Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005783 endoplasmic reticulum	IBA GO_REF:0000033	ACCEPT	Summary: P3H2 acts in the endoplasmic reticulum, where collagen prolyl hydroxylation occurs prior to secretion. The phylogenetic (IBA) ER localization is consistent with direct experimental evidence (IDA) and the C-terminal ER-retention motif. Reason: ER is the correct catalytic compartment; supported by IDA (PMID:15063763), the KDEL-type ER-retention motif, and the UniProt subcellular location. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum
GO:0019797 procollagen-proline 3-dioxygenase activity	IBA GO_REF:0000033	ACCEPT	Summary: Procollagen-proline 3-dioxygenase activity is the core molecular function of P3H2, conserved across the P3H/leprecan family and directly demonstrated for human P3H2 on collagen IV-derived peptides. Reason: Core molecular function; corroborated by IDA (PMID:18487197), EC 1.14.11.7, and family-level conservation. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Prolyl 3-hydroxylase that catalyzes the post-translational formation of 3-hydroxyproline on collagens
GO:0032963 collagen metabolic process	IBA GO_REF:0000033	ACCEPT	Summary: By 3-hydroxylating procollagen prolyl residues, P3H2 participates in collagen biosynthesis/metabolism; the phylogenetic annotation is consistent with the experimental IDA evidence. Reason: Correct biological process; redundant with IDA (PMID:18487197) collagen metabolic process annotation. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt post-translational formation of 3-hydroxyproline on collagens
GO:0005506 iron ion binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: As a 2-oxoglutarate/Fe(II)-dependent dioxygenase, P3H2 coordinates a catalytic Fe(II) ion (binding residues 580/582/652) required for hydroxylation. This cofactor binding supports, but is subsidiary to, the informative procollagen-proline 3-dioxygenase activity. Reason: Accurate catalytic cofactor attribute (Fe cation cofactor; Fe-binding residues in the Fe2OG domain) but a supporting feature rather than the standalone core function. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Name=Fe cation
GO:0005783 endoplasmic reticulum	IEA GO_REF:0000044	ACCEPT	Summary: Electronic transfer of ER localization from the UniProt subcellular location, consistent with the stronger IDA/IBA evidence. Reason: Correct compartment; redundant with experimental ER localization. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum
GO:0005794 Golgi apparatus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Electronic transfer of the Golgi localization from the UniProt subcellular location. Golgi residence is a reported secondary localization; the catalytic site of action is the ER lumen. Reason: Accurate reported localization (UniProt/IDA) but secondary to the ER, where collagen prolyl hydroxylation occurs; not the core site of action. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Golgi apparatus
GO:0016529 sarcoplasmic reticulum	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: The sarcoplasmic reticulum is the specialized ER of muscle; this localization is consistent with the strong muscle expression and muscle-specific transcript of P3H2 reported by Jaernum et al. Reason: Accurate UniProt-derived localization reflecting muscle-tissue ER, but a tissue-specific variant of the ER compartment rather than a distinct core function. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Sarcoplasmic 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: This is the parent oxidoreductase class for the dioxygenase reaction P3H2 catalyzes (it incorporates one atom of O2 into proline while reducing 2-oxoglutarate). Correct but less informative than the specific procollagen-proline 3-dioxygenase activity. Reason: Correct but generic parent term; the specific GO:0019797 captures the core catalytic activity. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt EC=1.14.11.7
GO:0019797 procollagen-proline 3-dioxygenase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (multi-method, EC/Rhea-based) assignment of the core procollagen-proline 3-dioxygenase activity, consistent with the experimental IDA evidence and EC 1.14.11.7. Reason: Correct core molecular function; redundant with IDA/IBA evidence. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt EC=1.14.11.7
GO:0031418 L-ascorbic acid binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: P3H2 uses L-ascorbate (vitamin C) as a cofactor to maintain the active-site iron in the reduced state, a hallmark of collagen prolyl hydroxylases. This cofactor binding supports the catalytic activity. Reason: Accurate catalytic cofactor attribute (L-ascorbate cofactor; KM=110 uM for ascorbate) but subsidiary to the informative procollagen-proline 3-dioxygenase activity. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Name=L-ascorbate
GO:0032963 collagen metabolic process	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment of the collagen metabolic process, consistent with the experimental IDA evidence. Reason: Correct biological process; redundant with IDA (PMID:18487197). Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt 3-hydroxyproline on collagens
GO:0005604 basement membrane	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Basement membrane is the location of P3H2's collagen IV substrate/product, not where the enzyme itself acts. P3H2 is an ER-resident enzyme (KDEL-type retention motif) that modifies procollagen in the ER lumen before secretion; it is not a structural component of the assembled basement membrane. This annotation is transferred electronically from the mouse ortholog. Reason: Ortholog-transferred (Ensembl/ISS from Q8CG71) localization to basement membrane conflates the enzyme's ER site of action with the destination of its collagen IV substrate; P3H2 acts in the ER and is retained there by a KDEL-type motif. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Prevents secretion from ER
GO:0005794 Golgi apparatus	IDA GO_REF:0000052	KEEP AS NON CORE	Summary: Immunofluorescence (HPA) evidence for Golgi localization, consistent with the reported ER-and-Golgi distribution of P3H2. The catalytic site of action remains the ER lumen. Reason: Direct (IDA) reported localization but secondary to the ER catalytic compartment; not the core site of action. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Golgi apparatus
GO:0005788 endoplasmic reticulum lumen	TAS Reactome:R-HSA-1980233	ACCEPT	Summary: Reactome curation places P3H2 in the ER lumen, the precise compartment where collagen prolyl 3-hydroxylation occurs. This is the most informative cellular-component term for the enzyme. Reason: Correct and precise catalytic compartment; consistent with the ER localization and ER-retention motif. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen	TAS Reactome:R-HSA-8948226	ACCEPT	Summary: Reactome curation of P3H2 in the ER lumen during the collagen 3-hydroxylation reaction cycle. Reason: Correct precise catalytic compartment; redundant with the other ER lumen TAS annotation. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen	TAS Reactome:R-HSA-8948230	ACCEPT	Summary: Reactome curation of P3H2 in the ER lumen, where it binds 4-Hyp collagen propeptides. Reason: Correct precise catalytic compartment; redundant with the other ER lumen TAS annotations. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum
GO:0005604 basement membrane	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: Sequence-similarity (ISS, from mouse ortholog Q8CG71) transfer of basement membrane localization. As with the IEA version, this reflects the location of the collagen IV substrate/product rather than the ER-resident enzyme's site of action. Reason: ISS transfer from the mouse ortholog conflates enzyme site of action (ER) with the destination of its collagen IV substrate; P3H2 is ER-retained via a KDEL-type motif. Supporting Evidence: file:human/P3H2/P3H2-uniprot.txt Prevents secretion from ER
GO:0019511 peptidyl-proline hydroxylation	IDA PMID:18487197 Characterization of recombinant human prolyl 3-hydroxylase i...	ACCEPT	Summary: P3H2 directly hydroxylates peptidyl-proline residues; the recombinant enzyme assay demonstrated robust activity on (Gly-Pro-4Hyp)5 and collagen IV-derived peptides. This is the biological-process view of the core catalytic function. Reason: Directly demonstrated peptidyl-proline hydroxylation activity (IDA); the central biological process of P3H2. Supporting Evidence: PMID:18487197 A large amount of P3H activity was found in the P3H2 samples with (Gly-Pro-4Hyp)5 as a substrate
GO:0019797 procollagen-proline 3-dioxygenase activity	IDA PMID:18487197 Characterization of recombinant human prolyl 3-hydroxylase i...	ACCEPT	Summary: Direct experimental demonstration that recombinant human P3H2 catalyzes prolyl 3-hydroxylation, with high activity toward collagen IV sequences. This is the core molecular function of the enzyme. Reason: Core molecular function with direct experimental (IDA) support; defines P3H2 as the collagen IV-preferring prolyl 3-hydroxylase isoenzyme (EC 1.14.11.7). Supporting Evidence: PMID:18487197 P3H2 hydroxylated more effectively two synthetic peptides corresponding to sequences that are hydroxylated in collagen IV than a peptide corresponding to the 3-hydroxylation site in collagen I
GO:0032963 collagen metabolic process	IDA PMID:18487197 Characterization of recombinant human prolyl 3-hydroxylase i...	ACCEPT	Summary: P3H2 contributes to collagen metabolism by modifying procollagen prolyl residues, with a preference for the basement-membrane collagen IV. Reason: Directly supported (IDA) collagen-modifying process; central to P3H2's biological role. Supporting Evidence: PMID:18487197 P3H2 is responsible for the hydroxylation of collagen IV, which has the highest 3-hydroxyproline content of all collagens
GO:0005783 endoplasmic reticulum	IDA PMID:15063763 LEPREL1, a novel ER and Golgi resident member of the Lepreca...	ACCEPT	Summary: Direct immunofluorescence evidence that LEPREL1/P3H2 localizes to the ER, consistent with its role as an ER-lumenal collagen-modifying enzyme and its KDEL-type retention motif. Reason: IDA-supported ER localization agrees with the catalytic site of action and the ER-retention motif. Supporting Evidence: PMID:15063763 LEPREL1 is localized to the ER and Golgi network
GO:0005794 Golgi apparatus	IDA PMID:15063763 LEPREL1, a novel ER and Golgi resident member of the Lepreca...	KEEP AS NON CORE	Summary: Direct immunofluorescence evidence that LEPREL1/P3H2 also localizes to the Golgi. This is a reported secondary localization; the ER lumen is the catalytic compartment. Reason: Direct (IDA) reported localization but secondary to the ER site of action for collagen prolyl hydroxylation. Supporting Evidence: PMID:15063763 LEPREL1 is localized to the ER and Golgi network
GO:0008285 negative regulation of cell population proliferation	IDA PMID:19436308 The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets fo...	KEEP AS NON CORE	Summary: P3H2 is epigenetically silenced by promoter CpG methylation in breast cancer, and ectopic re-expression suppresses colony formation, indicating a tumor-suppressor-like anti-proliferative effect. The colony-suppression assay was performed with P3H2 cDNA in P3H2-silenced breast cancer cell lines (MCF7, T47D), so the experimental annotation is gene-specific and should be retained. However, this is a context-dependent, likely indirect phenotype rather than the enzyme's core ER collagen-modifying function. Reason: Real gene-specific experimental (IDA) phenotype, but an indirect/context-dependent tumor-suppressor effect of overexpression in cancer cell lines, not the core catalytic function; retained as non-core per guidelines. Supporting Evidence: PMID:19436308 Ectopic expression of P3H2 and P3H3 in cell lines with silencing of the endogenous gene results in suppression of colony growth

Core Functions

ER-lumenal 2-oxoglutarate/Fe(II)-dependent prolyl 3-hydroxylase that catalyzes post-translational 3-hydroxylation of specific prolyl residues in procollagen (the first Pro of Gly-Pro-4Hyp triplets), acting preferentially on basement-membrane collagen type IV.

