PIGA (phosphatidylinositol N-acetylglucosaminyltransferase subunit A) is the catalytic subunit of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex, which catalyzes the first, committed step of glycosylphosphatidylinositol (GPI) anchor biosynthesis. PIGA transfers N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine (UDP-GlcNAc) onto phosphatidylinositol (PI) to form GlcNAc-PI (EC 2.4.1.198), a reaction occurring on the cytoplasmic face of the endoplasmic reticulum membrane. PIGA is a single-pass ER membrane protein with a large cytoplasmic catalytic domain (homologous to bacterial GlcNAc transferases, glycosyltransferase group 1 / GT4 family) and a small lumenal domain that mediates rough-ER localization. The GPI-GnT complex additionally contains PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2, with PIGA as the catalytic component. Somatic loss-of-function mutations of the X-linked PIGA gene in hematopoietic stem cells cause paroxysmal nocturnal hemoglobinuria (PNH), through loss of GPI-anchored complement regulators on blood cells; germline hypomorphic mutations cause X-linked recessive multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2) and related neurodevelopmental disorders.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PIGA is a subunit of the GPI-GnT complex. This phylogenetically inferred complex membership is directly supported by experimental studies of the human complex and is a core aspect of PIGA biology.
Reason: PIGA is the catalytic subunit of the GPI-GnT complex, which comprises at least PIGA, PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2. The IBA call is corroborated by direct experimental identification of the human complex.
Supporting Evidence:
PMID:8900170
PIG-A and PIG-H are subunits of the GPI GlcNAc transferase that transfers GlcNAc to PI on the cytoplasmic side of the ER.
PMID:9463366
four mammalian gene products form a protein complex in the endoplasmic reticulum membrane.
|
|
GO:0006506
GPI anchor biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: PIGA catalyzes the first, committed step of GPI anchor biosynthesis, so involvement in the GPI anchor biosynthetic process is a core biological process annotation.
Reason: The catalytic first step (GlcNAc transfer to PI) initiates the GPI biosynthesis pathway. This is well established experimentally and consistent with the phylogenetic inference.
Supporting Evidence:
PMID:9463366
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI).
|
|
GO:0017176
phosphatidylinositol N-acetylglucosaminyltransferase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: This is the exact, correct molecular function of PIGA - the catalytic subunit that transfers GlcNAc from UDP-GlcNAc to phosphatidylinositol (EC 2.4.1.198).
Reason: PIGA is the catalytic component of the GPI-GnT enzyme; this specific transferase activity is the core molecular function and is directly supported by biochemistry.
Supporting Evidence:
PMID:9463366
The protein complex had GPI-GlcNAc transferase (GPI-GnT) activity in vitro.
PMID:16162815
binding directly to the catalytic subunit PIG-A.
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-based electronic annotation of GPI-GnT complex membership (via the PIG-A/GPI3 signature IPR039507). Correct and consistent with experimental data.
Reason: The IEA mapping from the PIG-A/GPI3 InterPro entry to the GPI-GnT complex is biologically correct; PIGA is an experimentally verified complex member.
Supporting Evidence:
PMID:8900170
PIG-A and PIG-H are subunits of the GPI GlcNAc transferase that transfers GlcNAc to PI on the cytoplasmic side of the ER.
|
|
GO:0006506
GPI anchor biosynthetic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (InterPro/UniPathway) annotation to the GPI anchor biosynthetic process, matching the experimentally established role of PIGA.
Reason: The pathway mapping (UPA00196 GPI-anchor biosynthesis) is correct; PIGA initiates this pathway.
Supporting Evidence:
PMID:9463366
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI).
|
|
GO:0016757
glycosyltransferase activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: Generic glycosyltransferase activity from the InterPro glycosyltransferase family 1 domain (IPR001296). Correct but a broad parent of the specific PIGA activity.
Reason: This term is a general ancestor of the specific and experimentally supported GO:0017176 (phosphatidylinositol N-acetylglucosaminyltransferase activity), which is annotated separately. The generic term is not informative for PIGA's core function.
Supporting Evidence:
PMID:9463366
The protein complex had GPI-GlcNAc transferase (GPI-GnT) activity in vitro.
|
|
GO:0017176
phosphatidylinositol N-acetylglucosaminyltransferase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic annotation of the specific catalytic activity based on the RHEA/EC mapping (RHEA:14789, EC 2.4.1.198). This is the correct core molecular function.
Reason: The EC/RHEA-derived assignment matches the experimentally established catalytic activity of PIGA and is the specific, informative molecular function term.
