Affinage

GNPAT

Dihydroxyacetone phosphate acyltransferase · UniProt O15228

Length
680 aa
Mass
77.2 kDa
Annotated
2026-06-10
21 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

GNPAT (DHAPAT) is a peroxisomal acyltransferase that catalyzes the committed step of de novo plasmalogen (ether-phospholipid) biosynthesis; its isolated deficiency causes rhizomelic chondrodysplasia punctata type 2 while leaving all other peroxisomal functions intact, and GNPAT is the sole gene responsible for this disorder (PMID:8466247, PMID:11237722). Catalytic activity is restricted to the membrane-bound form of the enzyme, with an N-terminal lipid-binding domain whose binding is enhanced by phosphatidic acid (PMID:37204785), and full activity depends on its luminal-membrane partner AGPS through substrate channeling from GNPAT to AGPS (PMID:21990100). The enzyme exhibits high latency that requires reduced glutathione and intact peroxisomal membrane thiol groups, with ATP stimulating the latent activity through a cation-dependent mechanism (PMID:1657193). Loss of GNPAT-dependent plasmalogen synthesis disrupts myelin integrity (PMID:10972423). Beyond plasmalogen production, GNPAT is regulated by SIRT4-mediated deacetylation that lowers its protein level and activity and thereby modulates cigarette-smoke-induced ferroptosis (PMID:38041059), and it has been linked to mitochondrial fission via recruitment of USP30 to deubiquitinate and stabilize DRP1 (PMID:40709564). A proposed role in hepatocyte hepcidin/iron regulation is contested: a HepG2 knockdown reduced hepcidin expression (PMID:25605615), but comprehensive Gnpat knockout mouse models showed no systemic iron or hepcidin phenotype (PMID:32108988).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1991 Medium

    Established the biochemical behavior of the enzyme by showing its peroxisomal latency depends on reduced glutathione and membrane thiol integrity, defining the conditions under which it is catalytically active.

    Evidence selective permeabilization of human fibroblasts with defined-medium enzyme assays manipulating GSH/GSSG, ATP, and cations

    PMID:1657193

    Open questions at the time
    • molecular basis of thiol-dependent latency not defined
    • no structural mechanism for ATP/cation stimulation
  2. 1993 Medium

    Defined the disease relevance of GNPAT by showing that its isolated deficiency causes RCDP with selectively deficient plasmalogen synthesis, establishing the enzyme as essential and non-redundant in this pathway.

    Evidence enzyme activity assay in patient fibroblasts with a comprehensive peroxisomal function panel

    PMID:8466247

    Open questions at the time
    • causative gene mutation not yet identified at this stage
    • tissue-level consequences beyond fibroblasts not addressed
  3. 2000 Medium

    Linked a specific GNPAT missense mutation to deficient plasmalogen synthesis and abnormal myelin, connecting the enzyme's biochemical role to a downstream physiological consequence.

    Evidence patient fibroblast enzyme assays, cDNA mutation identification (R211H), and white-matter MRI

    PMID:10972423

    Open questions at the time
    • mechanism connecting plasmalogen loss to myelin defect not established
    • single mutation
  4. 2001 Medium

    Confirmed GNPAT as the sole gene underlying RCDP type 2 by cataloguing diverse loss-of-function mutations, cementing the genotype-phenotype relationship.

    Evidence genomic sequencing, exon mapping, and mutation analysis across 12 patients

    PMID:11237722

    Open questions at the time
    • functional impact of individual mutation classes on protein not resolved
  5. 2011 Medium

    Identified AGPS as a physical partner required for full GNPAT activity via substrate channeling, revealing that the enzyme functions within a coupled complex rather than alone.

    Evidence protein quantification, structural modeling, transcript analysis, and functional assays across patient cell lines

    PMID:21990100

    Open questions at the time
    • direct structural interface of GNPAT-AGPS not defined
    • channeling mechanism inferred rather than reconstituted
  6. 2023 Medium

    Resolved which form of the enzyme is active and identified an N-terminal regulatory lipid-binding domain, explaining the soluble-versus-membrane activity difference.

    Evidence heterologous expression of Xenopus Gnpat in yeast, subcellular fractionation, activity assays, and phosphatidic-acid lipid-binding assays

    PMID:37204785

    Open questions at the time
    • functional role of N-terminal lipid binding in human enzyme regulation not demonstrated in vivo
    • ortholog system
  7. 2023 Medium

    Established post-translational control of GNPAT by SIRT4 deacetylation and connected the enzyme to ferroptosis susceptibility, extending its role beyond constitutive plasmalogen synthesis.

