DPM2 is the small (84-residue), multi-pass endoplasmic reticulum (ER) membrane regulatory subunit of the dolichol-phosphate mannose (Dol-P-Man) synthase complex, which is composed of the catalytic subunit DPM1 together with DPM2 and DPM3. DPM2 is non-catalytic: it stabilizes the complex and enhances its activity rather than performing the mannosyltransfer itself. DPM2 forms a complex with DPM1 that is required for the correct ER localization and stable expression of DPM1, stabilizes DPM3, and enhances the enzyme's binding of the substrate dolichyl phosphate, increasing Dol-P-Man synthase activity roughly ten-fold. Dol-P-Man is the mannosyl donor used for glycosylphosphatidylinositol (GPI) anchor synthesis, the dolichol-linked oligosaccharide precursor of N-glycosylation, and protein O- and C-mannosylation. DPM2 additionally associates with, and enhances the activity of, the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex that initiates GPI-anchor biosynthesis, although it is not essential for that complex. In humans, loss-of-function variants cause DPM2-CDG (congenital disorder of glycosylation type Iu), a muscular dystrophy-dystroglycanopathy with severe epilepsy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005783
endoplasmic reticulum
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment that DPM2 is active in the endoplasmic reticulum. This is correct but less specific than the well-supported ER membrane localization; retained as an accurate, broader localization.
Reason: DPM2 is an ER membrane protein and the Dol-P-Man synthase complex acts in the ER. The more specific GO:0005789 (ER membrane) is separately annotated and preferred for the core localization.
Supporting Evidence:
PMID:9724629
DPM2, an 84 amino acid
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0006488
dolichol-linked oligosaccharide biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment linking DPM2 to biosynthesis of the dolichol-linked oligosaccharide N-glycan precursor. Dol-P-Man produced by the DPM synthase complex is the mannosyl donor for elongation of the lipid-linked oligosaccharide, so DPM2's regulatory role is upstream of and required for this process.
Reason: Consistent with the established role of Dol-P-Man synthase in supplying mannose to the dolichol-linked oligosaccharide (LLO) pathway.
Supporting Evidence:
PMID:10835346
Dolichol-phosphate-mannose (DPM) synthase generates mannosyl donors for
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of DPM2 as part of the dolichol-phosphate-mannose synthase complex. This is the core structural context of DPM2 and is strongly supported experimentally.
Reason: DPM2 is a bona fide subunit of the three-subunit human DPM synthase complex (DPM1/DPM2/DPM3).
Supporting Evidence:
PMID:10835346
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
|
|
GO:0030234
enzyme regulator activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of enzyme regulator activity, capturing DPM2's non-catalytic regulatory role in the DPM synthase complex. DPM2 enhances DPM synthase activity and substrate (dolichyl phosphate) binding without itself being catalytic.
Reason: Matches the experimentally supported function of DPM2 as a regulatory subunit. The more specific GO:0008047 (enzyme activator activity), separately annotated by IDA, better reflects the activating nature of this regulation.
Supporting Evidence:
PMID:10835346
DPM synthase activity was 10 times
PMID:9724629
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (IEA) assignment of ER membrane localization from InterPro/UniProt subcellular-location mapping. Correct and consistent with the experimentally determined multi-pass ER membrane topology of DPM2.
Reason: DPM2 is a multi-pass ER membrane protein; this is the core cellular location.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0030234
enzyme regulator activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Electronic (IEA) InterPro2GO assignment of enzyme regulator activity based on the DPM2 domain (IPR009914). Consistent with the experimental IDA/IBA evidence for DPM2's regulatory role.
Reason: Correct molecular-function class for the DPM2 regulatory subunit; the more specific enzyme activator activity (GO:0008047) is also annotated.
Supporting Evidence:
PMID:10835346
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
|
|
GO:0180047
dolichol phosphate mannose biosynthetic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Electronic (IEA) InterPro2GO assignment to Dol-P-Man biosynthesis. This is the core biological process that the DPM synthase complex, and hence DPM2 as its regulatory subunit, carries out.
Reason: Directly matches DPM2's function as regulatory subunit of Dol-P-Man synthase; also supported by an experimental IDA annotation (PMID:10835346).
Supporting Evidence:
PMID:9724629
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
|
|
GO:0005515
protein binding
|
IPI
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
MARK AS OVER ANNOTATED |
Summary: IPI protein-binding annotation from co-purification/interaction of DPM2 with DPM3 (UniProtKB:Q9P2X0) in the DPM synthase complex. The interaction is real and biologically meaningful for complex assembly, but the bare "protein binding" term is uninformative about molecular function.