Supporting Evidence:
PMID:16162815
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting of at least six proteins.
file:human/PIGA/PIGA-uniprot.txt
EC=2.4.1.198
|
|
GO:0030867
rough endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: UniProt subcellular-location keyword mapping to rough ER membrane. Correct and consistent with experimental localization data.
Reason: PIGA localizes to the rough ER membrane; this specific location is experimentally verified (the small lumenal domain targets it to the rough ER).
Supporting Evidence:
PMID:8900170
part of the small lumenal domain of PIG-A plays an essential functional role in targeting itself to the rough ER.
|
|
GO:0005515
protein binding
|
IPI
PMID:10944123 Initial enzyme for glycosylphosphatidylinositol biosynthesis... |
MARK AS OVER ANNOTATED |
Summary: IntAct-curated binary interactions of PIGA with GPI-GnT complex components (DPM2/O94777, PIGP/P57054, PIGH/Q14442, PIGQ/Q9BRB3). These reflect PIGA's role as a scaffolding/catalytic member of the GPI-GnT complex.
Reason: The generic 'protein binding' term is uninformative. The underlying interactions are real and are the physical basis of the GPI-GnT complex, which is captured by the specific GO:0000506 (GPI-GnT complex) annotation. Per curation guidelines the bare protein binding IPI is not retained as a core function.
Supporting Evidence:
PMID:10944123
PIG-P, a 134-amino acid protein having two hydrophobic domains, associates with PIG-A and GPI1.
PMID:10944123
DPM2, but not two other components of dolichol-phosphate-mannose synthase, associates with GPI-GnT through interactions with PIG-A, PIG-C and GPI1.
|
|
GO:0005515
protein binding
|
IPI
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
MARK AS OVER ANNOTATED |
Summary: IntAct-curated interactions of PIGA with GPI-GnT complex components including the directly associated regulatory subunit PIGY (Q3MUY2), plus DPM2, PIGP, PIGH, PIGQ. Real interactions underpinning complex assembly.
Reason: Bare 'protein binding' is uninformative and is subsumed by the specific GPI-GnT complex (GO:0000506) annotation. The interactions themselves are genuine.
Supporting Evidence:
PMID:16162815
PIG-Y appeared to be directly associated with PIG-A.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: High-throughput BioPlex 3.0 AP-MS interactions of PIGA (recovering PIGP and PIGH). Consistent with GPI-GnT complex membership but low information content.
Reason: Generic 'protein binding' from a proteome-scale AP-MS screen; not a core function term. The recovered partners are GPI-GnT complex members captured by GO:0000506.
Supporting Evidence:
PMID:33961781
BioPlex suggests function, localization, and complex membership for thousands of proteins.
|
|
GO:0005515
protein binding
|
IPI
PMID:8900170 PIG-A and PIG-H, which participate in glycosylphosphatidylin... |
MARK AS OVER ANNOTATED |
Summary: IntAct-curated interaction of PIGA with PIGH (Q14442), the earliest characterized binary interaction within the GPI-GnT complex.
Reason: The PIGA-PIGH interaction is real and foundational to the complex, but the generic 'protein binding' term is uninformative and is captured by the specific GPI-GnT complex (GO:0000506) annotation.
Supporting Evidence:
PMID:8900170
they form a protein complex.
|
|
GO:0005515
protein binding
|
IPI
PMID:9463366 The first step of glycosylphosphatidylinositol biosynthesis ... |
MARK AS OVER ANNOTATED |
Summary: IntAct-curated interaction of PIGA with PIGQ/GPI1 (Q9BRB3), a component of the four-subunit GPI-GnT complex characterized in this study.
Reason: Real interaction within the GPI-GnT complex, but the generic 'protein binding' term is uninformative and subsumed by GO:0000506 (GPI-GnT complex).
Supporting Evidence:
PMID:9463366
four mammalian gene products form a protein complex in the endoplasmic reticulum membrane.
|
|
GO:0006506
GPI anchor biosynthetic process
|
TAS
Reactome:R-HSA-162710 |
ACCEPT |
Summary: Reactome traceable-author-statement placing PIGA in the GPI synthesis pathway. Matches PIGA's established role initiating GPI anchor biosynthesis.
Reason: PIGA catalyzes the first reaction of GPI anchor biosynthesis; the Reactome pathway assignment is correct and core.
Supporting Evidence:
PMID:9463366
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI).
|
|
GO:0030867
rough endoplasmic reticulum membrane
|
EXP
PMID:8900170 PIG-A and PIG-H, which participate in glycosylphosphatidylin... |
ACCEPT |
Summary: Experimental demonstration that PIGA is an ER transmembrane protein localizing to the rough ER, with its small lumenal domain required for rough-ER targeting.