Molecular Function:

procollagen-proline 3-dioxygenase activity

Directly Involved In:

peptidyl-proline hydroxylation collagen metabolic process

Cellular Locations:

endoplasmic reticulum lumen

Supporting Evidence:

PMID:18487197
P3H2 hydroxylated more effectively two synthetic peptides corresponding to sequences that are hydroxylated in collagen IV than a peptide corresponding to the 3-hydroxylation site in collagen I
file:human/P3H2/P3H2-uniprot.txt
Prolyl 3-hydroxylase that catalyzes the post-translational formation of 3-hydroxyproline on collagens

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:15063763

LEPREL1, a novel ER and Golgi resident member of the Leprecan family.

LEPREL1/P3H2 is an 80 kDa, 708-residue ER/Golgi-resident protein of the leprecan family with a signal sequence, four TPRs, a P4Halpha domain, and a C-terminal KDEL ER-retention motif; over-expression perturbs ER PDI staining.

PMID:18487197

Characterization of recombinant human prolyl 3-hydroxylase isoenzyme 2, an enzyme modifying the basement membrane collagen IV.

Recombinant human P3H2 has prolyl 3-hydroxylase activity on (Gly-Pro-4Hyp)5 and preferentially hydroxylates collagen IV-derived peptides over a collagen I site, identifying P3H2 as the collagen IV-modifying isoenzyme; it is enriched in basement-membrane-rich tissues such as kidney and does not require CRTAP.

PMID:19436308

The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic silencing in breast cancer.

P3H2 (and P3H3) are silenced by promoter CpG hypermethylation in breast cancer; ectopic re-expression of P3H2 in silenced breast cancer cell lines suppresses colony growth, implying tumor-suppressor-like anti-proliferative activity.

PMID:29491144

Post-translational modification of type IV collagen with 3-hydroxyproline affects its interactions with glycoprotein VI and nidogens 1 and 2.

Using P3H2-knockout PFHR-9 cells and tandem MS, P3H2 is shown to be the major (but not the only) 3-hydroxyproline-modifying enzyme of type IV collagen; 3-Hyp on collagen IV modulates its interactions with glycoprotein VI (reduced 3-Hyp increases GP6 binding) and is required for nidogen 1/2 binding.

PMID:33918807

Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis.

P3H2 is induced by VEGF-A in human endothelial cells via VEGFR-2/p38 MAPK signaling; through its activity on type IV collagen it is required for angiogenic properties in vitro, and P3H2 knockdown prevents pathological angiogenesis in a laser-induced choroidal neovascularization model.

PMID:35499085

Loss of the collagen IV modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy.

P3H2 was identified as a glomerular basement membrane (GBM) modifier in a cohort of patients with albuminuria; it 3-hydroxylates prolines in collagen IV subchains in the ER, and podocyte-specific loss in mice produces a thin basement membrane nephropathy (TBMN) phenotype with progressive microhematuria and microalbuminuria. Loss/mutation of P3H2 causes TBMN and focal segmental glomerulosclerosis (FSGS) in mice and humans.

Reactome:R-HSA-1980233

Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen

Reactome:R-HSA-8948226

Prolyl 3-hydroxylases:Fe2+:3,4-Hyp collagen propeptides dissociates

Reactome:R-HSA-8948230

P3HB binds 4-Hyp-collagen propeptides

file:human/P3H2/P3H2-uniprot.txt

UniProt entry Q8IVL5 (P3H2_HUMAN), prolyl 3-hydroxylase 2

ER-lumenal 2-oxoglutarate/Fe(II)-dependent dioxygenase (EC 1.14.11.7) that 3-hydroxylates procollagen prolyl residues (high activity on collagen IV/COL4A1, lower on COL1A1); uses Fe cation and L-ascorbate cofactors; contains an Fe2OG dioxygenase domain and a C-terminal KDEL-type ER-retention motif; ER/sarcoplasmic reticulum/Golgi localization; loss-of-function variant causes MCVD high myopia.

Suggested Experiments

Experiment: Quantitative mass spectrometry of 3-hydroxyproline sites on collagen IV (and other basement-membrane collagens) from P3H2-knockout versus wild-type cells/tissues to define the in vivo substrate site repertoire and confirm collagen IV specificity.

Experiment: Structure-function analysis of the MCVD G508V variant (and active-site mutants) measuring prolyl 3-hydroxylase activity, folding/solubility, and ER retention to establish the molecular basis of the loss of function underlying high myopia.

Deep Research

Falcon

(P3H2-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 24 citations 2 artifacts 2026-06-12T04:42:18.959405

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000013 The requested information is presented in the following figures: - **GBM thickness and TEM images**: Figure 3 (image-007) provides (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive research report: Human P3H2 / LEPREL1 (UniProt Q8IVL5) functional annotation

0) Target verification (gene/protein identity)

The UniProt accession Q8IVL5 corresponds to human Prolyl 3-hydroxylase 2 (P3H2), encoded by LEPREL1 (syn. Leprecan-like protein 1; sometimes referenced as MLAT4). The P3H family includes paralogs P3H1 (LEPRE1) and P3H3 (LEPREL2) and related non-enzymatic partners (e.g., CRTAP, P3H4/SC65), so P3H2-specific claims must be distinguished from other P3H genes. (gjaltema2017molecularinsightsinto pages 4-5, marini2007componentsofthe pages 5-5)

1) Key concepts, definitions, and current understanding

1.1 What does P3H2 do? (enzyme class and reaction)

P3H2 is a collagen-modifying enzyme that catalyzes formation of 3-hydroxyproline (3Hyp) on collagen polypeptides (i.e., proline 3-hydroxylation), a post-translational modification occurring during collagen biosynthesis. (pignata2021prolyl3hydroxylase2 pages 1-2, pasanen2011prolyl3hydroxylasesand pages 1-5)

P3H2 is part of the broader 2-oxoglutarate/Fe(II)-dependent dioxygenase (2OGDD) enzyme superfamily. This class uses Fe2+, 2-oxoglutarate, molecular oxygen, and ascorbate to hydroxylate substrates, consistent with other collagen hydroxylases. (pasanen2011prolyl3hydroxylasesand pages 1-5, fonsen2007prolylhydroxylasescloning pages 1-7)

1.2 Substrate specificity: collagen IV as the dominant physiological target

Multiple sources support that P3H2 preferentially targets basement membrane type IV collagen, i.e., it is a principal prolyl 3-hydroxylase acting on collagen IV. (aypek2022lossofthe pages 1-2, pasanen2011prolyl3hydroxylasesand pages 1-5, salo2021prolylandlysyl pages 7-9)

Quantitatively, one review/experimental synthesis reports that while P3H1 modifies type I collagen at low frequency (~1 3Hyp per 1000 aa), P3H2’s principal substrate is collagen IV, with much higher modification levels (~10–15 prolines per 1000 aa). (pignata2021prolyl3hydroxylase2 pages 1-2)

1.3 Domain architecture and family features (what makes it a leprecan-family enzyme)

P3H2 is placed in the leprecan/prolyl-3-hydroxylase family, characterized by an N-terminal domain with protein–protein interaction features (including TPR motifs) and conserved cysteine motifs (e.g., CXXXC motifs), and a C-terminal 2OG/Fe(II) dioxygenase catalytic domain. (gjaltema2017molecularinsightsinto pages 4-5, onursal2023differentialeffectsof pages 41-46, marini2007componentsofthe pages 5-5)

A key complication is that some family members (e.g., CRTAP, P3H4) can lack the catalytic dioxygenase domain and instead function as complex partners, so catalytic activity should be specifically attributed to P3H1/2/3. (onursal2023differentialeffectsof pages 41-46, marini2007componentsofthe pages 5-5)

1.4 Where does P3H2 function in the cell? (subcellular localization)

P3H2 is a secretory-pathway enzyme reported to localize to the endoplasmic reticulum (ER) (and in some contexts ER/Golgi network), consistent with its role modifying collagens before secretion/assembly into basement membranes. (pignata2021prolyl3hydroxylase2 pages 1-2, aypek2022lossofthe pages 1-2)

In kidney/podocyte systems, imaging evidence supports ER-like localization of re-expressed P3H2 in podocyte cell lines, and in vivo podocyte-associated signal in wild-type kidney tissue. (aypek2022lossofthe media 6cf8aab0, aypek2022lossofthe media 45d6b292)

2) Primary biological roles and pathway context

2.1 Basement membrane collagen IV maturation and interactome

Basement membrane integrity depends heavily on collagen IV networks. P3H2-mediated proline 3-hydroxylation contributes to collagen IV post-translational patterning and can modulate collagen IV interactions with partners.

A primary study focusing on collagen IV shows that altered 3Hyp content (via P3H2 loss) changes collagen IV interactions with glycoprotein VI (GP6) and nidogens 1/2—reduced 3Hyp increased GP6 binding, whereas 3Hyp was required for nidogen binding. (montgomery2018posttranslationalmodificationof pages 1-2)

2.2 Angiogenesis link via ECM remodeling downstream of VEGF signaling

P3H2 has been proposed as a mechanistic link between VEGF signaling and basement membrane remodeling in angiogenesis. In endothelial cells, P3H2 is induced by VEGF-A/VEGFR2 signaling via p38 MAPK, and functional gain/loss experiments suggest that P3H2 activity on collagen IV supports angiogenic properties in vitro. (pignata2021prolyl3hydroxylase2 pages 1-2)

3) Disease relevance (human genetics and mechanistic models)

3.1 Kidney disease: thin basement membrane nephropathy (TBMN) and FSGS

A 2022 JCI study identified P3H2 as an important glomerular basement membrane (GBM) modifier: P3H2 hydroxylates prolines in collagen IV subchains in the ER, and podocyte-specific loss in mice produced a thin basement membrane nephropathy phenotype with thinner GBM, plus progressive microhematuria and microalbuminuria over time. (aypek2022lossofthe pages 1-2)

The same work links P3H2 loss/mutation to disease spanning TBMN and focal segmental glomerulosclerosis (FSGS) in mice and humans, including a reported nonsense variant (c.1213C>T) leading to a premature stop codon in a human pedigree. (aypek2022lossofthe pages 1-2)

Quantitative/visual evidence: The paper’s TEM images and quantification show reduced GBM thickness in podocyte-specific knockout mice at multiple ages, and proteomics indicates decreased abundance of collagen IV subchains in GBM preparations. (aypek2022lossofthe media f8c46f40, aypek2022lossofthe media 01d7b518)