Reason: Per curation guidelines, bare protein binding (GO:0005515) is uninformative and is not retained as a core function. The underlying DPM2-DPM3 interaction is better captured by complex membership (GO:0033185) and by enzyme regulator/ activator activity. Experimental IPI is kept, not removed.
Supporting Evidence:
PMID:10835346
with DPM2 via its N-terminal portion
|
|
GO:0005515
protein binding
|
IPI
PMID:10944123 Initial enzyme for glycosylphosphatidylinositol biosynthesis... |
MARK AS OVER ANNOTATED |
Summary: IPI protein-binding annotations from interactions of DPM2 with GPI-GnT components (PIGA/P37287, PIGC/Q92535, PIGQ/Q9BRB3). These interactions underlie DPM2's association with, and enhancement of, the GPI-GnT complex, but the bare term itself is uninformative.
Reason: Bare protein binding is not retained as a core function per curation guidelines. The interactions are more informatively represented by GPI-GnT complex membership (GO:0000506) and enzyme regulator activity. Experimental IPI kept.
Supporting Evidence:
PMID:10944123
associates with GPI-GnT through interactions with PIG-A, PIG-C and
|
|
GO:0005515
protein binding
|
IPI
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
MARK AS OVER ANNOTATED |
Summary: IPI protein-binding annotation from DPM2's identification as a component of the seven-subunit GPI-GnT complex (with PIGA/P37287). Real interaction but the bare term is uninformative.
Reason: Bare protein binding is not retained as a core function per curation guidelines; complex membership (GO:0000506) captures the biology. Experimental IPI kept.
Supporting Evidence:
PMID:16162815
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
|
|
GO:0005789
endoplasmic reticulum membrane
|
NAS
PMID:9724629 DPM2 regulates biosynthesis of dolichol phosphate-mannose in... |
ACCEPT |
Summary: NAS assignment of ER membrane localization based on the original DPM2 characterization. DPM2 was shown to be an ER-expressed membrane protein.
Reason: Consistent with experimental IDA/IEA support for ER membrane localization; this is the core cellular location of DPM2.
Supporting Evidence:
PMID:9724629
DPM2, an 84 amino acid
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IPI
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IPI (ComplexPortal) annotation of DPM2 as part of the DPM synthase complex, based on the physical characterization of the three-subunit human complex. This is a core annotation for DPM2.
Reason: Direct experimental support for DPM2 membership in the DPM1/DPM2/DPM3 complex.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
MARK AS OVER ANNOTATED |
Summary: IDA annotation to "dolichyl monophosphate biosynthetic process". PMID:10835346 concerns dolichol-phosphate-MANNOSE (Dol-P-Man) synthesis, i.e. the transfer of mannose onto dolichyl phosphate, rather than the biosynthesis of dolichyl monophosphate itself. The chosen term is therefore an imprecise/misleading match for the underlying experiment.
Reason: DPM2 regulates addition of mannose to dolichyl phosphate to form Dol-P-Man; it is not shown to be involved in synthesis of the dolichyl monophosphate acceptor. Kept (experimental, not removed) but flagged; the accurate BP is GO:0180047 (dolichol phosphate mannose biosynthetic process), which is separately annotated.
Supporting Evidence:
PMID:10835346
Dolichol-phosphate-mannose (DPM) synthase generates mannosyl donors for
|
|
GO:0180047
dolichol phosphate mannose biosynthetic process
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA annotation to Dol-P-Man biosynthesis, the core biological process of the DPM synthase complex. DPM2 was shown to be required for and to enhance this activity (~10-fold), and to be required for the ER localization/stability of the catalytic subunit DPM1.
Reason: Strong experimental support; this is the central biological process DPM2 participates in as regulatory subunit of Dol-P-Man synthase.
Supporting Evidence:
PMID:10835346
DPM synthase activity was 10 times
PMID:9724629
that is essential for the ER localization and stable expression of
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IPI
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
KEEP AS NON CORE |
Summary: IPI (ComplexPortal) annotation of DPM2 as a component of the GPI-GnT complex. DPM2 co-purifies with the GPI-GnT machinery, but it is a secondary/moonlighting membership: DPM2 is not essential for GPI-GnT and its primary role is in the DPM synthase complex.
Reason: Real, experimentally supported association, but non-core relative to DPM2's primary role as regulatory subunit of Dol-P-Man synthase; DPM2 is dispensable for GPI-GnT activity (though it enhances it).