Reason: Directly supported by experimental localization/topology work; the rough ER membrane is a verified, specific location for PIGA.
Supporting Evidence:
PMID:8900170
PIG-A is an ER transmembrane protein with a large cytoplasmic domain that has homology to a bacterial GlcNAc transferase and a small lumenal domain.
PMID:8900170
part of the small lumenal domain of PIG-A plays an essential functional role in targeting itself to the rough ER.
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IPI
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
ACCEPT |
Summary: ComplexPortal (CPX-6502) assertion of PIGA as part of the GPI-GnT complex, based on the study identifying the seven-component complex including PIGY.
Reason: PIGA is an experimentally established member (catalytic subunit) of the GPI-GnT complex; complex membership is a core annotation.
Supporting Evidence:
PMID:16162815
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting of at least six proteins.
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
ACCEPT |
Summary: Direct-assay localization of PIGA to the ER membrane, where the GPI-GnT complex assembles and functions.
Reason: The ER membrane is the verified site of PIGA action and GPI-GnT complex assembly; this is a core cellular component annotation.
Supporting Evidence:
PMID:9463366
four mammalian gene products form a protein complex in the endoplasmic reticulum membrane.
|
|
GO:0008194
UDP-glycosyltransferase activity
|
TAS
Reactome:R-HSA-162730 |
MODIFY |
Summary: Reactome describes the reaction as using the UDP-sugar donor UDP-GlcNAc. The term correctly captures the UDP-sugar donor class but is less specific than the exact enzyme activity.
Reason: UDP-glycosyltransferase activity is a broad donor-class term. The specific, experimentally supported activity is phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176, EC 2.4.1.198), which uses UDP-GlcNAc as donor and PI as acceptor.
Proposed replacements:
phosphatidylinositol N-acetylglucosaminyltransferase activity
Supporting Evidence:
PMID:9463366
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI).
|
|
GO:0016020
membrane
|
HDA
PMID:19946888 Defining the membrane proteome of NK cells. |
MARK AS OVER ANNOTATED |
Summary: High-throughput identification of PIGA in an NK-cell membrane proteome. Only confirms membrane association without specifying the organelle.
Reason: The 'membrane' term is a very general location from a proteome-scale study; PIGA's informative location is the ER membrane (GO:0005789 / GO:0030867), which is annotated separately with direct evidence.
Supporting Evidence:
PMID:19946888
approximately 40% of the identified proteins were predicted as plausible membrane proteins.
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-162730 |
ACCEPT |
Summary: Reactome traceable-author-statement placing the GlcNAc-PI synthesis reaction (and PIGA) at the ER membrane. Consistent with direct experimental data.
Reason: The ER membrane is the verified site of the PIGA-catalyzed reaction; a core cellular component annotation.
Supporting Evidence:
PMID:8900170
PIG-A is an ER transmembrane protein with a large cytoplasmic domain that has homology to a bacterial GlcNAc transferase and a small lumenal domain.
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IDA
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
ACCEPT |
Summary: Direct-assay identification of PIGA as a component of the seven-subunit GPI-GnT complex (adding PIGY as the seventh component directly associated with PIGA).
Reason: Experimentally established core complex membership; PIGA is the catalytic subunit.
Supporting Evidence:
PMID:16162815
PIG-Y appeared to be directly associated with PIG-A.
|
|
GO:0017176
phosphatidylinositol N-acetylglucosaminyltransferase activity
|
TAS
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
ACCEPT |
Summary: Traceable-author-statement of PIGA's phosphatidylinositol N-acetylglucosaminyltransferase activity, from the study establishing catalytic activity and the seven-component complex.
Reason: This is the specific, experimentally supported core molecular function of PIGA (catalytic subunit; EC 2.4.1.198).
Supporting Evidence:
PMID:16162815
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting of at least six proteins.
|
Human PIGA / PIG-A / Phosphatidylinositol N-acetylglucosaminyltransferase subunit A.
HGNC:8957, X-linked (Xp22.2), 484 aa, EC 2.4.1.198. CAZy GT4 (glycosyltransferase group 1 family, GT4 subfamily).
Deep research: falcon provider was OUT OF CREDITS (HTTP 402) at the time of review, so no
-deep-research-falcon.md was generated. This review is grounded in the UniProt record,
the seeded GOA, cached primary publications, and the two cached Reactome entries.
