GNPAT (O15228) — review notes

Identity and function

GNPAT = glyceronephosphate O-acyltransferase, aka dihydroxyacetone phosphate
acyltransferase (DHAPAT / DAP-AT / DAPAT / DHAP-AT), EC 2.3.1.42. A 680-aa
peroxisomal enzyme.

• Catalyzes: dihydroxyacetone phosphate (glycerone phosphate, DHAP) + acyl-CoA
  → 1-acylglycerone 3-phosphate (acyl-DHAP) + CoA (EC 2.3.1.42). This is the
  first committed step of ether-glycerolipid (plasmalogen) biosynthesis.
  [file:human/GNPAT/GNPAT-uniprot.txt "Reaction=dihydroxyacetone phosphate + an acyl-CoA = a 1-acylglycerone"]
  [file:human/GNPAT/GNPAT-uniprot.txt "Dihydroxyacetonephosphate acyltransferase catalyzing the"]
• The acyl-DHAP product is then handed to AGPS (alkyl-DHAP synthase / alkylglycerone
  phosphate synthase), which replaces the acyl group with a fatty alcohol to create
  the characteristic ether (later vinyl-ether) bond of plasmalogens.
• GO term for the MF is GO:0016287 glycerone-phosphate O-acyltransferase activity
  (OLS: "Catalysis of the reaction: acyl-CoA + glycerone phosphate = 1-acylglycerone
  3-phosphate + CoA").

Subcellular localization

• Peroxisome membrane, peripheral membrane protein, matrix (lumenal) side.
  [file:human/GNPAT/GNPAT-uniprot.txt "SUBCELLULAR LOCATION: Peroxisome membrane"]
  [file:human/GNPAT/GNPAT-uniprot.txt "Exclusively localized to the"] (…lumenal side of the peroxisomal membrane).
• Has a C-terminal type-1 peroxisomal targeting signal (PTS1). Human C-terminus is
  ...PATAKL; mouse ortholog ends AKL.
  PMID:9459311
  PMID:10395968
• Experimental localization to peroxisome / peroxisomal membrane in human cells:
  PMID:15687349 (EXP/IDA). Consistent Reactome placement in peroxisomal matrix /
  membrane. HDA proteomics also placed it in "membrane" (generic) and peroxisomal
  membrane (PMID:19946888, PMID:21525035 — both large-scale, generic-membrane or
  co-purification contexts).

Quaternary structure

• Native enzyme isolated as a trimeric complex from peroxisomes.
  PMID:9459311
• UniProt: "Part of a heterotrimeric complex composed of GNPAT, AGPS and a modified
  form of GNPAT."
  [file:human/GNPAT/GNPAT-uniprot.txt "Part of a heterotrimeric complex composed of GNPAT, AGPS and a"]
• Reactome R-HSA-75879: "The active form of the enzyme is one subunit of a heterotrimer
  with two molecules of the alkylglycerone phosphate synthase (AGPS) enzyme."
• (An earlier placental-purification paper reported an apparent monomer of ~65 kDa,
  PMID:8186247 "these results suggest that DHAPAT is a monomeric protein" — likely a
  solubilized single subunit; superseded by the trimeric-complex view.)

Catalytic / functional evidence

• Catalytic activity (EC 2.3.1.42) established via cDNA expression in yeast and enzyme
  assays: mouse cDNA PMID:10395968, human RCDP2 characterization PMID:11152660, and
  functional rescue PMID:15687349.
• Rescue of DHAPAT-deficient CHO variant (NRel-4) by human DHAPAT cDNA restores
  DHAPAT activity and plasmalogen biosynthesis; peroxisomal DHAPAT is essential for
  plasmalogen synthesis.
  PMID:15687349
  PMID:15687349
• Importantly, GNPAT/DHAPAT does not normally contribute to non-ether (diacyl)
  glycerolipid biosynthesis:
  PMID:15687349
  → This argues the "phosphatidic acid biosynthetic process" (GO:0006654) annotation is
  peripheral/non-core for GNPAT, even though acyl-DHAP feeds a minor glycerolipid branch.

Disease

• Biallelic GNPAT mutations cause rhizomelic chondrodysplasia punctata type 2 (RCDP2;
  MIM 222765) — defective plasmalogen biosynthesis.
  [file:human/GNPAT/GNPAT-uniprot.txt "Rhizomelic chondrodysplasia punctata 2 (RCDP2)"]
  PMID:9536089
• Disease variants (e.g. R211H) cause loss of glycerone-phosphate O-acyltransferase
  activity (UniProt VARIANT annotations, PMID:9536089, PMID:11152660).

Annotation review reasoning

• Core MF: GO:0016287 glycerone-phosphate O-acyltransferase activity — strong
  experimental support (multiple IDA). ACCEPT all; IEA/IBA/TAS copies also ACCEPT (own
  correct core function).
• Core BP: GO:0008611 ether lipid biosynthetic process — IDA + IBA + IEA + TAS;
  ACCEPT.
• Core CC: GO:0005778 peroxisomal membrane (EXP/IDA/IBA/IEA/HDA) and GO:0005777
  peroxisome — ACCEPT. GO:0005782 peroxisomal matrix (Reactome TAS) is compatible with
  the lumenal/matrix-side localization — KEEP_AS_NON_CORE (matrix vs membrane nuance).
• Generic/parent MF: GO:0016746, GO:0016747 acyltransferase activity (IEA parents of
  the specific MF) — MARK_AS_OVER_ANNOTATED (uninformative parents).
• Broad BP: GO:0006629 lipid metabolic process, GO:0006650 glycerophospholipid
  metabolic process — correct but general; KEEP_AS_NON_CORE.
• GO:0006654 phosphatidic acid biosynthetic process (Reactome TAS) — peripheral;
  PMID:15687349 shows GNPAT does not normally contribute to nonether glycerolipids →
  KEEP_AS_NON_CORE.
• GO:0016020 membrane (HDA) — generic; KEEP_AS_NON_CORE (true but uninformative).
• GO:0005829 cytosol (Reactome TAS, from Peroxisomal-protein-import pathway) —
  reflects the transient cytosolic state of newly synthesized PTS1 cargo before import,
  not steady-state localization → MARK_AS_OVER_ANNOTATED (as a location claim for the
  mature enzyme).