Supporting Evidence:
PMID:16162815
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
PMID:10944123
indicating that DPM2 is not essential for GPI-GnT; however, the enzyme activity
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
ACCEPT |
Summary: IDA (ComplexPortal) annotation of ER membrane localization, consistent with the ER-membrane topology of DPM2 and the ER location of the GPI-GnT and DPM synthase complexes.
Reason: Core cellular location, well supported across multiple lines of evidence.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IDA
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
KEEP AS NON CORE |
Summary: IDA (UniProt) annotation of DPM2 as a component of the GPI-GnT complex, from the seven-component characterization of GPI-GnT (PIGA/PIGC/PIGH/PIGP/PIGQ/PIGY/DPM2). Secondary/moonlighting membership relative to DPM2's DPM-synthase role.
Reason: Experimentally supported but non-core; DPM2 is not essential for GPI-GnT.
Supporting Evidence:
PMID:16162815
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
|
|
GO:0006506
GPI anchor biosynthetic process
|
IDA
PMID:16162815 The initial enzyme for glycosylphosphatidylinositol biosynth... |
KEEP AS NON CORE |
Summary: IDA annotation linking DPM2 to GPI anchor biosynthesis via its membership in GPI-GnT, the first enzyme of the GPI pathway. This is a genuine but secondary role; DPM2 also contributes to GPI biosynthesis indirectly by supplying Dol-P-Man as a mannosyl donor.
Reason: Real involvement but non-core; DPM2 enhances rather than is essential for GPI-GnT, and its core role is Dol-P-Man synthesis.
Supporting Evidence:
PMID:10944123
DPM2, which regulates
PMID:16162815
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually
|
|
GO:0008047
enzyme activator activity
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA annotation of enzyme activator activity. DPM2 increases Dol-P-Man synthase activity ~10-fold and enhances dolichyl phosphate substrate binding, acting as a positive (activating) regulator of the catalytic DPM1 subunit. This is the most precise molecular-function term for DPM2.
Reason: Directly supported by the ~10x activation of DPM synthase in the presence of DPM2 and by enhanced substrate (dolichyl phosphate) binding; this is DPM2's core molecular function.
Supporting Evidence:
PMID:10835346
DPM synthase activity was 10 times
PMID:9724629
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4719375 |
ACCEPT |
Summary: TAS (Reactome) ER membrane localization from the "Defective DPM2 does not transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
Reason: Consistent with the well-established ER membrane localization of DPM2.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-162721 |
ACCEPT |
Summary: TAS (Reactome) ER membrane localization from the dolichyl phosphate + GDP-mannose -> Dol-P-Man reaction. Correct localization.
Reason: Consistent with the ER membrane localization of DPM2 and the DPM synthase complex.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-162730 |
ACCEPT |
Summary: TAS (Reactome) ER membrane localization from the GPI-GnT reaction (PI + UDP-GlcNAc -> GlcNAc-PI + UDP). Correct localization.
Reason: Consistent with the ER membrane localization of DPM2 and the GPI-GnT complex.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4717406 |
ACCEPT |
Summary: TAS (Reactome) ER membrane localization from the "Defective DPM1 does not transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
Reason: Consistent with the ER membrane localization of DPM2.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4719354 |
ACCEPT |
Summary: TAS (Reactome) ER membrane localization from the "Defective DPM3 does not transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
Reason: Consistent with the ER membrane localization of DPM2.
Supporting Evidence:
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
IDA
PMID:10944123 Initial enzyme for glycosylphosphatidylinositol biosynthesis... |
KEEP AS NON CORE |
Summary: IDA (MGI) annotation of DPM2 as a component of the GPI-GnT complex, from the demonstration that DPM2 associates with GPI-GnT via PIG-A, PIG-C and GPI1. Secondary/moonlighting membership.
Reason: Experimentally supported but non-core relative to DPM2's DPM synthase role; DPM2 is not essential for GPI-GnT.
Supporting Evidence:
PMID:10944123
associates with GPI-GnT through interactions with PIG-A, PIG-C and
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA (UniProt) annotation of DPM2 as part of the DPM synthase complex, from the physical characterization of the three-subunit human complex. Core annotation.
Reason: Directly supported experimental evidence for DPM2 membership in the DPM1/DPM2/ DPM3 complex.
Supporting Evidence:
PMID:10835346
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
|
|
GO:0000506
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
|
TAS
PMID:16280320 DPM1, the catalytic subunit of dolichol-phosphate mannose sy... |
KEEP AS NON CORE |
Summary: TAS annotation of GPI-GnT complex membership. PMID:16280320 focuses on DPM3 tethering/stabilizing DPM1 and notes DPM3 was co-purified with DPM1 and DPM2; the GPI-GnT membership of DPM2 is more directly established elsewhere (PMID:10944123, PMID:16162815). Secondary/moonlighting membership.