PIGA is the catalytic subunit of the GPI-GlcNAc transferase (GPI-GnT) complex that
catalyses the first, committed step of GPI (glycosylphosphatidylinositol) anchor biosynthesis:
transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc onto phosphatidylinositol (PI) to give
GlcNAc-PI, on the cytoplasmic face of the ER membrane [PMID:8900170; PMID:9463366; PMID:16162815].
At least PIGA, PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2 (PIGA is the catalytic component)
[UniProt SUBUNIT; PMID:16162815]. Historical assembly picture:
- PMID:8900170 (1996): PIG-A + PIG-H form an ER complex; PIG-A is a transmembrane protein with a large
cytoplasmic (catalytic) domain homologous to a bacterial GlcNAc transferase and a small lumenal domain;
small lumenal domain targets it to the rough ER. GlcNAc-PI is made on the cytoplasmic side of the ER.
- PMID:9463366 (1998): four-component complex PIG-A/PIG-H/PIG-C/GPI1 (=PIGQ) in the ER membrane; complex
has GPI-GlcNAc transferase (GPI-GnT) activity in vitro; PIG-L (2nd step, de-N-acetylation) not in complex.
- PMID:10944123 (2000): adds PIG-P as essential component; DPM2 associates and regulates (enhances activity
~3-fold), coupling GPI-GnT to Dol-P-Man synthase.
- PMID:16162815 (2005): adds PIG-Y (7th component); PIG-Y associates directly with catalytic PIG-A and
regulates GPI-GnT activity. Establishes catalytic activity/function; assigns EC 2.4.1.198.
IntAct/BioPlex interactors used in GOA GO:0005515 IPIs map to complex members:
O94777=DPM2, P57054=PIGP, Q14442=PIGH, Q9BRB3=PIGQ, Q3MUY2=PIGY (all confirmed in UniProt INTERACTION block).
PMID:33961781 = BioPlex 3.0 AP-MS (high-throughput interactome) — recovers PIGP, PIGH.
Rough ER membrane; single-pass membrane protein. TOPO_DOM 1..421 cytoplasmic (catalytic), TRANSMEM
422..442, TOPO_DOM 443..484 lumenal; region 443..465 required for rough-ER localization PMID:8900170.
GOA carries both GO:0030867 (rough ER membrane) and GO:0005789 (ER membrane); the latter is the general
parent and is the cleaner "located_in" for core functions.
MF:
- GO:0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity — CORE. IBA, IEA(EC 2.4.1.198/RHEA:14789),
TAS(PMID:16162815). ACCEPT (the specific, correct catalytic activity).
- GO:0016757 glycosyltransferase activity (IEA InterPro) — parent of GO:0017176; MARK_AS_OVER_ANNOTATED
(correct but less informative; the specific child is annotated).
- GO:0008194 UDP-glycosyltransferase activity (TAS Reactome) — describes UDP-sugar donor; less specific/slightly
off-branch vs the exact EC. MODIFY -> GO:0017176.
- GO:0005515 protein binding (IPI x several, partners = complex members) — bare "protein binding";
MARK_AS_OVER_ANNOTATED (real interactions but uninformative MF; captured by GPI-GnT complex membership).
BP:
- GO:0006506 GPI anchor biosynthetic process — CORE. IBA, IEA, TAS(Reactome). ACCEPT.
CC:
- GO:0000506 GPI-GnT complex — CORE. IBA, IEA, IPI, IDA(PMID:16162815). ACCEPT (part_of).
- GO:0005789 endoplasmic reticulum membrane — IDA(PMID:16162815), TAS(Reactome). ACCEPT (core location).
- GO:0030867 rough endoplasmic reticulum membrane — EXP(PMID:8900170), IEA. ACCEPT (specific location, verified).
- GO:0016020 membrane (HDA, PMID:19946888 NK membrane proteome) — MARK_AS_OVER_ANNOTATED (too general;
high-throughput proteome; ER membrane is the informative location).
id: P37287
gene_symbol: PIGA
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: PIGA (phosphatidylinositol N-acetylglucosaminyltransferase subunit A)
is the catalytic subunit of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase
(GPI-GnT) complex, which catalyzes the first, committed step of glycosylphosphatidylinositol
(GPI) anchor biosynthesis. PIGA transfers N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine
(UDP-GlcNAc) onto phosphatidylinositol (PI) to form GlcNAc-PI (EC 2.4.1.198), a reaction
occurring on the cytoplasmic face of the endoplasmic reticulum membrane. PIGA is a
single-pass ER membrane protein with a large cytoplasmic catalytic domain (homologous
to bacterial GlcNAc transferases, glycosyltransferase group 1 / GT4 family) and a small
lumenal domain that mediates rough-ER localization. The GPI-GnT complex additionally
contains PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2, with PIGA as the catalytic component.