3.2 Ocular phenotypes: high myopia and cataract/vitreoretinal degeneration

Genetic association evidence supports that LEPREL1 (P3H2) variants can cause or be associated with severe ocular disease. A clinical genetics review in JCI emphasizes that recessive LEPREL1 mutations can cause severe non-syndromic high myopia (with additional lens/vitreoretinal features referenced in the collagen IV 3Hyp literature). (montgomery2018posttranslationalmodificationof pages 13-14, pignata2021prolyl3hydroxylase2 pages 14-15)

Separately, a major clinical genetics paper on myopia/deafness notes that high myopia is a significant clinical problem and cites that a missense variant in LEPREL1 (P3H2)—a collagen-hydroxylating 2OG dioxygenase—was associated with an autosomal recessive form of high myopia with early-onset cataracts. This provides additional support that LEPREL1/P3H2 is implicated in ocular structural disease consistent with collagen/basement membrane biology. (tekin2013slitrk6mutationscause pages 1-2)

4) Current applications and real-world implementations

4.1 Diagnostics/clinical genetics (implemented use)

The most direct real-world implementation is in molecular diagnosis and interpretation of inherited or familial basement membrane diseases. The evidence supporting P3H2 as a GBM modifier and a cause of TBMN/FSGS indicates LEPREL1 should be considered in genetic workups of hematuria/albuminuria phenotypes when collagen IV-related disease is suspected but COL4A genes are not explanatory. (aypek2022lossofthe pages 1-2)

4.2 Therapeutic concepts (preclinical)

A preclinical therapeutic concept is anti-angiogenic targeting. In an in vivo laser-induced choroidal neovascularization (CNV) model, P3H2 knockdown reduced pathological angiogenesis, suggesting P3H2 could be explored as a candidate anti-angiogenesis target—potentially via modulation of collagen IV organization in the vascular basement membrane. (pignata2021prolyl3hydroxylase2 pages 14-15)

5) Expert opinions and synthesis (authoritative review perspectives)

A highly cited collagen hydroxylase review synthesizes that P3H2/LEPREL1 is one of the three vertebrate collagen prolyl-3-hydroxylases and contains the canonical C-terminal 2OG dioxygenase domain, with tissue distribution enriched in basement membrane–rich tissues—supporting a primary role in basement membrane collagen modification rather than fibrillar collagen remodeling. (gjaltema2017molecularinsightsinto pages 4-5)

A 2021 expert review of collagen prolyl/lysyl hydroxylases cites biochemical and genetic evidence that P3H2 is active on collagen IV and that P3H2 loss produces abnormal collagens, supporting a mechanistic link to high myopia and basement membrane biology. (salo2021prolylandlysyl pages 21-24)

6) Relevant statistics and data points

Collagen IV modification frequency: P3H2 modifies collagen IV at high frequency (~10–15 prolines per 1000 aa), contrasted with P3H1’s low-frequency modification of collagen I (~1 per 1000 aa). (pignata2021prolyl3hydroxylase2 pages 1-2)
Myopia epidemiology (contextual burden): Myopia affects >25% of adults in Western Europe/America and can exceed 70% in some urban East Asian populations; high myopia affects ~1–3% of the population. (tekin2013slitrk6mutationscause pages 1-2)
Kidney pathology readouts: TEM and GBM thickness quantification demonstrate a thinner GBM in podocyte-specific P3h2 knockout mice, and GBM proteomics indicates reduced collagen IV subchains abundance. (aypek2022lossofthe media f8c46f40, aypek2022lossofthe media 01d7b518)

7) 2023–2024 research update (evidence-limited in retrieved corpus)

Although the request prioritizes 2023–2024, tool-based retrieval in this run did not surface accessible 2023–2024 primary mechanistic studies specifically focused on human P3H2/LEPREL1 beyond indirect mentions. The most recent high-confidence, P3H2-focused primary evidence available here is Aypek et al., 2022 (JCI) on kidney basement membrane disease and Pignata et al., 2021 (IJMS) on angiogenesis, supported by 2021–2018 reviews/primary studies on collagen IV modification. (aypek2022lossofthe pages 1-2, pignata2021prolyl3hydroxylase2 pages 1-2, montgomery2018posttranslationalmodificationof pages 1-2)

Summary table (quick reference)

Category	Summary	Key evidence (cite first-author year)	URL	Publication date
Identity/Names	Human P3H2 corresponds to LEPREL1 (also called Leprecan-like protein 1), one of three vertebrate prolyl 3-hydroxylase isoenzymes; it belongs to the leprecan family and contains a C-terminal 2-oxoglutarate-dependent dioxygenase catalytic domain. Literature distinguishes it from paralogs P3H1/LEPRE1 and P3H3/LEPREL2, which is important because substrate specificities differ. (gjaltema2017molecularinsightsinto pages 4-5, marini2007componentsofthe pages 5-5)	Marini 2007; Gjaltema 2017	https://doi.org/10.4161/cc.6.14.4474 ; https://doi.org/10.1080/10409238.2016.1269716	2007-07 ; 2017-01
Enzymatic reaction	P3H2 is a prolyl 3-hydroxylase that catalyzes formation of 3-hydroxyproline (3Hyp) on collagen chains, hydroxylating proline residues in collagenous Gly-X-Y motifs; reviews and primary studies identify collagen IV as its main physiological substrate. (pignata2021prolyl3hydroxylase2 pages 1-2, aypek2022lossofthe pages 1-2, pasanen2011prolyl3hydroxylasesand pages 1-5, salo2021prolylandlysyl pages 21-24, montgomery2018posttranslationalmodificationof pages 13-14)	Pasanen 2011; Aypek 2022; Salo & Myllyharju 2021; Montgomery 2018	https://doi.org/10.1172/jci147253 ; https://doi.org/10.1111/exd.14197 ; https://doi.org/10.1074/jbc.ra117.000406	2011 ; 2022-05 ; 2021-10 ; 2018-04
Cofactors	As a member of the 2-oxoglutarate/Fe(II)-dependent dioxygenase family, P3H2 requires Fe2+, 2-oxoglutarate, O2, and ascorbate for catalysis, consistent with the catalytic chemistry of collagen hydroxylases. (pasanen2011prolyl3hydroxylasesand pages 1-5, onursal2023differentialeffectsof pages 41-46, fonsen2007prolylhydroxylasescloning pages 1-7)	Pasanen 2011; Onursal 2023; Fonsén 2007	https://doi.org/10.1101/2023.06.28.546985	2011 ; 2023-06 ; 2007
Substrate specificity	Evidence supports collagen IV as the principal substrate of P3H2. Recombinant/enrichment studies place P3H2 in basement-membrane-rich tissues and show greater activity on peptide substrates representing type IV collagen hydroxylation sites than on type I collagen sites; type IV collagen is likely the major substrate, though P3H2 may also modify other collagens to a lesser extent. (pignata2021prolyl3hydroxylase2 pages 1-2, montgomery2018posttranslationalmodificationof pages 1-2, pasanen2011prolyl3hydroxylasesand pages 1-5, montgomery2018posttranslationalmodificationof pages 13-14, salo2021prolylandlysyl pages 7-9)	Pasanen 2011; Montgomery 2018; Salo & Myllyharju 2021; Pignata 2021	https://doi.org/10.1074/jbc.ra117.000406 ; https://doi.org/10.1111/exd.14197 ; https://doi.org/10.3390/ijms22083896	2011 ; 2018-04 ; 2021-10 ; 2021-04
Subcellular localization	P3H2 is reported as endoplasmic reticulum (ER)-localized, with some evidence also noting ER/Golgi network localization; family-level evidence indicates ER-association/ER-retention features for prolyl 3-hydroxylases. In podocytes and endothelial cells, localization is consistent with a secretory-pathway collagen-modifying enzyme. (pignata2021prolyl3hydroxylase2 pages 1-2, aypek2022lossofthe pages 1-2, marini2007componentsofthe pages 5-5, aypek2022lossofthe media 6cf8aab0)	Marini 2007; Pignata 2021; Aypek 2022	https://doi.org/10.4161/cc.6.14.4474 ; https://doi.org/10.3390/ijms22083896 ; https://doi.org/10.1172/jci147253	2007-07 ; 2021-04 ; 2022-05
Biological role/pathways	P3H2 functions in the collagen biosynthesis/post-translational modification pathway for basement membranes, especially the glomerular basement membrane (GBM) and vascular basement membrane. By generating 3Hyp on collagen IV, it influences collagen IV organization and interactions with binding partners such as nidogens 1/2 and glycoprotein VI; it is also induced by VEGF-A/VEGFR2/p38 MAPK signaling in endothelial cells, linking collagen IV modification to angiogenesis. (montgomery2018posttranslationalmodificationof pages 1-2, aypek2022lossofthe pages 1-2, pignata2021prolyl3hydroxylase2 pages 1-2, pignata2021prolyl3hydroxylase2 pages 14-15)	Montgomery 2018; Pignata 2021; Aypek 2022	https://doi.org/10.1074/jbc.ra117.000406 ; https://doi.org/10.3390/ijms22083896 ; https://doi.org/10.1172/jci147253	2018-04 ; 2021-04 ; 2022-05
Key phenotypes/disease links	Loss or mutation of P3H2/LEPREL1 is linked to ocular disease (autosomal-recessive high myopia with early cataract/vitreoretinal degeneration) and to renal disease including thin basement membrane nephropathy (TBMN) and focal segmental glomerulosclerosis (FSGS). In the kidney, podocyte-specific loss causes thinner GBM with progressive microhematuria and microalbuminuria; in human pedigrees, truncating variants have been reported. (aypek2022lossofthe pages 1-2, tekin2013slitrk6mutationscause pages 1-2, montgomery2018posttranslationalmodificationof pages 13-14, pignata2021prolyl3hydroxylase2 pages 14-15, salo2021prolylandlysyl pages 7-9)	Tekin 2013; Aypek 2022; Montgomery 2018; Pignata 2021; Salo & Myllyharju 2021	https://doi.org/10.1172/JCI65853 ; https://doi.org/10.1172/jci147253 ; https://doi.org/10.1074/jbc.ra117.000406 ; https://doi.org/10.3390/ijms22083896 ; https://doi.org/10.1111/exd.14197	2013-05 ; 2022-05 ; 2018-04 ; 2021-04 ; 2021-10
Therapeutic/real-world applications	P3H2 currently has no established approved therapy directly targeting it, but experimental work suggests translational potential in anti-angiogenic therapy: P3H2 knockdown reduced pathological angiogenesis in a laser-induced choroidal neovascularization model. In nephrology, P3H2 is emerging as a disease gene and GBM modifier relevant to diagnosis/mechanistic interpretation of TBMN/FSGS. (aypek2022lossofthe pages 1-2, pignata2021prolyl3hydroxylase2 pages 14-15)	Pignata 2021; Aypek 2022	https://doi.org/10.3390/ijms22083896 ; https://doi.org/10.1172/jci147253	2021-04 ; 2022-05
Key quantitative data	Reported quantitative details include: P3H2 modifies ~10–15 proline residues per 1000 amino acids in collagen IV, whereas P3H1 modifies ~1 per 1000 aa in collagen I; type IV collagen α1 chain contains about 15 3Hyp residues; VEGF-A-stimulated HUVEC RNA-seq identified 459 differentially expressed genes including P3H2; myopia affects >25% of adults in Western Europe/America and >70% in some urban East Asian populations, while high myopia affects about 1–3% of the population. A human renal pedigree described a c.1213C>T nonsense variant causing premature truncation. (pignata2021prolyl3hydroxylase2 pages 1-2, salo2021prolylandlysyl pages 7-9, tekin2013slitrk6mutationscause pages 1-2, aypek2022lossofthe pages 1-2)	Pignata 2021; Salo & Myllyharju 2021; Tekin 2013; Aypek 2022	https://doi.org/10.3390/ijms22083896 ; https://doi.org/10.1111/exd.14197 ; https://doi.org/10.1172/JCI65853 ; https://doi.org/10.1172/jci147253	2021-04 ; 2021-10 ; 2013-05 ; 2022-05

Table: This table summarizes the core functional annotation of human P3H2/LEPREL1 (UniProt Q8IVL5), including enzymatic activity, localization, substrates, disease links, and quantitative findings. It condenses the most relevant supported evidence for rapid reference in the final report.