Reason: Real but non-core association; DPM2's primary complex is the DPM synthase complex.
Supporting Evidence:
PMID:16280320
co-purified with DPM1 and DPM2
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
PMID:16280320 DPM1, the catalytic subunit of dolichol-phosphate mannose sy... |
ACCEPT |
Summary: TAS ER membrane localization. Consistent with the ER-membrane setting of the DPM synthase and GPI-GnT complexes.
Reason: Consistent with the well-established ER membrane localization of DPM2.
Supporting Evidence:
PMID:16280320
tethered
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
PMID:9724629 DPM2 regulates biosynthesis of dolichol phosphate-mannose in... |
ACCEPT |
Summary: TAS ER membrane localization from the original DPM2 characterization, which described DPM2 as an ER-expressed membrane protein.
Reason: Core cellular location, supported by the primary DPM2 paper and consistent with multi-pass ER membrane topology.
Supporting Evidence:
PMID:9724629
DPM2, an 84 amino acid
file:human/DPM2/DPM2-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
UniProtKB: O94777. HGNC:3006. 84 aa, two predicted TM helices (11–31, 49–69),
ER membrane multi-pass protein. Pfam PF07297 (DPM2); InterPro IPR009914 (DPM2).
Pharos Tdark. Belongs to the DPM2 family.
Deep research: falcon provider is OUT OF CREDITS (HTTP 402); no
-deep-research-falcon.md was generated. Review grounded in the UniProt record,
the seeded GOA, and the cached abstract-only publications below.
DPM2 is the regulatory/stabilizing subunit of the dolichol-phosphate mannose
(Dol-P-Man) synthase complex (DPM1 catalytic / DPM2 / DPM3). It is non-catalytic.
DPM2 is also a component of the GPI-N-acetylglucosaminyltransferase (GPI-GnT)
complex and enhances GPI-GnT activity, but is NOT essential for it:
- PMID:10944123; DPM2 "associates with GPI-GnT through interactions with PIG-A, PIG-C and GPI1"; "indicating that DPM2 is not essential for GPI-GnT; however, the enzyme activity is enhanced 3-fold in the presence of DPM2."
- PMID:16162815 GPI-GnT is the initial GPI-biosynthesis enzyme (transfers GlcNAc from UDP-GlcNAc to PI); DPM2 is one of its components (PIG-Y is the seventh). This paper's DPM2 annotations (GPI-GnT complex, ER membrane) are ComplexPortal/UniProt IDA.
DPM2-CDG (congenital disorder of glycosylation type Iu / CDG1U, MIM:615042):
muscular dystrophy-dystroglycanopathy with severe epilepsy. Variant Y23C (CDG1U).
Ref PMID:23109149 (Barone et al. 2012) — NOT in GOA, not cached; cited only in
UniProt disease block, so not used as a supporting_text source here.
id: O94777
gene_symbol: DPM2
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
DPM2 is the small (84-residue), multi-pass endoplasmic reticulum (ER) membrane
regulatory subunit of the dolichol-phosphate mannose (Dol-P-Man) synthase complex,
which is composed of the catalytic subunit DPM1 together with DPM2 and DPM3.
DPM2 is non-catalytic: it stabilizes the complex and enhances its activity rather
than performing the mannosyltransfer itself. DPM2 forms a complex with DPM1 that is
required for the correct ER localization and stable expression of DPM1, stabilizes
DPM3, and enhances the enzyme's binding of the substrate dolichyl phosphate,
increasing Dol-P-Man synthase activity roughly ten-fold. Dol-P-Man is the mannosyl
donor used for glycosylphosphatidylinositol (GPI) anchor synthesis, the
dolichol-linked oligosaccharide precursor of N-glycosylation, and protein O- and
C-mannosylation. DPM2 additionally associates with, and enhances the activity of,
the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex that initiates GPI-anchor
biosynthesis, although it is not essential for that complex. In humans, loss-of-function
variants cause DPM2-CDG (congenital disorder of glycosylation type Iu), a muscular
dystrophy-dystroglycanopathy with severe epilepsy.
existing_annotations:
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetic (IBA) assignment that DPM2 is active in the endoplasmic reticulum.