Somatic loss-of-function mutations of the X-linked PIGA gene in hematopoietic stem cells
cause paroxysmal nocturnal hemoglobinuria (PNH), through loss of GPI-anchored complement
regulators on blood cells; germline hypomorphic mutations cause X-linked recessive
multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2) and related
neurodevelopmental disorders.
alternative_products:
- name: '1'
id: P37287-1
- name: '2'
id: P37287-2
sequence_note: VSP_001802
- name: '3'
id: P37287-3
sequence_note: VSP_043366, VSP_043367
existing_annotations:
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: part_of
review:
summary: PIGA is a subunit of the GPI-GnT complex. This phylogenetically inferred
complex membership is directly supported by experimental studies of the human
complex and is a core aspect of PIGA biology.
action: ACCEPT
reason: PIGA is the catalytic subunit of the GPI-GnT complex, which comprises at
least PIGA, PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2. The IBA call is corroborated
by direct experimental identification of the human complex.
supported_by:
- reference_id: PMID:8900170
supporting_text: PIG-A and PIG-H are subunits of the GPI GlcNAc transferase that
transfers GlcNAc to PI on the cytoplasmic side of the ER.
- reference_id: PMID:9463366
supporting_text: four mammalian gene products form a protein complex in the endoplasmic
reticulum membrane.
- term:
id: GO:0006506
label: GPI anchor biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: PIGA catalyzes the first, committed step of GPI anchor biosynthesis, so
involvement in the GPI anchor biosynthetic process is a core biological process
annotation.
action: ACCEPT
reason: The catalytic first step (GlcNAc transfer to PI) initiates the GPI biosynthesis
pathway. This is well established experimentally and consistent with the phylogenetic
inference.
supported_by:
- reference_id: PMID:9463366
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol
(PI).
- term:
id: GO:0017176
label: phosphatidylinositol N-acetylglucosaminyltransferase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: This is the exact, correct molecular function of PIGA - the catalytic subunit
that transfers GlcNAc from UDP-GlcNAc to phosphatidylinositol (EC 2.4.1.198).
action: ACCEPT
reason: PIGA is the catalytic component of the GPI-GnT enzyme; this specific transferase
activity is the core molecular function and is directly supported by biochemistry.
supported_by:
- reference_id: PMID:9463366
supporting_text: The protein complex had GPI-GlcNAc transferase (GPI-GnT) activity
in vitro.
- reference_id: PMID:16162815
supporting_text: binding directly to the catalytic subunit PIG-A.
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: part_of
review:
summary: InterPro-based electronic annotation of GPI-GnT complex membership (via
the PIG-A/GPI3 signature IPR039507). Correct and consistent with experimental data.
action: ACCEPT
reason: The IEA mapping from the PIG-A/GPI3 InterPro entry to the GPI-GnT complex
is biologically correct; PIGA is an experimentally verified complex member.
supported_by:
- reference_id: PMID:8900170
supporting_text: PIG-A and PIG-H are subunits of the GPI GlcNAc transferase that
transfers GlcNAc to PI on the cytoplasmic side of the ER.
- term:
id: GO:0006506
label: GPI anchor biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: Electronic (InterPro/UniPathway) annotation to the GPI anchor biosynthetic
process, matching the experimentally established role of PIGA.
action: ACCEPT
reason: The pathway mapping (UPA00196 GPI-anchor biosynthesis) is correct; PIGA initiates
this pathway.
supported_by:
- reference_id: PMID:9463366
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol
(PI).
- term:
id: GO:0016757
label: glycosyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: Generic glycosyltransferase activity from the InterPro glycosyltransferase
family 1 domain (IPR001296). Correct but a broad parent of the specific PIGA activity.
action: MARK_AS_OVER_ANNOTATED
reason: This term is a general ancestor of the specific and experimentally supported
GO:0017176 (phosphatidylinositol N-acetylglucosaminyltransferase activity), which
is annotated separately. The generic term is not informative for PIGA's core function.
supported_by:
- reference_id: PMID:9463366
supporting_text: The protein complex had GPI-GlcNAc transferase (GPI-GnT) activity
in vitro.