Key references (publication date and URL)

Marini et al. Cell Cycle (2007-07): https://doi.org/10.4161/cc.6.14.4474 (marini2007componentsofthe pages 5-5)
Pasanen (2011): prolyl 3-hydroxylases overview and collagen IV hydroxylation by P3H2 (pasanen2011prolyl3hydroxylasesand pages 1-5)
Gjaltema & Bank Crit Rev Biochem Mol Biol (2017-01): https://doi.org/10.1080/10409238.2016.1269716 (gjaltema2017molecularinsightsinto pages 4-5)
Montgomery et al. J Biol Chem (2018-04): https://doi.org/10.1074/jbc.ra117.000406 (montgomery2018posttranslationalmodificationof pages 1-2)
Pignata et al. Int J Mol Sci (2021-04): https://doi.org/10.3390/ijms22083896 (pignata2021prolyl3hydroxylase2 pages 1-2, pignata2021prolyl3hydroxylase2 pages 14-15)
Salo & Myllyharju Exp Dermatol (2021-10): https://doi.org/10.1111/exd.14197 (salo2021prolylandlysyl pages 21-24, salo2021prolylandlysyl pages 7-9)
Aypek et al. J Clin Invest (2022-05): https://doi.org/10.1172/jci147253 (aypek2022lossofthe pages 1-2, aypek2022lossofthe media f8c46f40, aypek2022lossofthe media 01d7b518, aypek2022lossofthe media 45d6b292)
Tekin et al. J Clin Invest (2013-05): https://doi.org/10.1172/JCI65853 (LEPREL1/P3H2 cited in myopia genetics background; includes population burden statistics) (tekin2013slitrk6mutationscause pages 1-2)

References

(gjaltema2017molecularinsightsinto pages 4-5): Rutger A. F. Gjaltema and Ruud A. Bank. Molecular insights into prolyl and lysyl hydroxylation of fibrillar collagens in health and disease. Critical Reviews in Biochemistry and Molecular Biology, 52:74-95, Jan 2017. URL: https://doi.org/10.1080/10409238.2016.1269716, doi:10.1080/10409238.2016.1269716. This article has 208 citations and is from a peer-reviewed journal.
(marini2007componentsofthe pages 5-5): Joan C. Marini, Wayne A. Cabral, Aileen M. Barnes, and Weizhong Chang. Components of the collagen prolyl 3-hydroxylation complex are crucial for normal bone development. Cell Cycle, 6:1675-1681, Jul 2007. URL: https://doi.org/10.4161/cc.6.14.4474, doi:10.4161/cc.6.14.4474. This article has 168 citations and is from a peer-reviewed journal.
(pignata2021prolyl3hydroxylase2 pages 1-2): Paola Pignata, Ivana Apicella, Valeria Cicatiello, Caterina Puglisi, Sara Magliacane Trotta, Remo Sanges, Valeria Tarallo, and Sandro De Falco. Prolyl 3-hydroxylase 2 is a molecular player of angiogenesis. International Journal of Molecular Sciences, 22:3896, Apr 2021. URL: https://doi.org/10.3390/ijms22083896, doi:10.3390/ijms22083896. This article has 13 citations.
(pasanen2011prolyl3hydroxylasesand pages 1-5): A Pasanen. Prolyl 3-hydroxylases and hypoxia-inducible factor 3: their roles in collagen synthesis and hypoxia response, respectively. Unknown journal, 2011.
(fonsen2007prolylhydroxylasescloning pages 1-7): P Fonsén. Prolyl hydroxylases: cloning and characterization of novel human and plant prolyl 4-hydroxylases, and three human prolyl 3-hydroxylases. Unknown journal, 2007.
(aypek2022lossofthe pages 1-2): Hande Aypek, Christoph Krisp, Shun Lu, Shuya Liu, Dominik Kylies, Oliver Kretz, Guochao Wu, Manuela Moritz, Kerstin Amann, Kerstin Benz, Ping Tong, Zheng-mao Hu, Sulaiman M. Alsulaiman, Arif O. Khan, Maik Grohmann, Timo Wagner, Janina Müller-Deile, Hartmut Schlüter, Victor G. Puelles, Carsten Bergmann, Tobias B. Huber, and Florian Grahammer. Loss of the collagen iv modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. The Journal of Clinical Investigation, May 2022. URL: https://doi.org/10.1172/jci147253, doi:10.1172/jci147253. This article has 42 citations.
(salo2021prolylandlysyl pages 7-9): Antti M. Salo and Johanna Myllyharju. Prolyl and lysyl hydroxylases in collagen synthesis. Experimental Dermatology, 30:38-49, Oct 2021. URL: https://doi.org/10.1111/exd.14197, doi:10.1111/exd.14197. This article has 146 citations and is from a domain leading peer-reviewed journal.
(onursal2023differentialeffectsof pages 41-46): C Onursal. Differential effects of prolyl-3-hydroxylases 1 and 4 on collagen biosynthesis highlight prolyl-3-hydroxylase 4 as a potential novel drug target in pulmonary …. Unknown journal, 2023.
(aypek2022lossofthe media 6cf8aab0): Hande Aypek, Christoph Krisp, Shun Lu, Shuya Liu, Dominik Kylies, Oliver Kretz, Guochao Wu, Manuela Moritz, Kerstin Amann, Kerstin Benz, Ping Tong, Zheng-mao Hu, Sulaiman M. Alsulaiman, Arif O. Khan, Maik Grohmann, Timo Wagner, Janina Müller-Deile, Hartmut Schlüter, Victor G. Puelles, Carsten Bergmann, Tobias B. Huber, and Florian Grahammer. Loss of the collagen iv modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. The Journal of Clinical Investigation, May 2022. URL: https://doi.org/10.1172/jci147253, doi:10.1172/jci147253. This article has 42 citations.
(aypek2022lossofthe media 45d6b292): Hande Aypek, Christoph Krisp, Shun Lu, Shuya Liu, Dominik Kylies, Oliver Kretz, Guochao Wu, Manuela Moritz, Kerstin Amann, Kerstin Benz, Ping Tong, Zheng-mao Hu, Sulaiman M. Alsulaiman, Arif O. Khan, Maik Grohmann, Timo Wagner, Janina Müller-Deile, Hartmut Schlüter, Victor G. Puelles, Carsten Bergmann, Tobias B. Huber, and Florian Grahammer. Loss of the collagen iv modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. The Journal of Clinical Investigation, May 2022. URL: https://doi.org/10.1172/jci147253, doi:10.1172/jci147253. This article has 42 citations.
(montgomery2018posttranslationalmodificationof pages 1-2): Nathan T. Montgomery, Keith D. Zientek, Elena N. Pokidysheva, and Hans Peter Bächinger. Post-translational modification of type iv collagen with 3-hydroxyproline affects its interactions with glycoprotein vi and nidogens 1 and 2. Journal of Biological Chemistry, 293:5987-5999, Apr 2018. URL: https://doi.org/10.1074/jbc.ra117.000406, doi:10.1074/jbc.ra117.000406. This article has 35 citations and is from a domain leading peer-reviewed journal.
(aypek2022lossofthe media f8c46f40): Hande Aypek, Christoph Krisp, Shun Lu, Shuya Liu, Dominik Kylies, Oliver Kretz, Guochao Wu, Manuela Moritz, Kerstin Amann, Kerstin Benz, Ping Tong, Zheng-mao Hu, Sulaiman M. Alsulaiman, Arif O. Khan, Maik Grohmann, Timo Wagner, Janina Müller-Deile, Hartmut Schlüter, Victor G. Puelles, Carsten Bergmann, Tobias B. Huber, and Florian Grahammer. Loss of the collagen iv modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. The Journal of Clinical Investigation, May 2022. URL: https://doi.org/10.1172/jci147253, doi:10.1172/jci147253. This article has 42 citations.
(aypek2022lossofthe media 01d7b518): Hande Aypek, Christoph Krisp, Shun Lu, Shuya Liu, Dominik Kylies, Oliver Kretz, Guochao Wu, Manuela Moritz, Kerstin Amann, Kerstin Benz, Ping Tong, Zheng-mao Hu, Sulaiman M. Alsulaiman, Arif O. Khan, Maik Grohmann, Timo Wagner, Janina Müller-Deile, Hartmut Schlüter, Victor G. Puelles, Carsten Bergmann, Tobias B. Huber, and Florian Grahammer. Loss of the collagen iv modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. The Journal of Clinical Investigation, May 2022. URL: https://doi.org/10.1172/jci147253, doi:10.1172/jci147253. This article has 42 citations.
(montgomery2018posttranslationalmodificationof pages 13-14): Nathan T. Montgomery, Keith D. Zientek, Elena N. Pokidysheva, and Hans Peter Bächinger. Post-translational modification of type iv collagen with 3-hydroxyproline affects its interactions with glycoprotein vi and nidogens 1 and 2. Journal of Biological Chemistry, 293:5987-5999, Apr 2018. URL: https://doi.org/10.1074/jbc.ra117.000406, doi:10.1074/jbc.ra117.000406. This article has 35 citations and is from a domain leading peer-reviewed journal.
(pignata2021prolyl3hydroxylase2 pages 14-15): Paola Pignata, Ivana Apicella, Valeria Cicatiello, Caterina Puglisi, Sara Magliacane Trotta, Remo Sanges, Valeria Tarallo, and Sandro De Falco. Prolyl 3-hydroxylase 2 is a molecular player of angiogenesis. International Journal of Molecular Sciences, 22:3896, Apr 2021. URL: https://doi.org/10.3390/ijms22083896, doi:10.3390/ijms22083896. This article has 13 citations.
(tekin2013slitrk6mutationscause pages 1-2): Mustafa Tekin, Barry A. Chioza, Yoshifumi Matsumoto, Oscar Diaz-Horta, Harold E. Cross, Duygu Duman, Haris Kokotas, Heather L. Moore-Barton, Kazuto Sakoori, Maya Ota, Yuri S. Odaka, Joseph Foster, F. Basak Cengiz, Suna Tokgoz-Yilmaz, Oya Tekeli, Maria Grigoriadou, Michael B. Petersen, Ajith Sreekantan-Nair, Kay Gurtz, Xia-Juan Xia, Arti Pandya, Michael A. Patton, Juan I. Young, Jun Aruga, and Andrew H. Crosby. Slitrk6 mutations cause myopia and deafness in humans and mice. The Journal of clinical investigation, 123 5:2094-102, May 2013. URL: https://doi.org/10.1172/jci65853, doi:10.1172/jci65853. This article has 79 citations.
(salo2021prolylandlysyl pages 21-24): Antti M. Salo and Johanna Myllyharju. Prolyl and lysyl hydroxylases in collagen synthesis. Experimental Dermatology, 30:38-49, Oct 2021. URL: https://doi.org/10.1111/exd.14197, doi:10.1111/exd.14197. This article has 146 citations and is from a domain leading peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