This is correct but less specific than the well-supported ER membrane
localization; retained as an accurate, broader localization.
action: ACCEPT
reason: >-
DPM2 is an ER membrane protein and the Dol-P-Man synthase complex acts in the
ER. The more specific GO:0005789 (ER membrane) is separately annotated and
preferred for the core localization.
supported_by:
- reference_id: PMID:9724629
supporting_text: >-
DPM2, an 84 amino acid
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetic (IBA) assignment linking DPM2 to biosynthesis of the
dolichol-linked oligosaccharide N-glycan precursor. Dol-P-Man produced by the
DPM synthase complex is the mannosyl donor for elongation of the lipid-linked
oligosaccharide, so DPM2's regulatory role is upstream of and required for this
process.
action: ACCEPT
reason: >-
Consistent with the established role of Dol-P-Man synthase in supplying mannose
to the dolichol-linked oligosaccharide (LLO) pathway.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
Dolichol-phosphate-mannose (DPM) synthase generates mannosyl donors for
- term:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: part_of
review:
summary: >-
Phylogenetic (IBA) assignment of DPM2 as part of the dolichol-phosphate-mannose
synthase complex. This is the core structural context of DPM2 and is strongly
supported experimentally.
action: ACCEPT
reason: >-
DPM2 is a bona fide subunit of the three-subunit human DPM synthase complex
(DPM1/DPM2/DPM3).
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
- term:
id: GO:0030234
label: enzyme regulator activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) assignment of enzyme regulator activity, capturing DPM2's
non-catalytic regulatory role in the DPM synthase complex. DPM2 enhances DPM
synthase activity and substrate (dolichyl phosphate) binding without itself
being catalytic.
action: ACCEPT
reason: >-
Matches the experimentally supported function of DPM2 as a regulatory subunit.
The more specific GO:0008047 (enzyme activator activity), separately annotated
by IDA, better reflects the activating nature of this regulation.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
DPM synthase activity was 10 times
- reference_id: PMID:9724629
supporting_text: >-
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: >-
Electronic (IEA) assignment of ER membrane localization from InterPro/UniProt
subcellular-location mapping. Correct and consistent with the experimentally
determined multi-pass ER membrane topology of DPM2.
action: ACCEPT
reason: >-
DPM2 is a multi-pass ER membrane protein; this is the core cellular location.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0030234
label: enzyme regulator activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
Electronic (IEA) InterPro2GO assignment of enzyme regulator activity based on
the DPM2 domain (IPR009914). Consistent with the experimental IDA/IBA evidence
for DPM2's regulatory role.
action: ACCEPT
reason: >-
Correct molecular-function class for the DPM2 regulatory subunit; the more
specific enzyme activator activity (GO:0008047) is also annotated.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
- term:
id: GO:0180047
label: dolichol phosphate mannose biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
Electronic (IEA) InterPro2GO assignment to Dol-P-Man biosynthesis. This is the
core biological process that the DPM synthase complex, and hence DPM2 as its
regulatory subunit, carries out.
action: ACCEPT
reason: >-
Directly matches DPM2's function as regulatory subunit of Dol-P-Man synthase;
also supported by an experimental IDA annotation (PMID:10835346).
supported_by:
- reference_id: PMID:9724629
supporting_text: >-
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:10835346
qualifier: enables
review:
summary: >-
IPI protein-binding annotation from co-purification/interaction of DPM2 with
DPM3 (UniProtKB:Q9P2X0) in the DPM synthase complex. The interaction is real and
biologically meaningful for complex assembly, but the bare "protein binding"
term is uninformative about molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Per curation guidelines, bare protein binding (GO:0005515) is uninformative and
is not retained as a core function. The underlying DPM2-DPM3 interaction is
better captured by complex membership (GO:0033185) and by enzyme regulator/
activator activity. Experimental IPI is kept, not removed.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
with DPM2 via its N-terminal portion
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:10944123
qualifier: enables
review:
summary: >-
IPI protein-binding annotations from interactions of DPM2 with GPI-GnT
components (PIGA/P37287, PIGC/Q92535, PIGQ/Q9BRB3). These interactions underlie
DPM2's association with, and enhancement of, the GPI-GnT complex, but the bare
term itself is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Bare protein binding is not retained as a core function per curation guidelines.