- term:
id: GO:0017176
label: phosphatidylinositol N-acetylglucosaminyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic annotation of the specific catalytic activity based on the RHEA/EC
mapping (RHEA:14789, EC 2.4.1.198). This is the correct core molecular function.
action: ACCEPT
reason: The EC/RHEA-derived assignment matches the experimentally established catalytic
activity of PIGA and is the specific, informative molecular function term.
supported_by:
- reference_id: PMID:16162815
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting
of at least six proteins.
- reference_id: file:human/PIGA/PIGA-uniprot.txt
supporting_text: "EC=2.4.1.198"
- term:
id: GO:0030867
label: rough endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: UniProt subcellular-location keyword mapping to rough ER membrane. Correct
and consistent with experimental localization data.
action: ACCEPT
reason: PIGA localizes to the rough ER membrane; this specific location is experimentally
verified (the small lumenal domain targets it to the rough ER).
supported_by:
- reference_id: PMID:8900170
supporting_text: part of the small lumenal domain of PIG-A plays an essential functional
role in targeting itself to the rough ER.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:10944123
qualifier: enables
review:
summary: IntAct-curated binary interactions of PIGA with GPI-GnT complex components
(DPM2/O94777, PIGP/P57054, PIGH/Q14442, PIGQ/Q9BRB3). These reflect PIGA's role
as a scaffolding/catalytic member of the GPI-GnT complex.
action: MARK_AS_OVER_ANNOTATED
reason: The generic 'protein binding' term is uninformative. The underlying interactions
are real and are the physical basis of the GPI-GnT complex, which is captured by
the specific GO:0000506 (GPI-GnT complex) annotation. Per curation guidelines the
bare protein binding IPI is not retained as a core function.
supported_by:
- reference_id: PMID:10944123
supporting_text: PIG-P, a 134-amino acid protein having two hydrophobic domains,
associates with PIG-A and GPI1.
- reference_id: PMID:10944123
supporting_text: DPM2, but not two other components of dolichol-phosphate-mannose
synthase, associates with GPI-GnT through interactions with PIG-A, PIG-C and GPI1.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16162815
qualifier: enables
review:
summary: IntAct-curated interactions of PIGA with GPI-GnT complex components including
the directly associated regulatory subunit PIGY (Q3MUY2), plus DPM2, PIGP, PIGH,
PIGQ. Real interactions underpinning complex assembly.
action: MARK_AS_OVER_ANNOTATED
reason: Bare 'protein binding' is uninformative and is subsumed by the specific GPI-GnT
complex (GO:0000506) annotation. The interactions themselves are genuine.
supported_by:
- reference_id: PMID:16162815
supporting_text: PIG-Y appeared to be directly associated with PIG-A.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: High-throughput BioPlex 3.0 AP-MS interactions of PIGA (recovering PIGP and
PIGH). Consistent with GPI-GnT complex membership but low information content.
action: MARK_AS_OVER_ANNOTATED
reason: Generic 'protein binding' from a proteome-scale AP-MS screen; not a core function
term. The recovered partners are GPI-GnT complex members captured by GO:0000506.
supported_by:
- reference_id: PMID:33961781
supporting_text: BioPlex suggests function, localization, and complex membership
for thousands of proteins.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:8900170
qualifier: enables
review:
summary: IntAct-curated interaction of PIGA with PIGH (Q14442), the earliest characterized
binary interaction within the GPI-GnT complex.
action: MARK_AS_OVER_ANNOTATED
reason: The PIGA-PIGH interaction is real and foundational to the complex, but the
generic 'protein binding' term is uninformative and is captured by the specific
GPI-GnT complex (GO:0000506) annotation.
supported_by:
- reference_id: PMID:8900170
supporting_text: they form a protein complex.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:9463366
qualifier: enables
review:
summary: IntAct-curated interaction of PIGA with PIGQ/GPI1 (Q9BRB3), a component of
the four-subunit GPI-GnT complex characterized in this study.
action: MARK_AS_OVER_ANNOTATED
reason: Real interaction within the GPI-GnT complex, but the generic 'protein binding'
term is uninformative and subsumed by GO:0000506 (GPI-GnT complex).
supported_by:
- reference_id: PMID:9463366
supporting_text: four mammalian gene products form a protein complex in the endoplasmic
reticulum membrane.
- term:
id: GO:0006506
label: GPI anchor biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162710
qualifier: involved_in
review:
summary: Reactome traceable-author-statement placing PIGA in the GPI synthesis pathway.
Matches PIGA's established role initiating GPI anchor biosynthesis.
action: ACCEPT
reason: PIGA catalyzes the first reaction of GPI anchor biosynthesis; the Reactome
pathway assignment is correct and core.
supported_by:
- reference_id: PMID:9463366
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol
(PI).