    Evidence immunoprecipitation for acetylation plus knockdown/overexpression rescue with ferroptosis readouts in A549 cells

    PMID:38041059

    Open questions at the time
    • acetylated residues not mapped
    • link between GNPAT activity and ferroptosis lipid species not defined
  8. 2025 Medium

    Proposed a non-enzymatic scaffolding role in which GNPAT recruits USP30 to stabilize DRP1 and drive mitochondrial fission, broadening its function into mitochondrial dynamics.

    Evidence co-immunoprecipitation, overexpression/knockdown rescue, electron microscopy, and a mouse COPD model in A549 cells

    PMID:40709564

    Open questions at the time
    • reciprocal validation and endogenous-level interaction not shown
    • how a peroxisomal enzyme engages mitochondrial machinery unexplained
  9. 2020 High

    Tested whether GNPAT directly controls systemic iron homeostasis and found no requirement, with multiple knockout models showing normal iron and hepcidin, refining the contested hepcidin hypothesis.

    Evidence germline, double, and hepatocyte-specific Gnpat knockout mice with dietary iron challenge and primary hepatocyte BMP6 stimulation

    PMID:32108988

    Open questions at the time
    • conflicting in vitro knockdown data unresolved
    • any conditional BMP6-stimulated role mechanistically undefined
  10. 2026 Low

    Extended GNPAT function to the tumor microenvironment by linking its plasmalogen output to PPARγ-driven M2 macrophage polarization in hepatocellular carcinoma.

    Evidence overexpression in HCC cell lines, macrophage co-culture polarization, plasmalogen quantification, and PPAR pathway readouts

    PMID:41816340

    Open questions at the time
    • single low-confidence study with limited mechanistic depth
    • autocrine PPARγ activation not validated in vivo
    • specific plasmalogen ligand not identified

Open questions

Synthesis pass · forward-looking unresolved questions
  • How GNPAT's enzymatic plasmalogen-synthesis function mechanistically connects to its reported roles in ferroptosis, mitochondrial fission, and macrophage polarization remains unresolved.
  • no unified mechanism linking peroxisomal lipid synthesis to mitochondrial and immune phenotypes
  • structural basis of catalysis and partner binding undetermined
  • in vivo relevance of non-enzymatic functions untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 4 GO:0008289 lipid binding 1
Localization
GO:0005777 peroxisome 3
Pathway
R-HSA-1430728 Metabolism 3
Partners
AGPSDRP1SIRT4USP30

