulum with P3H3 and lysyl hydroxylase 1 (LH1), and loss of this complex leads to defective collagen lysyl hydroxylation, low bone mass, and skin fragility. Co-complex biochemical characterization; KO mouse phenotypic analysis with collagen PTM readouts AIMS genetics Medium 30417103
2021 P3H3 is involved in collagen lysyl hydroxylation particularly at cross-link formation sites in type I collagen and at additional sites in type V collagen, but is not required for all lysyl hydroxylation sites. Unlike LH1, which plays a global enzymatic role in type I collagen lysyl hydroxylation, P3H3 and LH1 have two distinct mechanisms to recognize different collagen types and to distinguish cross-link formation sites from other sites. Notably, type V collagen from LH1-null mice retains normal hydroxylysine levels, whereas P3H3-null mice show reduced hydroxylysine in type V collagen. Comparative analysis of hydroxylysine amount and location in type I and V collagen from P3H3-null, LH1-null, and wild-type mice using tandem mass spectrometry The Journal of biological chemistry High 33631195
2014 SC65 and P3H3 are co-expressed in the endoplasmic reticulum of bone, skin, and reproductive tissues, consistent with their forming a functional complex in that compartment. Immunolocalization, co-expression analysis in Sc65-KO and wild-type tissues Journal of bone and mineral research Low 23959653
2009 Ectopic expression of P3H3 (Leprel2) in breast cancer cell lines with endogenous gene silencing results in suppression of colony growth, establishing a tumor-suppressive functional activity for P3H3. Ectopic expression (stable transfection) in cell lines with epigenetically silenced endogenous P3H3; colony formation assay British journal of cancer Medium 19436308
2018 Ectopic expression of Leprel2 (P3H3) inhibits melanoma cell proliferation, consistent with a tumor suppressor function; this was observed in melanoma cell lines where the endogenous gene is subject to methylation-dependent transcriptional silencing. Ectopic expression in melanoma cell lines; proliferation assays The Journal of investigative dermatology Medium 30452903
2017 Ectopic expression of P3H3 in lung cancer cell lines inhibits cell proliferation, colony formation, migration, and invasion, and induces apoptosis with G2/M cell cycle arrest. These effects are accompanied by increased p21, decreased cyclin A1, and increased caspase 3/7 activity. Knockdown of P3H3 increases migratory and invasive potential. Stable transfection (ectopic expression) and RNA interference (knockdown) in lung cancer cell lines; proliferation, colony formation, migration/invasion assays; flow cytometry for cell cycle; caspase activity assay; western blotting Experimental cell research Medium 29277505
2024 Proteome thermal profiling of dextromethorphan-treated lung fibroblasts showed increased thermal stability of P3H3 (alongside P3H2, P3H4, P4HA1, P4HA2), suggesting a change in P3H3 enzymatic activity; coinciding with collagen hyperhydroxylation and intracellular trafficking block of collagen type I. Thermal proteome profiling (proteome stability assay); mass spectrometry of collagen PTMs Science translational medicine Low 39693409
2026 P3H1 deficiency leads to compensatory increases in P3H3 protein levels (and P3H2), indicating that P3H3 participates in a feedback network regulating collagen biosynthesis and that its expression is upregulated when P3H1 activity is lost. P3H1 KO mouse tendon and P3H1 siRNA knockdown in human lung fibroblasts; proteomics and gene expression analysis The Journal of biological chemistry Medium 41932442
2024 ZNF334 directly transcriptionally regulates P3H3 expression in cervical cancer cells, as shown by dual-luciferase reporter and chromatin immunoprecipitation assays. Knockdown of P3H3 attenuates ZNF334-induced reversal of epithelial-to-mesenchymal transition (EMT), placing P3H3 downstream of ZNF334 in an EMT-suppressive pathway. Dual-luciferase reporter assay; chromatin immunoprecipitation (ChIP); siRNA knockdown of P3H3 with EMT phenotype readout Medical oncology Medium 38954116

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 Prolyl 3-hydroxylase 1, enzyme characterization and identification of a novel family of enzymes. The Journal of biological chemistry 157 15044469
2013 Collagen prolyl 3-hydroxylation: a major role for a minor post-translational modification? Connective tissue research 86 23772978
2009 The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic silencing in breast cancer. British journal of cancer 59 19436308
2018 Collagen Prolyl Hydroxylases Are Bifunctional Growth Regulators in Melanoma. The Journal of investigative dermatology 47 30452903
2015 Post-translationally abnormal collagens of prolyl 3-hydroxylase-2 null mice offer a pathobiological mechanism for the high myopia linked to human LEPREL1 mutations. The Journal of biological chemistry 46 25645914
2017 P3h3-null and Sc65-null Mice Phenocopy the Collagen Lysine Under-hydroxylation and Cross-linking Abnormality of Ehlers-Danlos Syndrome Type VIA. The Journal of biological chemistry 35 28115524
2021 Type I and type V procollagen triple helix uses different subsets of the molecular ensemble for lysine posttranslational modifications in the rER. The Journal of biological chemistry 23 33631195
2016 Genome-wide analysis identifies differential promoter methylation of Leprel2, Foxf1, Mmp25, Igfbp6, and Peg12 in murine tendinopathy. Journal of orthopaedic research : official publication of the Orthopaedic Research Society 23 27517731
2014 Sc65 is a novel endoplasmic reticulum protein that regulates bone mass homeostasis. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 20 23959653
2012 The collagen prolyl hydroxylases are novel transcriptionally silenced genes in lymphoma. British journal of cancer 20 22955849
2017 Collagen prolyl hydroxylase 3 has a tumor suppressive activity in human lung cancer. Experimental cell research 14 29277505
2024 Dextromethorphan inhibits collagen and collagen-like cargo secretion to ameliorate lung fibrosis. Science translational medicine 13 39693409
2023 The development of radioresistant oral squamous carcinoma cell lines and identification of radiotherapy-related biomarkers. Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 8 37029240
2023 Identifying Immune Cell Infiltration and Hub Genes During the Myocardial Remodeling Process After Myocardial Infarction. Journal of inflammation research 6 37456781
2018 Expression characterization and functional implication of the collagen-modifying Leprecan proteins in mouse gonadal tissue and mature sperm. AIMS genetics 5 30417103
2023 Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection. bioRxiv : the preprint server for biology 2 36712077
2024 Role of ZNF334 in cervical cancer: implications for EMT reversal and tumor suppression. Medical oncology (Northwood, London, England) 1 38954116
2026 Prolyl-3-hydroxylase 1 is a central regulator of collagen post-translational modifications and the collagen biosynthetic network. The Journal of biological chemistry 0 41932442
2025 Novel genetic associations with childhood adipocytokines in Indian adolescents. Cytokine 0 40187068

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