- term:
id: GO:0030867
label: rough endoplasmic reticulum membrane
evidence_type: EXP
original_reference_id: PMID:8900170
qualifier: located_in
review:
summary: Experimental demonstration that PIGA is an ER transmembrane protein localizing
to the rough ER, with its small lumenal domain required for rough-ER targeting.
action: ACCEPT
reason: Directly supported by experimental localization/topology work; the rough ER
membrane is a verified, specific location for PIGA.
supported_by:
- reference_id: PMID:8900170
supporting_text: PIG-A is an ER transmembrane protein with a large cytoplasmic domain
that has homology to a bacterial GlcNAc transferase and a small lumenal domain.
- reference_id: PMID:8900170
supporting_text: part of the small lumenal domain of PIG-A plays an essential functional
role in targeting itself to the rough ER.
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IPI
original_reference_id: PMID:16162815
qualifier: part_of
review:
summary: ComplexPortal (CPX-6502) assertion of PIGA as part of the GPI-GnT complex,
based on the study identifying the seven-component complex including PIGY.
action: ACCEPT
reason: PIGA is an experimentally established member (catalytic subunit) of the GPI-GnT
complex; complex membership is a core annotation.
supported_by:
- reference_id: PMID:16162815
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting
of at least six proteins.
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:16162815
qualifier: located_in
review:
summary: Direct-assay localization of PIGA to the ER membrane, where the GPI-GnT complex
assembles and functions.
action: ACCEPT
reason: The ER membrane is the verified site of PIGA action and GPI-GnT complex assembly;
this is a core cellular component annotation.
supported_by:
- reference_id: PMID:9463366
supporting_text: four mammalian gene products form a protein complex in the endoplasmic
reticulum membrane.
- term:
id: GO:0008194
label: UDP-glycosyltransferase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162730
qualifier: enables
review:
summary: Reactome describes the reaction as using the UDP-sugar donor UDP-GlcNAc. The
term correctly captures the UDP-sugar donor class but is less specific than the exact
enzyme activity.
action: MODIFY
reason: UDP-glycosyltransferase activity is a broad donor-class term. The specific,
experimentally supported activity is phosphatidylinositol N-acetylglucosaminyltransferase
activity (GO:0017176, EC 2.4.1.198), which uses UDP-GlcNAc as donor and PI as acceptor.
proposed_replacement_terms:
- id: GO:0017176
label: phosphatidylinositol N-acetylglucosaminyltransferase activity
supported_by:
- reference_id: PMID:9463366
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol
(PI).
- term:
id: GO:0016020
label: membrane
evidence_type: HDA
original_reference_id: PMID:19946888
qualifier: located_in
review:
summary: High-throughput identification of PIGA in an NK-cell membrane proteome. Only
confirms membrane association without specifying the organelle.
action: MARK_AS_OVER_ANNOTATED
reason: The 'membrane' term is a very general location from a proteome-scale study;
PIGA's informative location is the ER membrane (GO:0005789 / GO:0030867), which is
annotated separately with direct evidence.
supported_by:
- reference_id: PMID:19946888
supporting_text: approximately 40% of the identified proteins were predicted as plausible
membrane proteins.
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162730
qualifier: located_in
review:
summary: Reactome traceable-author-statement placing the GlcNAc-PI synthesis reaction
(and PIGA) at the ER membrane. Consistent with direct experimental data.
action: ACCEPT
reason: The ER membrane is the verified site of the PIGA-catalyzed reaction; a core
cellular component annotation.
supported_by:
- reference_id: PMID:8900170
supporting_text: PIG-A is an ER transmembrane protein with a large cytoplasmic domain
that has homology to a bacterial GlcNAc transferase and a small lumenal domain.
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IDA
original_reference_id: PMID:16162815
qualifier: part_of
review:
summary: Direct-assay identification of PIGA as a component of the seven-subunit GPI-GnT
complex (adding PIGY as the seventh component directly associated with PIGA).
action: ACCEPT
reason: Experimentally established core complex membership; PIGA is the catalytic subunit.
supported_by:
- reference_id: PMID:16162815
supporting_text: PIG-Y appeared to be directly associated with PIG-A.