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1991 GNPAT (DHAP-AT) is a peroxisomal enzyme with ~80% latency in selectively permeabilized fibroblasts. Its latency is critically dependent on reduced glutathione (GSH) in the medium, and ATP stimulates latent DHAP-AT activity through a mechanism involving cations but not a proton gradient. The integrity of peroxisomal membrane thiol-groups is essential for maintaining DHAP-AT latency. Selective permeabilization of human skin fibroblasts, enzyme activity assays with defined medium components (GSH/GSSG manipulation, ATP, cation chelation) Biochimica et biophysica acta Medium 1657193
1993 Isolated deficiency of the peroxisomal enzyme DHAP-AT (GNPAT) causes rhizomelic chondrodysplasia punctata with deficient de novo plasmalogen biosynthesis, establishing GNPAT as essential for the plasmalogen synthesis pathway in humans, with all other peroxisomal functions normal. Enzyme activity measurement in patient fibroblasts, clinical phenotype characterization, peroxisomal function panel Archives of disease in childhood Medium 8466247
1995 GNPAT (DHAPAT) enzymatic activity can be reliably measured in chorionic villous samples, blood cells, cultured skin fibroblasts, cultured chorionic villus fibroblasts, and cultured amniocytes, establishing the enzyme's presence and activity across multiple human cell types and its utility for prenatal diagnosis. Enzyme activity assay in multiple human cell types and tissue samples Journal of inherited metabolic disease Medium 9053559
2000 A missense mutation in GNPAT (R211H) causes isolated DHAPAT deficiency, resulting in deficient de novo plasmalogen synthesis in patient fibroblasts while alkyl-DHAP synthase activity, VLCFA profile, phytanic acid concentration, and peroxisomal thiolase remain normal. The deficiency leads to abnormal myelin formation, linking GNPAT-dependent plasmalogen biosynthesis to myelin integrity. Enzyme activity assays in patient fibroblasts, mutation identification by cDNA sequencing, MRI of white matter Developmental medicine and child neurology Medium 10972423
2001 The human GNPAT gene spans ~28 kb on chromosome 1q42.12-43, consists of 16 exons and 15 introns, and nine distinct mutations (missense, deletions, insertion, splice site mutations) in GNPAT cause DHAPAT enzyme deficiency and impaired etherphospholipid biosynthesis. This confirmed GNPAT as the sole gene responsible for RCDP type 2. Genomic sequencing, exon mapping, patient mutation analysis across 12 GNPAT-deficient patients, splice site and transcript analysis Biochemical and biophysical research communications Medium 11237722
2011 GNPAT and AGPS physically partner on the luminal peroxisomal membrane surface; the presence of AGPS is required for full GNPAT activity, and full GNPAT activity also depends on intact substrate channeling from GNPAT to AGPS. Milder RCDP phenotypes correlate with residual GNPAT or AGPS protein function. Cell line protein quantification (GNPAT and AGPS levels compared across patient and control lines), protein modeling for structural consequences, transcript analysis, functional enzyme assays in patient fibroblasts Human mutation Medium 21990100
2015 siRNA-mediated knockdown of GNPAT in HepG2/C3A human liver-derived cells resulted in a >17-fold decrease in hepcidin (HAMP) mRNA expression, indicating that GNPAT participates in hepcidin regulation in hepatocytes. siRNA knockdown of GNPAT in HepG2/C3A cells, quantitative RT-PCR for hepcidin mRNA Hepatology (Baltimore, Md.) Low 25605615
2020 Gnpat knockout mice (Gnpat-/-, Gnpat-/-Hfe-/-, hepatocyte-specific Gnpat-/-) showed no significant difference in serum or tissue iron levels or hepcidin expression compared to controls under normal or high-iron diet conditions. However, Gnpat knockdown in primary hepatocytes repressed BMP6-induced hepcidin expression, suggesting a specific role only under BMP6-stimulated conditions. This NEGATIVE result contradicts the earlier HepG2 siRNA study and the hypothesis that GNPAT directly mediates systemic iron homeostasis. Gnpat knockout mouse models (germline and hepatocyte-specific), high-iron diet challenge, serum iron measurement, tissue iron quantification, hepcidin mRNA expression, primary hepatocyte knockdown with BMP6 stimulation Journal of cellular and molecular medicine High 32108988
2020 Gnpat heterozygous mice fed a high-iron diet had lower hepatic hepcidin mRNA expression but significantly higher serum iron levels and transferrin saturation compared to wild-type littermates, suggesting that reduced GNPAT expression impairs the hepcidin response to dietary iron challenge. Gnpat+/- mouse model, high-iron diet challenge, hepatic hepcidin (HAMP) mRNA quantification, serum iron and transferrin saturation measurements Bioscience reports Medium 32766721
2023 CSE (cigarette smoke extract) downregulates SIRT4 expression, which leads to increased acetylation of GNPAT protein; SIRT4 directly deacetylates GNPAT, and this deacetylation reduces GNPAT protein levels and activity. Knockdown of GNPAT mitigated CSE-induced ferroptosis in A549 cells, while GNPAT overexpression reversed SIRT4-mediated inhibition of ferroptosis, establishing a SIRT4→GNPAT acetylation axis in CSE-induced ferroptosis. Immunoprecipitation for GNPAT acetylation level, siRNA knockdown and overexpression in A549 cells, cell viability, LDH, ROS, lipid ROS, GSH, GPX4, and MDA measurement, western blot, qRT-PCR, immunofluorescence Respiratory research Medium 38041059
2023 Xenopus GNPAT is present in both soluble and membrane fractions, but only the membrane-bound enzyme displays acyltransferase activity. The amino-terminal domain of GNPAT, conserved in humans, shows lipid-binding capacity that is enhanced by phosphatidic acid, identifying a regulatory lipid-binding function of the N-terminus. Heterologous expression of Xenopus Gnpat in yeast, subcellular fractionation, enzyme activity assay in soluble vs. membrane fractions, lipid-binding assay with phosphatidic acid Investigative ophthalmology & visual science Medium 37204785
2025 GNPAT recruits USP30 (ubiquitin-specific protease 30), which stabilizes DRP1 protein (dynamin-related protein 1) by deubiquitination, promoting mitochondrial fission, mitochondrial dysfunction, and cell apoptosis in CSE-exposed A549 cells. Co-immunoprecipitation confirmed direct binding among GNPAT, USP30, and DRP1. Co-immunoprecipitation assay in A549 cells, plasmid overexpression and knockdown of GNPAT/USP30/DRP1, transmission electron microscopy for mitochondrial morphology, cell viability, apoptosis, LDH, ATP production, ROS measurement, western blot, qRT-PCR, mouse COPD model The Kaohsiung journal of medical sciences Medium 40709564
2026 GNPAT promotes M2 macrophage polarization in hepatocellular carcinoma via a plasmalogen-PPARγ pathway: GNPAT overexpression in HCC cells enhances plasmalogen synthesis, activates PPAR signaling in an autocrine manner, and polarizes macrophages to an M2-like immunosuppressive phenotype. Functional overexpression experiments in HCC cell lines, macrophage co-culture polarization assay, plasmalogen quantification, PPARγ pathway readouts, migration, proliferation, and apoptosis assays Frontiers in immunology Low 41816340