montgomery2018posttranslationalmodificationof pages 1-2
aypek2022lossofthe pages 1-2
gjaltema2017molecularinsightsinto pages 4-5
salo2021prolylandlysyl pages 21-24
marini2007componentsofthe pages 5-5
fonsen2007prolylhydroxylasescloning pages 1-7
salo2021prolylandlysyl pages 7-9
onursal2023differentialeffectsof pages 41-46
montgomery2018posttranslationalmodificationof pages 13-14
https://doi.org/10.4161/cc.6.14.4474
https://doi.org/10.1080/10409238.2016.1269716
https://doi.org/10.1172/jci147253
https://doi.org/10.1111/exd.14197
https://doi.org/10.1074/jbc.ra117.000406
https://doi.org/10.1101/2023.06.28.546985
https://doi.org/10.3390/ijms22083896
https://doi.org/10.1172/JCI65853
https://doi.org/10.1080/10409238.2016.1269716,
https://doi.org/10.4161/cc.6.14.4474,
https://doi.org/10.3390/ijms22083896,
https://doi.org/10.1172/jci147253,
https://doi.org/10.1111/exd.14197,
https://doi.org/10.1074/jbc.ra117.000406,
https://doi.org/10.1172/jci65853,

📚 Additional Documentation

Notes

(P3H2-notes.md)

P3H2 (Prolyl 3-hydroxylase 2; LEPREL1) — review notes

UniProt: Q8IVL5 (P3H2_HUMAN), 708 aa precursor, EC 1.14.11.7. Synonyms: LEPREL1, MLAT4 (Leprecan-like protein 1 / myxoid liposarcoma-associated protein 4). HGNC:19317. Member of the leprecan/prolyl 3-hydroxylase family (P3H1/P3H2/P3H3).

Core molecular function

P3H2 is an ER-lumenal 2-oxoglutarate/Fe(II)-dependent dioxygenase that catalyzes the post-translational formation of (trans-)3-hydroxyproline on collagen prolyl residues.

Catalytic reaction (UniProt): "L-prolyl-[collagen] + 2-oxoglutarate + O2 = trans-3-hydroxy-L-prolyl-[collagen] + succinate + CO2" [EC 1.14.11.7; ECO:0000269|PubMed:18487197].
UniProt FUNCTION: "Prolyl 3-hydroxylase that catalyzes the post-translational formation of 3-hydroxyproline on collagens (PubMed:18487197)." and "Catalyzes hydroxylation of the first Pro in Gly-Pro-Hyp sequences where Hyp is 4-hydroxyproline (PubMed:18487197). Has no activity on substrates that lack 4-hydroxyproline in the third position (PubMed:18487197)."
Substrate preference for basement-membrane collagen IV: UniProt "Has high activity with the type IV collagen COL4A1, and lower activity with COL1A1 (PubMed:18487197)."

Experimental characterization PMID:18487197 and PMID:18487197. The enzyme is distinct from P3H1 in that it does not require CRTAP for activity PMID:18487197, and its 2-oxoglutarate Km/Ki resemble lysyl hydroxylases rather than C-P4Hs PMID:18487197.

Cofactors (catalytic supporting, non-core)

As a 2-OG/Fe(II) dioxygenase, P3H2 requires Fe(II) and uses L-ascorbate (vitamin C) as cofactor.
- UniProt COFACTOR "Name=Fe cation" and "Name=L-ascorbate" [ECO:0000305|PubMed:18487197]; kinetic parameters "KM=0.5 uM for Fe(2+)" and "KM=110 uM for ascorbate".
- UniProt KW: "Iron; Metal-binding; Oxidoreductase; Vitamin C." and the Fe2OG dioxygenase domain (residues 557-671) with Fe-binding residues 580/582/652.
Iron ion binding (GO:0005506), L-ascorbic acid binding (GO:0031418), and the oxidoreductase-on-paired-donors parent (GO:0016705) are accurate catalytic/structural attributes but subsidiary to the informative MF (procollagen-proline 3-dioxygenase activity, GO:0019797).

Subcellular location

ER lumen / ER is the site of action (collagen modification occurs co/post-translationally in the ER before secretion). UniProt: "SUBCELLULAR LOCATION: Endoplasmic reticulum ... Sarcoplasmic reticulum ... Golgi apparatus." Contains a C-terminal ER-retention signal (residues 705-708, "Prevents secretion from ER"; PROSITE ER_TARGET; the KDEL-type motif).
- ER + Golgi localization shown by IF PMID:15063763.
- Reactome (TAS) places it in ER lumen (R-HSA-1980233, R-HSA-8948226, R-HSA-8948230) — consistent and the most precise CC term.
- Sarcoplasmic reticulum is the specialized ER of muscle; consistent with strong muscle expression and the 200 kDa muscle-specific transcript PMID:15063763. Keep but non-core.
- Basement membrane (GO:0005604, ISS/IEA from mouse ortholog Q8CG71) is the location of the COLLAGEN IV substrate/product, not where the enzyme itself acts; the enzyme is ER-resident. Treat as non-core (mark over-annotated) — P3H2 acts in the ER on procollagen, not in the assembled basement membrane.

Biological process

collagen metabolic process (GO:0032963) and peptidyl-proline hydroxylation (GO:0019511) — both correct and directly supported by IDA PMID:18487197.
Contributes to 3-hydroxylation of COL4A1 and COL1A1 in tendon, eye sclera, lens capsule (UniProt, by similarity).

Disease

Loss-of-function variant (G508V) causes autosomal-recessive high myopia with cataract and vitreoretinal degeneration (MCVD, MIM:614292) [UniProt DISEASE; PubMed:21885030]. Consistent with a role in basement-membrane/eye collagen biogenesis.

Cancer / proliferation annotation (PMID:19436308)

P3H2 (and P3H3) are epigenetically silenced by promoter CpG methylation in breast cancer; ectopic re-expression suppresses colony formation, suggesting a tumor-suppressor-like activity PMID:19436308. This is the basis for the GO:0008285 (negative regulation of cell population proliferation) IDA annotation. The colony-suppression assay is real and gene-specific (P3H2 cDNA into MCF7 and T47D), so the experimental annotation should not be removed; however this is a context-dependent/indirect phenotype (overexpression in cancer cell lines), not the enzyme's core ER collagen-modifying function. Keep as non-core. Full text available and verified.

Annotation strategy summary

Core MF: GO:0019797 procollagen-proline 3-dioxygenase activity — ACCEPT as core (IDA PMID:18487197; IBA; IEA all converge).
ER (GO:0005783) / ER lumen (GO:0005788) — ACCEPT (IDA, TAS); ER lumen is most precise.
collagen metabolic process (GO:0032963), peptidyl-proline hydroxylation (GO:0019511) — ACCEPT.
iron ion binding (GO:0005506), L-ascorbic acid binding (GO:0031418), oxidoreductase activity on paired donors (GO:0016705) — KEEP_AS_NON_CORE (catalytic cofactor/structural support).
Golgi (GO:0005794), sarcoplasmic reticulum (GO:0016529) — KEEP_AS_NON_CORE (secondary localizations).
basement membrane (GO:0005604) — MARK_AS_OVER_ANNOTATED (location of substrate, not enzyme; ortholog transfer).
negative regulation of cell population proliferation (GO:0008285) — KEEP_AS_NON_CORE (real IDA but indirect tumor-suppressor phenotype).
No bare protein binding (GO:0005515) annotation present in this GOA.

Falcon deep-research findings (incorporated 2026-06)

Falcon surfaced three genuinely new, verified P3H2-specific references (all PubMed-confirmed; none in publications cache, so added as reference ids without paraphrased supporting_text):

In vivo confirmation that P3H2 is the principal collagen IV 3-hydroxylase, via a P3H2-knockout cell line: "we confirm that P3H2 is the major, but not the only 3-Hyp-modifying enzyme of type IV collagen" [PMID:29491144 (DOI 10.1074/jbc.RA117.000406)]. This corroborates the existing IDA collagen IV substrate-specificity annotation with knockout (rather than recombinant-peptide) evidence.
3-Hyp on collagen IV modulates its protein interactions: reduced 3-Hyp increases glycoprotein VI (GP6) binding, whereas 3-Hyp is required for nidogen 1/2 binding PMID:29491144. Mechanistic link between P3H2 activity and basement-membrane assembly partners (not previously in review).
New renal disease association: P3H2 is a glomerular basement membrane (GBM) modifier; podocyte-specific loss in mice causes thin basement membrane nephropathy (TBMN) with progressive microhematuria/microalbuminuria, and P3H2 loss/mutation causes TBMN and FSGS in mice and humans [PMID:35499085 (DOI 10.1172/JCI147253) "P3H2 protein is the first identified GBM modifier, and loss or mutation of P3H2 causes TBMN and focal segmental glomerulosclerosis in mice and humans"]. Complements the previously-noted ocular MCVD high-myopia phenotype; in vivo proof of collagen IV as the physiological substrate (GBM proteomics shows decreased collagen IV subchains on P3H2 loss). Added as HIGH relevance.
Angiogenesis role: P3H2 is induced by VEGF-A via VEGFR-2/p38 MAPK in endothelial cells and, through its collagen IV activity, supports angiogenesis; knockdown reduces pathological choroidal neovascularization in vivo [PMID:33918807 (DOI 10.3390/ijms22083896) "P3H2 is a new molecular player involved in new vessels formation and could be considered as a potential target for anti-angiogenesis therapy"]. Added as MEDIUM relevance (context-dependent physiological role downstream of the core MF).
These are additive references only; no action: changes (review was COMPLETE). The findings reinforce, rather than alter, the core MF (GO:0019797, collagen IV-preferring prolyl 3-hydroxylase) and the ER site of action. The Aypek/Montgomery in vivo evidence further supports that "basement membrane" (GO:0005604) is the destination of the collagen IV substrate, consistent with the existing MARK_AS_OVER_ANNOTATED decision for that CC term on the enzyme itself.