- term:
id: GO:0017176
label: phosphatidylinositol N-acetylglucosaminyltransferase activity
evidence_type: TAS
original_reference_id: PMID:16162815
qualifier: enables
review:
summary: Traceable-author-statement of PIGA's phosphatidylinositol N-acetylglucosaminyltransferase
activity, from the study establishing catalytic activity and the seven-component complex.
action: ACCEPT
reason: This is the specific, experimentally supported core molecular function of PIGA
(catalytic subunit; EC 2.4.1.198).
supported_by:
- reference_id: PMID:16162815
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting
of at least six proteins.
core_functions:
- description: Catalytic subunit of the GPI-GnT complex that transfers N-acetylglucosamine
from UDP-GlcNAc to phosphatidylinositol (EC 2.4.1.198), catalyzing the first committed
step of GPI anchor biosynthesis at the ER membrane.
molecular_function:
id: GO:0017176
label: phosphatidylinositol N-acetylglucosaminyltransferase activity
directly_involved_in:
- id: GO:0006506
label: GPI anchor biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
in_complex:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
supported_by:
- reference_id: PMID:16162815
supporting_text: Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated
by an unusually complex GPI-N-acetylglucosaminyltransferase (GPI-GnT) consisting
of at least six proteins.
- reference_id: PMID:9463366
supporting_text: The protein complex had GPI-GlcNAc transferase (GPI-GnT) activity
in vitro.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
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:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:10944123
title: Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P
and is regulated by DPM2.
findings:
- statement: "GPI-GnT requires PIG-P as an essential component and is regulated by DPM2, which associates with the complex through interactions with PIG-A, PIG-C and GPI1 and enhances enzyme activity ~3-fold."
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Establishes PIG-P and DPM2 as components/regulator of
the PIGA-containing GPI-GnT complex; supports the protein-binding IPI to DPM2/PIGP.
- id: PMID:16162815
title: The initial enzyme for glycosylphosphatidylinositol biosynthesis requires
PIG-Y, a seventh component.
findings:
- statement: "PIGA is the catalytic subunit of the GPI-GnT complex; PIG-Y is directly associated with PIG-A and regulates GPI-GnT activity. This study established the catalytic activity and seven-component complex (EC 2.4.1.198)."
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Primary source for PIGA catalytic-subunit function,
EC 2.4.1.198, and the seven-component GPI-GnT complex.
- id: PMID:19946888
title: Defining the membrane proteome of NK cells.
findings:
- statement: "High-throughput membrane proteome of the NK-like cell line YTS; supports only a generic membrane localization for PIGA."
reference_section_type: ABSTRACT
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: PubMed-verified proteomics survey; supports only the general membrane
annotation, not organelle specificity.
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings:
- statement: "BioPlex 3.0 AP-MS interactome; recovers PIGA interactions with GPI-GnT complex members (PIGP, PIGH), supporting a generic protein-binding annotation."
reference_section_type: DISCUSSION
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: PubMed-verified proteome-scale AP-MS; low information content for PIGA's
specific function beyond complex membership.
- id: PMID:8900170
title: PIG-A and PIG-H, which participate in glycosylphosphatidylinositol anchor
biosynthesis, form a protein complex in the endoplasmic reticulum.
findings:
- statement: "PIG-A is an ER transmembrane protein with a large cytoplasmic (catalytic) domain and a small lumenal domain that targets it to the rough ER; PIG-A and PIG-H form a complex and transfer GlcNAc to PI on the cytoplasmic side of the ER."
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Primary source for PIGA ER-membrane localization, topology,
and cytoplasmic-face catalysis.
- id: PMID:9463366
title: The first step of glycosylphosphatidylinositol biosynthesis is mediated by
a complex of PIG-A, PIG-H, PIG-C and GPI1.
findings:
- statement: "The first step of GPI biosynthesis (GlcNAc transfer from UDP-GlcNAc to PI) is mediated by an ER-membrane complex of PIG-A, PIG-H, PIG-C and GPI1 that has GPI-GnT activity in vitro."
reference_section_type: ABSTRACT
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Establishes the multi-subunit GPI-GnT complex and its
in vitro GlcNAc-transferase activity.
- id: Reactome:R-HSA-162710
title: Synthesis of glycosylphosphatidylinositol (GPI)
findings: []
- id: Reactome:R-HSA-162730
title: phosphatidylinositol + UDP-N-acetyl-D-glucosamine -> N-acetylglucosaminyl-PI
+ UDP
findings: []
- id: file:human/PIGA/PIGA-uniprot.txt
title: UniProtKB P37287 (PIGA_HUMAN) record
findings:
- statement: "Catalytic subunit of the GPI-GnT complex that catalyzes transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol (EC 2.4.1.198); rough ER membrane, single-pass membrane protein; complex composed of PIGA, PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2."
reference_section_type: OTHER
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: UniProt curated record; primary source for EC number, catalytic activity,
subunit composition, and subcellular location.