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 Exome sequencing in HFE C282Y homozygous men with extreme phenotypes identifies a GNPAT variant associated with severe iron overload. Hepatology (Baltimore, Md.) 64 25605615
2011 Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. Human mutation 61 21990100
2006 A single nucleotide polymorphism fine mapping study of chromosome 1q42.1 reveals the vulnerability genes for schizophrenia, GNPAT and DISC1: Association with impairment of sustained attention. Biological psychiatry 55 16997000
1993 Rhizomelic chondrodysplasia punctata with isolated DHAP-AT deficiency. Archives of disease in childhood 29 8466247
2000 Abnormal myelin formation in rhizomelic chondrodysplasia punctata type 2 (DHAPAT-deficiency). Developmental medicine and child neurology 23 10972423
2023 CSE triggers ferroptosis via SIRT4-mediated GNPAT deacetylation in the pathogenesis of COPD. Respiratory research 21 38041059
1998 Developmental delay and growth failure caused by a peroxisomal disorder, dihydroxyacetonephosphate acyltransferase (DHAP-AT) deficiency. American journal of medical genetics 17 9843043
1995 Measurement of dihydroxyacetone-phosphate acyltransferase (DHAPAT) in chorionic villous samples, blood cells and cultured cells. Journal of inherited metabolic disease 16 9053559
1991 Factors influencing the latency of the peroxisomal enzyme dihydroxyacetone-phosphate acyltransferase (DHAP-AT) in permeabilized human skin fibroblasts. Biochimica et biophysica acta 14 1657193
2001 Etherphospholipid biosynthesis and dihydroxyactetone-phosphate acyltransferase: resolution of the genomic organization of the human gnpat gene and its use in the identification of novel mutations. Biochemical and biophysical research communications 11 11237722
2016 GNPAT variant (D519G) is not associated with an elevated serum ferritin or iron removed by phlebotomy in patients referred for C282Y-linked hemochromatosis. Annals of hepatology 6 27740525
2012 Synthesis and structure-activity relationships of o-sulfonamido-arylhydrazides as inhibitors of LL-diaminopimelate aminotransferase (LL-DAP-AT). Organic & biomolecular chemistry 6 22371097
2025 A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene. Genetics, selection, evolution : GSE 3 40394457
2023 Neonatal rhizomelic chondrodysplasia punctata type 2 caused by a novel homozygous variant in the GNPAT gene. Clinical case reports 3 37323250
2023 RNA N6-methyladenosine of DHAPAT and PAP involves in regulation of diapause of Bombyx mori via the lipid metabolism pathway. Bulletin of entomological research 3 37555240
2020 Gnpat does not play an essential role in systemic iron homeostasis in murine model. Journal of cellular and molecular medicine 3 32108988
2025 GNPAT/USP30 Stabilizes DRP1 Protein to Promote Mitochondrial Fission and Functional Damage in COPD Progression. The Kaohsiung journal of medical sciences 2 40709564
2023 Differential Eye Expression of Xenopus Acyltransferase Gnpat and Its Biochemical Characterization Shed Light on Lipid-Associated Ocular Pathologies. Investigative ophthalmology & visual science 1 37204785
2021 A new GNPAT variant of foetal rhizomelic chondrodysplasia punctata. Molecular genetics & genomic medicine 1 34110102
2026 GNPAT promotes immunosuppression in hepatocellular carcinoma by activating the plasmalogen-PPARγ pathway to drive M2 macrophage polarization. Frontiers in immunology 0 41816340
2020 Dysregulated hepcidin response to dietary iron in male mice with reduced Gnpat expression. Bioscience reports 0 32766721

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