Pn Notes

(P3H2-pn-notes.md)

P3H2 PN Consistency Notes

Generated: 2026-06-18
Project: PROTEOSTASIS
Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
UniProt: Q8IVL5
AIGR review status: COMPLETE
Review batch: proteostasis-batch-2026-06-11
Batch change status: added

Source Files Checked

AIGR review YAML: present - genes/human/P3H2/P3H2-ai-review.yaml
AIGR review HTML: missing - genes/human/P3H2/P3H2-ai-review.html
Gene notes: present - genes/human/P3H2/P3H2-notes.md
GOA TSV: present - genes/human/P3H2/P3H2-goa.tsv
UniProt record: present - genes/human/P3H2/P3H2-uniprot.txt
PN dossier: projects/PROTEOSTASIS/reports/phase1_dossiers/P3H2.md
PN consistency section: projects/PROTEOSTASIS/reports/phase1_dossiers/_sections/P3H2.md
PN projection report: projects/PROTEOSTASIS/reports/pn_projection/pn_projected_gene_go_summary.tsv
PN mapping audit: projects/PROTEOSTASIS/reports/pn_mapping_audit/current_mapping_scrutiny.tsv

Deep Research Files

genes/human/P3H2/P3H2-deep-research-falcon.md

AIGR Review Snapshot

Description: P3H2 (prolyl 3-hydroxylase 2, also LEPREL1/MLAT4) is an endoplasmic reticulum-lumenal, 2-oxoglutarate/Fe(II)-dependent dioxygenase (EC 1.14.11.7) of the leprecan/prolyl 3-hydroxylase family (P3H1/P3H2/P3H3). It catalyzes post-translational formation of (trans-)3-hydroxyproline on procollagen, hydroxylating the first proline in Gly-Pro-4Hyp triplets and requiring a pre-existing 4-hydroxyproline in the third position. P3H2 shows high activity toward the basement-membrane collagen type IV (COL4A1), which has the highest 3-hydroxyproline content of all collagens, and lower activity toward collagen I; it is thus considered the principal modifier of basement-membrane collagens, complementing the fibrillar-collagen isoenzyme P3H1. The enzyme uses Fe(II) and L-ascorbate (vitamin C) as cofactors and 2-oxoglutarate as a co-substrate. The 708-residue precursor has an N-terminal signal sequence, tetratricopeptide (TPR) repeats, an Fe2OG dioxygenase (prolyl 4-hydroxylase alpha-type) catalytic domain, and a C-terminal KDEL-type ER-retention motif that retains it in the ER/sarcoplasmic reticulum; it is also detected in the Golgi. P3H2 is broadly expressed with enrichment in basement-membrane-rich tissues such as kidney and in muscle. Loss-of-function variants cause autosomal-recessive high myopia with cataract and vitreoretinal degeneration (MCVD), consistent with a role in ocular/lens-capsule basement-membrane collagen biogenesis.
Existing/core annotation action counts: ACCEPT: 13; KEEP_AS_NON_CORE: 8; MARK_AS_OVER_ANNOTATED: 2

PN Consistency Summary

Consistency: Fully consistent. Deep research (notes + falcon), review YAML, PN annotation, and node mapping all describe an ER-lumenal 2-OG/Fe(II) prolyl 3-hydroxylase (EC 1.14.11.7) acting on procollagen, especially basement-membrane collagen IV. No contradictions. PN places it under collagen processing/folding; review core function is GO:0019797 procollagen-proline 3-dioxygenase activity in GO:0005788 ER lumen.
PN story / NEW pressure: PN asserts the shared "collagen biosynthetic process" role. This is essentially already captured: GOA has GO:0032963 collagen metabolic process (the direct parent of GO:0032964; verified via OLS), accepted in the review. GO:0032964 is one step more specific and defensible (verified real, child of GO:0032963). Conclusion: low-pressure ADD of GO:0032964 (or rely on existing GO:0032963) — the substrate-specific story is captured; the projection is a justified mild refinement, not an over-reach.
Evidence alignment: PN dossier carries no reference titles (mapping-only). Review evidence: IDA PMID:18487197 (collagen IV characterization), PMID:15063763 (ER/Golgi localization), plus KO/disease papers (PMID:29491144, 35499085). Substrate-specificity story (collagen IV) underpins the PN "collagen processing" placement; consistent.
Verdict: Consistent and well-curated; PN collagen-biosynthesis story already captured (GO:0032963) with GO:0032964 a defensible narrower ADD.

Full Consistency Review

UniProt: Q8IVL5 (LEPREL1) · batch: proteostasis-batch-2026-06-11 · review status: COMPLETE
PN placement: ER proteostasis | Maturation and folding of specific substrates | ER collagen processing and folding ; PN-node mapping: group=mapped, scope=ok_for_propagation_to_go, GO=GO:0032964 collagen biosynthetic process (class/branch = no_mapping). Projection goa_status=more_specific_than_existing_goa.
Consistency: Fully consistent. Deep research (notes + falcon), review YAML, PN annotation, and node mapping all describe an ER-lumenal 2-OG/Fe(II) prolyl 3-hydroxylase (EC 1.14.11.7) acting on procollagen, especially basement-membrane collagen IV. No contradictions. PN places it under collagen processing/folding; review core function is GO:0019797 procollagen-proline 3-dioxygenase activity in GO:0005788 ER lumen.
PN story / NEW pressure: PN asserts the shared "collagen biosynthetic process" role. This is essentially already captured: GOA has GO:0032963 collagen metabolic process (the direct parent of GO:0032964; verified via OLS), accepted in the review. GO:0032964 is one step more specific and defensible (verified real, child of GO:0032963). Conclusion: low-pressure ADD of GO:0032964 (or rely on existing GO:0032963) — the substrate-specific story is captured; the projection is a justified mild refinement, not an over-reach.
Mapping strategy: Correct. Group-level mapping with class/branch deliberately unmapped is sound (collagen processing group is substrate-coherent). GO:0032964 is narrower than P3H2's existing GO:0032963 and matches review BP framing; not broader (contrast TOMM20/HSPA8/RAB7A rejected-as-broader precedent). Catalytic gene, correctly handled.
Evidence alignment: PN dossier carries no reference titles (mapping-only). Review evidence: IDA PMID:18487197 (collagen IV characterization), PMID:15063763 (ER/Golgi localization), plus KO/disease papers (PMID:29491144, 35499085). Substrate-specificity story (collagen IV) underpins the PN "collagen processing" placement; consistent.
Verdict: Consistent and well-curated; PN collagen-biosynthesis story already captured (GO:0032963) with GO:0032964 a defensible narrower ADD.

PN Dossier Context

review_batch: proteostasis-batch-2026-06-11
review_yaml: genes/human/P3H2/P3H2-ai-review.yaml
PN workbook rows: 1

PN row 1: ER proteostasis | Maturation and folding of specific substrates | ER collagen processing and folding

UniProt: Q8IVL5
In branches: ER
PN-node mapping records (path + ancestors):
- [group] ER proteostasis|Maturation and folding of specific substrates|ER collagen processing and folding
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0032964 collagen biosynthetic process]
  rationale: This PN group contains ER factors dedicated to collagen maturation, processing, and folding. Collagen biosynthetic process captures the shared substrate-specific pathway context.
- [class] ER proteostasis|Maturation and folding of specific substrates
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a broad PN category rather than a single GO class. The member genes span multiple activities, complexes, or contexts, so direct propagation from this node would overstate the shared biology.
- [branch] ER proteostasis
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a top-level PN branch. This is a systems/taxonomy umbrella, not a direct GO assertion; narrower child curations carry any propagating GO mappings.

Projected GO annotations (1)

GO:0032964 collagen biosynthetic process | scope=ok_for_propagation_to_go | goa_status=more_specific_than_existing_goa | from=ER proteostasis|Maturation and folding of specific substrates|ER collagen processing and folding

Note

This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.