The interactions are more informatively represented by GPI-GnT complex
membership (GO:0000506) and enzyme regulator activity. Experimental IPI kept.
supported_by:
- reference_id: PMID:10944123
supporting_text: >-
associates with GPI-GnT through interactions with PIG-A, PIG-C and
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16162815
qualifier: enables
review:
summary: >-
IPI protein-binding annotation from DPM2's identification as a component of the
seven-subunit GPI-GnT complex (with PIGA/P37287). Real interaction but the bare
term is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Bare protein binding is not retained as a core function per curation guidelines;
complex membership (GO:0000506) captures the biology. Experimental IPI kept.
supported_by:
- reference_id: PMID:16162815
supporting_text: >-
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: NAS
original_reference_id: PMID:9724629
qualifier: located_in
review:
summary: >-
NAS assignment of ER membrane localization based on the original DPM2
characterization. DPM2 was shown to be an ER-expressed membrane protein.
action: ACCEPT
reason: >-
Consistent with experimental IDA/IEA support for ER membrane localization; this
is the core cellular location of DPM2.
supported_by:
- reference_id: PMID:9724629
supporting_text: >-
DPM2, an 84 amino acid
- term:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
evidence_type: IPI
original_reference_id: PMID:10835346
qualifier: part_of
review:
summary: >-
IPI (ComplexPortal) annotation of DPM2 as part of the DPM synthase complex,
based on the physical characterization of the three-subunit human complex. This
is a core annotation for DPM2.
action: ACCEPT
reason: >-
Direct experimental support for DPM2 membership in the DPM1/DPM2/DPM3 complex.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: involved_in
review:
summary: >-
IDA annotation to "dolichyl monophosphate biosynthetic process". PMID:10835346
concerns dolichol-phosphate-MANNOSE (Dol-P-Man) synthesis, i.e. the transfer of
mannose onto dolichyl phosphate, rather than the biosynthesis of dolichyl
monophosphate itself. The chosen term is therefore an imprecise/misleading match
for the underlying experiment.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DPM2 regulates addition of mannose to dolichyl phosphate to form Dol-P-Man; it
is not shown to be involved in synthesis of the dolichyl monophosphate acceptor.
Kept (experimental, not removed) but flagged; the accurate BP is GO:0180047
(dolichol phosphate mannose biosynthetic process), which is separately annotated.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
Dolichol-phosphate-mannose (DPM) synthase generates mannosyl donors for
- term:
id: GO:0180047
label: dolichol phosphate mannose biosynthetic process
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: involved_in
review:
summary: >-
IDA annotation to Dol-P-Man biosynthesis, the core biological process of the
DPM synthase complex. DPM2 was shown to be required for and to enhance this
activity (~10-fold), and to be required for the ER localization/stability of the
catalytic subunit DPM1.
action: ACCEPT
reason: >-
Strong experimental support; this is the central biological process DPM2
participates in as regulatory subunit of Dol-P-Man synthase.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
DPM synthase activity was 10 times
- reference_id: PMID:9724629
supporting_text: >-
that is essential for the ER localization and stable expression of
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IPI
original_reference_id: PMID:16162815
qualifier: part_of
review:
summary: >-
IPI (ComplexPortal) annotation of DPM2 as a component of the GPI-GnT complex.
DPM2 co-purifies with the GPI-GnT machinery, but it is a secondary/moonlighting
membership: DPM2 is not essential for GPI-GnT and its primary role is in the DPM
synthase complex.
action: KEEP_AS_NON_CORE
reason: >-
Real, experimentally supported association, but non-core relative to DPM2's
primary role as regulatory subunit of Dol-P-Man synthase; DPM2 is dispensable
for GPI-GnT activity (though it enhances it).
supported_by:
- reference_id: PMID:16162815
supporting_text: >-
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
- reference_id: PMID:10944123
supporting_text: >-
indicating that DPM2 is not essential for GPI-GnT; however, the enzyme activity
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:16162815
qualifier: located_in
review:
summary: >-
IDA (ComplexPortal) annotation of ER membrane localization, consistent with the
ER-membrane topology of DPM2 and the ER location of the GPI-GnT and DPM synthase
complexes.
action: ACCEPT
reason: >-
Core cellular location, well supported across multiple lines of evidence.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IDA
original_reference_id: PMID:16162815
qualifier: part_of
review:
summary: >-
IDA (UniProt) annotation of DPM2 as a component of the GPI-GnT complex, from the
seven-component characterization of GPI-GnT (PIGA/PIGC/PIGH/PIGP/PIGQ/PIGY/DPM2).
Secondary/moonlighting membership relative to DPM2's DPM-synthase role.
action: KEEP_AS_NON_CORE
reason: >-
Experimentally supported but non-core; DPM2 is not essential for GPI-GnT.
supported_by:
- reference_id: PMID:16162815
supporting_text: >-
complex GPI-N-acetylglucosaminyltransferase (GPI-GnT)
- term:
id: GO:0006506
label: GPI anchor biosynthetic process
evidence_type: IDA
original_reference_id: PMID:16162815
qualifier: involved_in
review:
summary: >-
IDA annotation linking DPM2 to GPI anchor biosynthesis via its membership in
GPI-GnT, the first enzyme of the GPI pathway. This is a genuine but secondary
role; DPM2 also contributes to GPI biosynthesis indirectly by supplying Dol-P-Man
as a mannosyl donor.