📄 View Raw YAML

id: Q8IVL5
gene_symbol: P3H2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: P3H2 (prolyl 3-hydroxylase 2, also LEPREL1/MLAT4) is an endoplasmic reticulum-lumenal,
  2-oxoglutarate/Fe(II)-dependent dioxygenase (EC 1.14.11.7) of the leprecan/prolyl 3-hydroxylase family
  (P3H1/P3H2/P3H3). It catalyzes post-translational formation of (trans-)3-hydroxyproline on procollagen,
  hydroxylating the first proline in Gly-Pro-4Hyp triplets and requiring a pre-existing 4-hydroxyproline in
  the third position. P3H2 shows high activity toward the basement-membrane collagen type IV (COL4A1), which
  has the highest 3-hydroxyproline content of all collagens, and lower activity toward collagen I; it is thus
  considered the principal modifier of basement-membrane collagens, complementing the fibrillar-collagen
  isoenzyme P3H1. The enzyme uses Fe(II) and L-ascorbate (vitamin C) as cofactors and 2-oxoglutarate as a
  co-substrate. The 708-residue precursor has an N-terminal signal sequence, tetratricopeptide (TPR) repeats,
  an Fe2OG dioxygenase (prolyl 4-hydroxylase alpha-type) catalytic domain, and a C-terminal KDEL-type ER-retention
  motif that retains it in the ER/sarcoplasmic reticulum; it is also detected in the Golgi. P3H2 is broadly
  expressed with enrichment in basement-membrane-rich tissues such as kidney and in muscle. Loss-of-function
  variants cause autosomal-recessive high myopia with cataract and vitreoretinal degeneration (MCVD), consistent
  with a role in ocular/lens-capsule basement-membrane collagen biogenesis.
alternative_products:
- name: '1'
  id: Q8IVL5-1
- name: '2'
  id: Q8IVL5-2
  sequence_note: VSP_053814
existing_annotations:
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: P3H2 acts in the endoplasmic reticulum, where collagen prolyl hydroxylation occurs prior to secretion.
      The phylogenetic (IBA) ER localization is consistent with direct experimental evidence (IDA) and the C-terminal
      ER-retention motif.
    action: ACCEPT
    reason: ER is the correct catalytic compartment; supported by IDA (PMID:15063763), the KDEL-type ER-retention
      motif, and the UniProt subcellular location.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum'
- term:
    id: GO:0019797
    label: procollagen-proline 3-dioxygenase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: Procollagen-proline 3-dioxygenase activity is the core molecular function of P3H2, conserved across the
      P3H/leprecan family and directly demonstrated for human P3H2 on collagen IV-derived peptides.
    action: ACCEPT
    reason: Core molecular function; corroborated by IDA (PMID:18487197), EC 1.14.11.7, and family-level conservation.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Prolyl 3-hydroxylase that catalyzes the post-translational
        formation of 3-hydroxyproline on collagens
- term:
    id: GO:0032963
    label: collagen metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: By 3-hydroxylating procollagen prolyl residues, P3H2 participates in collagen biosynthesis/metabolism;
      the phylogenetic annotation is consistent with the experimental IDA evidence.
    action: ACCEPT
    reason: Correct biological process; redundant with IDA (PMID:18487197) collagen metabolic process annotation.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: post-translational
        formation of 3-hydroxyproline on collagens
- term:
    id: GO:0005506
    label: iron ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: As a 2-oxoglutarate/Fe(II)-dependent dioxygenase, P3H2 coordinates a catalytic Fe(II) ion (binding
      residues 580/582/652) required for hydroxylation. This cofactor binding supports, but is subsidiary to, the
      informative procollagen-proline 3-dioxygenase activity.
    action: KEEP_AS_NON_CORE
    reason: Accurate catalytic cofactor attribute (Fe cation cofactor; Fe-binding residues in the Fe2OG domain) but a
      supporting feature rather than the standalone core function.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Name=Fe cation
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic transfer of ER localization from the UniProt subcellular location, consistent with the stronger
      IDA/IBA evidence.
    action: ACCEPT
    reason: Correct compartment; redundant with experimental ER localization.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum'
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic transfer of the Golgi localization from the UniProt subcellular location. Golgi residence is
      a reported secondary localization; the catalytic site of action is the ER lumen.
    action: KEEP_AS_NON_CORE
    reason: Accurate reported localization (UniProt/IDA) but secondary to the ER, where collagen prolyl hydroxylation
      occurs; not the core site of action.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Golgi apparatus
- term:
    id: GO:0016529
    label: sarcoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: The sarcoplasmic reticulum is the specialized ER of muscle; this localization is consistent with the
      strong muscle expression and muscle-specific transcript of P3H2 reported by Jaernum et al.
    action: KEEP_AS_NON_CORE
    reason: Accurate UniProt-derived localization reflecting muscle-tissue ER, but a tissue-specific variant of the
      ER compartment rather than a distinct core function.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Sarcoplasmic reticulum
- term:
    id: GO:0016705
    label: oxidoreductase activity, acting on paired donors, with incorporation or
      reduction of molecular oxygen
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: This is the parent oxidoreductase class for the dioxygenase reaction P3H2 catalyzes (it incorporates one
      atom of O2 into proline while reducing 2-oxoglutarate). Correct but less informative than the specific
      procollagen-proline 3-dioxygenase activity.
    action: KEEP_AS_NON_CORE
    reason: Correct but generic parent term; the specific GO:0019797 captures the core catalytic activity.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: EC=1.14.11.7
- term:
    id: GO:0019797
    label: procollagen-proline 3-dioxygenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Electronic (multi-method, EC/Rhea-based) assignment of the core procollagen-proline 3-dioxygenase
      activity, consistent with the experimental IDA evidence and EC 1.14.11.7.
    action: ACCEPT
    reason: Correct core molecular function; redundant with IDA/IBA evidence.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: EC=1.14.11.7
- term:
    id: GO:0031418
    label: L-ascorbic acid binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: P3H2 uses L-ascorbate (vitamin C) as a cofactor to maintain the active-site iron in the reduced state,
      a hallmark of collagen prolyl hydroxylases. This cofactor binding supports the catalytic activity.
    action: KEEP_AS_NON_CORE
    reason: Accurate catalytic cofactor attribute (L-ascorbate cofactor; KM=110 uM for ascorbate) but subsidiary to
      the informative procollagen-proline 3-dioxygenase activity.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Name=L-ascorbate
- term:
    id: GO:0032963
    label: collagen metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: Electronic assignment of the collagen metabolic process, consistent with the experimental IDA evidence.
    action: ACCEPT
    reason: Correct biological process; redundant with IDA (PMID:18487197).
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 3-hydroxyproline on collagens
- term:
    id: GO:0005604
    label: basement membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: Basement membrane is the location of P3H2's collagen IV substrate/product, not where the enzyme itself
      acts. P3H2 is an ER-resident enzyme (KDEL-type retention motif) that modifies procollagen in the ER lumen before
      secretion; it is not a structural component of the assembled basement membrane. This annotation is transferred
      electronically from the mouse ortholog.
    action: MARK_AS_OVER_ANNOTATED
    reason: Ortholog-transferred (Ensembl/ISS from Q8CG71) localization to basement membrane conflates the enzyme's ER
      site of action with the destination of its collagen IV substrate; P3H2 acts in the ER and is retained there by a
      KDEL-type motif.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Prevents secretion from ER
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: Immunofluorescence (HPA) evidence for Golgi localization, consistent with the reported ER-and-Golgi
      distribution of P3H2. The catalytic site of action remains the ER lumen.
    action: KEEP_AS_NON_CORE
    reason: Direct (IDA) reported localization but secondary to the ER catalytic compartment; not the core site of
      action.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Golgi apparatus
- term:
    id: GO:0005788
    label: endoplasmic reticulum lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1980233
  qualifier: located_in
  review:
    summary: Reactome curation places P3H2 in the ER lumen, the precise compartment where collagen prolyl
      3-hydroxylation occurs. This is the most informative cellular-component term for the enzyme.
    action: ACCEPT
    reason: Correct and precise catalytic compartment; consistent with the ER localization and ER-retention motif.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum'
- term:
    id: GO:0005788
    label: endoplasmic reticulum lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8948226
  qualifier: located_in
  review:
    summary: Reactome curation of P3H2 in the ER lumen during the collagen 3-hydroxylation reaction cycle.
    action: ACCEPT
    reason: Correct precise catalytic compartment; redundant with the other ER lumen TAS annotation.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum'
- term:
    id: GO:0005788
    label: endoplasmic reticulum lumen
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8948230
  qualifier: located_in
  review:
    summary: Reactome curation of P3H2 in the ER lumen, where it binds 4-Hyp collagen propeptides.
    action: ACCEPT
    reason: Correct precise catalytic compartment; redundant with the other ER lumen TAS annotations.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum'
- term:
    id: GO:0005604
    label: basement membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: Sequence-similarity (ISS, from mouse ortholog Q8CG71) transfer of basement membrane localization. As with
      the IEA version, this reflects the location of the collagen IV substrate/product rather than the ER-resident
      enzyme's site of action.
    action: MARK_AS_OVER_ANNOTATED
    reason: ISS transfer from the mouse ortholog conflates enzyme site of action (ER) with the destination of its
      collagen IV substrate; P3H2 is ER-retained via a KDEL-type motif.
    supported_by:
    - reference_id: file:human/P3H2/P3H2-uniprot.txt
      supporting_text: Prevents secretion from ER
- term:
    id: GO:0019511
    label: peptidyl-proline hydroxylation
  evidence_type: IDA
  original_reference_id: PMID:18487197
  qualifier: involved_in
  review:
    summary: P3H2 directly hydroxylates peptidyl-proline residues; the recombinant enzyme assay demonstrated robust
      activity on (Gly-Pro-4Hyp)5 and collagen IV-derived peptides. This is the biological-process view of the core
      catalytic function.
    action: ACCEPT
    reason: Directly demonstrated peptidyl-proline hydroxylation activity (IDA); the central biological process of P3H2.
    supported_by:
    - reference_id: PMID:18487197
      supporting_text: A large amount of P3H activity was found in the P3H2 samples
        with (Gly-Pro-4Hyp)5 as a substrate
- term:
    id: GO:0019797
    label: procollagen-proline 3-dioxygenase activity
  evidence_type: IDA
  original_reference_id: PMID:18487197
  qualifier: enables
  review:
    summary: Direct experimental demonstration that recombinant human P3H2 catalyzes prolyl 3-hydroxylation, with high
      activity toward collagen IV sequences. This is the core molecular function of the enzyme.
    action: ACCEPT
    reason: Core molecular function with direct experimental (IDA) support; defines P3H2 as the collagen IV-preferring
      prolyl 3-hydroxylase isoenzyme (EC 1.14.11.7).
    supported_by:
    - reference_id: PMID:18487197
      supporting_text: P3H2 hydroxylated more effectively two synthetic peptides corresponding
        to sequences that are hydroxylated in collagen IV than a peptide corresponding
        to the 3-hydroxylation site in collagen I
- term:
    id: GO:0032963
    label: collagen metabolic process
  evidence_type: IDA
  original_reference_id: PMID:18487197
  qualifier: involved_in
  review:
    summary: P3H2 contributes to collagen metabolism by modifying procollagen prolyl residues, with a preference for
      the basement-membrane collagen IV.
    action: ACCEPT
    reason: Directly supported (IDA) collagen-modifying process; central to P3H2's biological role.
    supported_by:
    - reference_id: PMID:18487197
      supporting_text: P3H2 is responsible for the hydroxylation of collagen IV, which
        has the highest 3-hydroxyproline content of all collagens
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:15063763
  qualifier: located_in
  review:
    summary: Direct immunofluorescence evidence that LEPREL1/P3H2 localizes to the ER, consistent with its role as an
      ER-lumenal collagen-modifying enzyme and its KDEL-type retention motif.
    action: ACCEPT
    reason: IDA-supported ER localization agrees with the catalytic site of action and the ER-retention motif.
    supported_by:
    - reference_id: PMID:15063763
      supporting_text: LEPREL1 is localized to the ER and Golgi network
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: PMID:15063763
  qualifier: located_in
  review:
    summary: Direct immunofluorescence evidence that LEPREL1/P3H2 also localizes to the Golgi. This is a reported
      secondary localization; the ER lumen is the catalytic compartment.
    action: KEEP_AS_NON_CORE
    reason: Direct (IDA) reported localization but secondary to the ER site of action for collagen prolyl hydroxylation.
    supported_by:
    - reference_id: PMID:15063763
      supporting_text: LEPREL1 is localized to the ER and Golgi network
- term:
    id: GO:0008285
    label: negative regulation of cell population proliferation
  evidence_type: IDA
  original_reference_id: PMID:19436308
  qualifier: involved_in
  review:
    summary: P3H2 is epigenetically silenced by promoter CpG methylation in breast cancer, and ectopic re-expression
      suppresses colony formation, indicating a tumor-suppressor-like anti-proliferative effect. The colony-suppression
      assay was performed with P3H2 cDNA in P3H2-silenced breast cancer cell lines (MCF7, T47D), so the experimental
      annotation is gene-specific and should be retained. However, this is a context-dependent, likely indirect
      phenotype rather than the enzyme's core ER collagen-modifying function.
    action: KEEP_AS_NON_CORE
    reason: Real gene-specific experimental (IDA) phenotype, but an indirect/context-dependent tumor-suppressor effect
      of overexpression in cancer cell lines, not the core catalytic function; retained as non-core per guidelines.
    supported_by:
    - reference_id: PMID:19436308
      supporting_text: Ectopic expression of P3H2 and P3H3 in cell lines with silencing
        of the endogenous gene results in suppression of colony growth
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:15063763
  title: LEPREL1, a novel ER and Golgi resident member of the Leprecan family.
  findings:
  - statement: LEPREL1/P3H2 is an 80 kDa, 708-residue ER/Golgi-resident protein of the leprecan family with a signal
      sequence, four TPRs, a P4Halpha domain, and a C-terminal KDEL ER-retention motif; over-expression perturbs ER
      PDI staining.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified original characterization of LEPREL1 (P3H2); establishes ER/Golgi localization and
      domain architecture. Abstract-only cache.
- id: PMID:18487197
  title: Characterization of recombinant human prolyl 3-hydroxylase isoenzyme 2, an
    enzyme modifying the basement membrane collagen IV.
  findings:
  - statement: Recombinant human P3H2 has prolyl 3-hydroxylase activity on (Gly-Pro-4Hyp)5 and preferentially
      hydroxylates collagen IV-derived peptides over a collagen I site, identifying P3H2 as the collagen IV-modifying
      isoenzyme; it is enriched in basement-membrane-rich tissues such as kidney and does not require CRTAP.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified; the definitive enzymatic characterization underpinning the IDA molecular-function
      and process annotations and EC 1.14.11.7. Abstract-only cache.
- id: PMID:19436308
  title: The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic
    silencing in breast cancer.
  findings:
  - statement: P3H2 (and P3H3) are silenced by promoter CpG hypermethylation in breast cancer; ectopic re-expression
      of P3H2 in silenced breast cancer cell lines suppresses colony growth, implying tumor-suppressor-like
      anti-proliferative activity.
    reference_section_type: RESULTS
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: PubMed-verified, full text available; supports the GO:0008285 IDA. The anti-proliferative effect is
      an indirect/context-dependent phenotype, not the core enzymatic function.
- id: PMID:29491144
  title: Post-translational modification of type IV collagen with 3-hydroxyproline
    affects its interactions with glycoprotein VI and nidogens 1 and 2.
  findings:
  - statement: Using P3H2-knockout PFHR-9 cells and tandem MS, P3H2 is shown to be
      the major (but not the only) 3-hydroxyproline-modifying enzyme of type IV collagen;
      3-Hyp on collagen IV modulates its interactions with glycoprotein VI (reduced
      3-Hyp increases GP6 binding) and is required for nidogen 1/2 binding.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.1074/jbc.RA117.000406). Direct P3H2 KO study
      confirming P3H2 as the principal collagen IV 3-hydroxylase and linking the 3-Hyp
      mark to collagen IV interaction partners (GP6, nidogens). Supports the
      collagen IV substrate specificity and basement-membrane biological role. Not
      cached; no verbatim supporting_text added.
- id: PMID:33918807
  title: Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis.
  findings:
  - statement: P3H2 is induced by VEGF-A in human endothelial cells via VEGFR-2/p38
      MAPK signaling; through its activity on type IV collagen it is required for
      angiogenic properties in vitro, and P3H2 knockdown prevents pathological
      angiogenesis in a laser-induced choroidal neovascularization model.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.3390/ijms22083896). Implicates P3H2 in
      VEGF-driven endothelial basement-membrane (collagen IV) remodeling and
      angiogenesis; a context-dependent physiological role downstream of the core
      collagen IV-modifying activity. Not cached; no verbatim supporting_text added.
- id: PMID:35499085
  title: Loss of the collagen IV modifier prolyl 3-hydroxylase 2 causes thin basement
    membrane nephropathy.
  findings:
  - statement: P3H2 was identified as a glomerular basement membrane (GBM) modifier
      in a cohort of patients with albuminuria; it 3-hydroxylates prolines in collagen
      IV subchains in the ER, and podocyte-specific loss in mice produces a thin
      basement membrane nephropathy (TBMN) phenotype with progressive microhematuria
      and microalbuminuria. Loss/mutation of P3H2 causes TBMN and focal segmental
      glomerulosclerosis (FSGS) in mice and humans.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.1172/JCI147253). First identification of
      P3H2 as a GBM modifier; in vivo confirmation of collagen IV as the physiological
      substrate and a new renal disease association (TBMN/FSGS) complementing the
      ocular (MCVD high myopia) phenotype. Not cached; no verbatim supporting_text
      added.
- id: Reactome:R-HSA-1980233
  title: Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
  findings: []
- id: Reactome:R-HSA-8948226
  title: Prolyl 3-hydroxylases:Fe2+:3,4-Hyp collagen propeptides dissociates
  findings: []
- id: Reactome:R-HSA-8948230
  title: P3HB binds 4-Hyp-collagen propeptides
  findings: []
- id: file:human/P3H2/P3H2-uniprot.txt
  title: UniProt entry Q8IVL5 (P3H2_HUMAN), prolyl 3-hydroxylase 2
  findings:
  - statement: ER-lumenal 2-oxoglutarate/Fe(II)-dependent dioxygenase (EC 1.14.11.7) that 3-hydroxylates procollagen
      prolyl residues (high activity on collagen IV/COL4A1, lower on COL1A1); uses Fe cation and L-ascorbate cofactors;
      contains an Fe2OG dioxygenase domain and a C-terminal KDEL-type ER-retention motif; ER/sarcoplasmic
      reticulum/Golgi localization; loss-of-function variant causes MCVD high myopia.
    reference_section_type: OTHER
core_functions:
- description: ER-lumenal 2-oxoglutarate/Fe(II)-dependent prolyl 3-hydroxylase that catalyzes post-translational
    3-hydroxylation of specific prolyl residues in procollagen (the first Pro of Gly-Pro-4Hyp triplets), acting
    preferentially on basement-membrane collagen type IV.
  molecular_function:
    id: GO:0019797
    label: procollagen-proline 3-dioxygenase activity
  locations:
  - id: GO:0005788
    label: endoplasmic reticulum lumen
  supported_by:
  - reference_id: PMID:18487197
    supporting_text: P3H2 hydroxylated more effectively two synthetic peptides corresponding
      to sequences that are hydroxylated in collagen IV than a peptide corresponding
      to the 3-hydroxylation site in collagen I
  - reference_id: file:human/P3H2/P3H2-uniprot.txt
    supporting_text: Prolyl 3-hydroxylase that catalyzes the post-translational
      formation of 3-hydroxyproline on collagens
  directly_involved_in:
  - id: GO:0019511
    label: peptidyl-proline hydroxylation
  - id: GO:0032963
    label: collagen metabolic process
proposed_new_terms: []
suggested_questions:
- question: Does P3H2 act as a monomer or within a multiprotein complex in the ER lumen, and does it (like P3H1/CRTAP/PPIB)
    have additional chaperone/foldase or non-catalytic roles in basement-membrane collagen biogenesis?
- question: Is the anti-proliferative/tumor-suppressor effect of P3H2 in breast cancer a consequence of its
    collagen-modifying enzymatic activity (e.g. altered ECM signaling) or an activity-independent moonlighting function?
suggested_experiments:
- description: Quantitative mass spectrometry of 3-hydroxyproline sites on collagen IV (and other basement-membrane
    collagens) from P3H2-knockout versus wild-type cells/tissues to define the in vivo substrate site repertoire and
    confirm collagen IV specificity.
- description: Structure-function analysis of the MCVD G508V variant (and active-site mutants) measuring prolyl
    3-hydroxylase activity, folding/solubility, and ER retention to establish the molecular basis of the loss of
    function underlying high myopia.

P3H2

Gene Description

Existing Annotations Review

Core Functions

ER-lumenal 2-oxoglutarate/Fe(II)-dependent prolyl 3-hydroxylase that catalyzes post-translational 3-hydroxylation of specific prolyl residues in procollagen (the first Pro of Gly-Pro-4Hyp triplets), acting preferentially on basement-membrane collagen type IV.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Comprehensive research report: Human P3H2 / LEPREL1 (UniProt Q8IVL5) functional annotation

0) Target verification (gene/protein identity)

1) Key concepts, definitions, and current understanding

1.1 What does P3H2 do? (enzyme class and reaction)

1.2 Substrate specificity: collagen IV as the dominant physiological target

1.3 Domain architecture and family features (what makes it a leprecan-family enzyme)

1.4 Where does P3H2 function in the cell? (subcellular localization)

2) Primary biological roles and pathway context

2.1 Basement membrane collagen IV maturation and interactome

2.2 Angiogenesis link via ECM remodeling downstream of VEGF signaling

3) Disease relevance (human genetics and mechanistic models)

3.1 Kidney disease: thin basement membrane nephropathy (TBMN) and FSGS

3.2 Ocular phenotypes: high myopia and cataract/vitreoretinal degeneration

4) Current applications and real-world implementations

4.1 Diagnostics/clinical genetics (implemented use)

4.2 Therapeutic concepts (preclinical)

5) Expert opinions and synthesis (authoritative review perspectives)

6) Relevant statistics and data points

7) 2023–2024 research update (evidence-limited in retrieved corpus)

Summary table (quick reference)

Key references (publication date and URL)

Artifacts

Citations

📚 Additional Documentation

Notes

P3H2 (Prolyl 3-hydroxylase 2; LEPREL1) — review notes

Core molecular function

Cofactors (catalytic supporting, non-core)

Subcellular location

Biological process

Disease

Cancer / proliferation annotation (PMID:19436308)

Annotation strategy summary

Falcon deep-research findings (incorporated 2026-06)

Pn Notes

P3H2 PN Consistency Notes

Source Files Checked

Deep Research Files

AIGR Review Snapshot

PN Consistency Summary

Full Consistency Review

PN Dossier Context

PN row 1: ER proteostasis | Maturation and folding of specific substrates | ER collagen processing and folding

Projected GO annotations (1)

Note

📄 View Raw YAML