action: KEEP_AS_NON_CORE
reason: >-
Real involvement but non-core; DPM2 enhances rather than is essential for
GPI-GnT, and its core role is Dol-P-Man synthesis.
supported_by:
- reference_id: PMID:10944123
supporting_text: >-
DPM2, which regulates
- reference_id: PMID:16162815
supporting_text: >-
Biosynthesis of glycosylphosphatidylinositol (GPI) is initiated by an unusually
- term:
id: GO:0008047
label: enzyme activator activity
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: enables
review:
summary: >-
IDA annotation of enzyme activator activity. DPM2 increases Dol-P-Man synthase
activity ~10-fold and enhances dolichyl phosphate substrate binding, acting as a
positive (activating) regulator of the catalytic DPM1 subunit. This is the most
precise molecular-function term for DPM2.
action: ACCEPT
reason: >-
Directly supported by the ~10x activation of DPM synthase in the presence of
DPM2 and by enhanced substrate (dolichyl phosphate) binding; this is DPM2's core
molecular function.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
DPM synthase activity was 10 times
- reference_id: PMID:9724629
supporting_text: >-
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4719375
qualifier: located_in
review:
summary: >-
TAS (Reactome) ER membrane localization from the "Defective DPM2 does not
transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
action: ACCEPT
reason: >-
Consistent with the well-established ER membrane localization of DPM2.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162721
qualifier: located_in
review:
summary: >-
TAS (Reactome) ER membrane localization from the dolichyl phosphate +
GDP-mannose -> Dol-P-Man reaction. Correct localization.
action: ACCEPT
reason: >-
Consistent with the ER membrane localization of DPM2 and the DPM synthase
complex.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162730
qualifier: located_in
review:
summary: >-
TAS (Reactome) ER membrane localization from the GPI-GnT reaction
(PI + UDP-GlcNAc -> GlcNAc-PI + UDP). Correct localization.
action: ACCEPT
reason: >-
Consistent with the ER membrane localization of DPM2 and the GPI-GnT complex.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4717406
qualifier: located_in
review:
summary: >-
TAS (Reactome) ER membrane localization from the "Defective DPM1 does not
transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
action: ACCEPT
reason: >-
Consistent with the ER membrane localization of DPM2.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4719354
qualifier: located_in
review:
summary: >-
TAS (Reactome) ER membrane localization from the "Defective DPM3 does not
transfer mannose to DOLP to form DOLPman" reaction. Correct localization.
action: ACCEPT
reason: >-
Consistent with the ER membrane localization of DPM2.
supported_by:
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: IDA
original_reference_id: PMID:10944123
qualifier: part_of
review:
summary: >-
IDA (MGI) annotation of DPM2 as a component of the GPI-GnT complex, from the
demonstration that DPM2 associates with GPI-GnT via PIG-A, PIG-C and GPI1.
Secondary/moonlighting membership.
action: KEEP_AS_NON_CORE
reason: >-
Experimentally supported but non-core relative to DPM2's DPM synthase role;
DPM2 is not essential for GPI-GnT.
supported_by:
- reference_id: PMID:10944123
supporting_text: >-
associates with GPI-GnT through interactions with PIG-A, PIG-C and
- term:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: part_of
review:
summary: >-
IDA (UniProt) annotation of DPM2 as part of the DPM synthase complex, from the
physical characterization of the three-subunit human complex. Core annotation.
action: ACCEPT
reason: >-
Directly supported experimental evidence for DPM2 membership in the DPM1/DPM2/
DPM3 complex.
supported_by:
- reference_id: PMID:10835346
supporting_text: >-
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
- term:
id: GO:0000506
label: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT)
complex
evidence_type: TAS
original_reference_id: PMID:16280320
qualifier: part_of
review:
summary: >-
TAS annotation of GPI-GnT complex membership. PMID:16280320 focuses on DPM3
tethering/stabilizing DPM1 and notes DPM3 was co-purified with DPM1 and DPM2;
the GPI-GnT membership of DPM2 is more directly established elsewhere
(PMID:10944123, PMID:16162815). Secondary/moonlighting membership.
action: KEEP_AS_NON_CORE
reason: >-
Real but non-core association; DPM2's primary complex is the DPM synthase
complex.
supported_by:
- reference_id: PMID:16280320
supporting_text: >-
co-purified with DPM1 and DPM2
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: PMID:16280320
qualifier: located_in
review:
summary: >-
TAS ER membrane localization. Consistent with the ER-membrane setting of the DPM
synthase and GPI-GnT complexes.
action: ACCEPT
reason: >-
Consistent with the well-established ER membrane localization of DPM2.
supported_by:
- reference_id: PMID:16280320
supporting_text: >-
tethered
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: PMID:9724629
qualifier: located_in
review:
summary: >-
TAS ER membrane localization from the original DPM2 characterization, which
described DPM2 as an ER-expressed membrane protein.
action: ACCEPT
reason: >-
Core cellular location, supported by the primary DPM2 paper and consistent with
multi-pass ER membrane topology.
supported_by:
- reference_id: PMID:9724629
supporting_text: >-
DPM2, an 84 amino acid
- reference_id: file:human/DPM2/DPM2-uniprot.txt
supporting_text: >-
Endoplasmic reticulum membrane; Multi-pass
core_functions:
- description: >-
Regulatory (non-catalytic) subunit of the dolichol-phosphate mannose (Dol-P-Man)
synthase complex. As an activating regulator, DPM2 stabilizes the complex
(required for ER localization/stability of catalytic DPM1 and for DPM3 stability),
enhances binding of the dolichyl phosphate substrate, and increases Dol-P-Man
synthase activity ~10-fold, thereby driving Dol-P-Man biosynthesis in the ER
membrane. Dol-P-Man is the mannosyl donor for N-glycosylation, GPI-anchor
synthesis, and protein O-/C-mannosylation.
molecular_function:
id: GO:0008047
label: enzyme activator activity
directly_involved_in:
- id: GO:0180047
label: dolichol phosphate mannose biosynthetic process
- id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
in_complex:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
supported_by:
- reference_id: PMID:9724629
supporting_text: >-
that is essential for the ER localization and stable expression of
- reference_id: PMID:9724629
supporting_text: >-
DPM2 enhances binding of dolichol phosphate, a substrate of DPM
- reference_id: PMID:10835346
supporting_text: >-
DPM synthase activity was 10 times
- reference_id: PMID:10835346
supporting_text: >-
mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2
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:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:human/DPM2/DPM2-uniprot.txt
title: UniProtKB entry O94777 (DPM2_HUMAN)
findings: []
- id: PMID:10835346
title: Human dolichol-phosphate-mannose synthase consists of three subunits, DPM1,
DPM2 and DPM3.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Primary paper establishing the three-subunit human DPM synthase (DPM1 catalytic,
DPM2 and DPM3 regulatory/stabilizing) and DPM2's ~10x enhancement of activity.
Abstract-only cache (full_text_available: false); claims anchored to the abstract.
- id: PMID:10944123
title: Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P
and is regulated by DPM2.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Establishes DPM2's association with, and ~3x enhancement of, GPI-GnT (via PIG-A,
PIG-C, GPI1), while showing DPM2 is not essential for GPI-GnT.
- id: PMID:16162815
title: The initial enzyme for glycosylphosphatidylinositol biosynthesis requires
PIG-Y, a seventh component.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Characterizes the seven-component GPI-GnT (including DPM2); primary focus is
PIG-Y. Supports DPM2's GPI-GnT complex membership.
- id: PMID:16280320
title: DPM1, the catalytic subunit of dolichol-phosphate mannose synthase, is tethered
to and stabilized on the endoplasmic reticulum membrane by DPM3.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Primarily about DPM3 tethering/stabilizing DPM1; confirms DPM3 co-purifies with
DPM1 and DPM2 in the DPM synthase complex.
- id: PMID:9724629
title: 'DPM2 regulates biosynthesis of dolichol phosphate-mannose in mammalian cells:
correct subcellular localization and stabilization of DPM1, and binding of dolichol
phosphate.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Original DPM2 characterization: ER membrane protein that complexes with DPM1,
required for DPM1 ER localization/stability, and enhances dolichyl phosphate
binding. Abstract-only cache; claims anchored to abstract.
- id: Reactome:R-HSA-162721
title: dolichyl phosphate + GDP-alpha-D-mannose -> dolichyl phosphate D-mannose
findings: []
- id: Reactome:R-HSA-162730
title: phosphatidylinositol + UDP-N-acetyl-D-glucosamine -> N-acetylglucosaminyl-PI
+ UDP
findings: []
- id: Reactome:R-HSA-4717406
title: Defective DPM1 does not transfer mannose to DOLP to form DOLPman
findings: []
- id: Reactome:R-HSA-4719354
title: Defective DPM3 does not transfer mannose to DOLP to form DOLPman
findings: []
- id: Reactome:R-HSA-4719375
title: Defective DPM2 does not transfer mannose to DOLP to form DOLPman
findings: []