DPM3 is the small (92-residue) membrane-anchoring and stabilizer subunit of the heterotrimeric dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex, which also comprises the catalytic subunit DPM1 and the regulatory subunit DPM2. DPM synthase transfers mannose from cytosolic GDP-mannose to dolichyl phosphate at the endoplasmic reticulum membrane to produce dolichol-phosphate-mannose (Dol-P-Man), the essential lumenal mannosyl donor for GPI-anchor biosynthesis, N-glycan precursor assembly, and protein O- and C-mannosylation. DPM3 is non-catalytic; because the catalytic DPM1 subunit lacks a transmembrane domain, DPM3 (a multi-pass ER membrane protein) tethers DPM1 to the ER membrane and bridges the complex, associating with DPM1 through its C-terminal region and with DPM2 through its N-terminal region. This scaffolding stabilizes DPM1 and is required for assembly and activity of the DPM synthase. Loss of DPM3 function causes DPM3-CDG, an alpha-dystroglycanopathy-type congenital muscular dystrophy (with elevated serum creatine kinase, reduced O-mannosylation of alpha-dystroglycan, and cardiomyopathy in some patients).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005789
endoplasmic reticulum membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) localization of DPM3 to the ER membrane, where the DPM synthase complex acts. This is consistent with the experimentally determined localization and with DPM3 being a multi-pass ER membrane protein.
Reason: The ER membrane is the established site of the DPM synthase complex and of DPM3, corroborated by IDA localization and the UniProt subcellular location.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0006488
dolichol-linked oligosaccharide biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) involvement in dolichol-linked oligosaccharide biosynthesis. DPM synthase produces Dol-P-Man, the mannosyl donor consumed during assembly of the dolichol-linked oligosaccharide (N-glycan precursor), so DPM3 contributes to this process as part of the complex.
Reason: DPM3 is required for DPM synthase activity, which supplies the Dol-P-Man mannosyl donor used in dolichol-linked oligosaccharide (LLO) assembly and downstream glycosylation.
Supporting Evidence:
PMID:10835346
N-glycan and protein O- and C-mannosylation.
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of DPM3 as part of the dolichol-phosphate-mannose synthase complex. This is the defining complex membership of DPM3 and is strongly supported experimentally.
Reason: DPM3 is one of the three subunits (DPM1/DPM2/DPM3) of the human DPM synthase complex; complex membership is directly established experimentally.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic annotation of ER membrane localization from the UniProt subcellular-location vocabulary mapping. Matches the curated UniProt location and the experimental IDA evidence.
Reason: The IEA ER-membrane localization agrees with the UniProt subcellular location and with experimental evidence; correctly mapped.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0009101
glycoprotein biosynthetic process
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: InterPro2GO (IEA) mapping to glycoprotein biosynthesis. This is a broad downstream process term - DPM synthase supplies the Dol-P-Man donor for protein glycosylation, so DPM3 contributes indirectly, but glycoprotein biosynthesis is a general consequence rather than DPM3's direct/core role.
Reason: Correct in direction (DPM synthase output feeds glycoprotein biosynthesis) but broad and downstream; retained as a non-core process. The core BP is the biosynthesis of the Dol-P-Man donor itself.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Protein modification; protein glycosylation.
|
|
GO:0005515
protein binding
|
IPI
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
MARK AS OVER ANNOTATED |
Summary: IPI protein-binding annotation capturing physical interaction of DPM3 with DPM1 (O60762), DPM2 (O94777), and Xenopus Dpm2 (Q9Z325). These are the functionally central interactions of DPM3, but the bare "protein binding" term is uninformative about the anchoring/adaptor role.
Reason: The DPM1/DPM2 interactions are real and central, but "protein binding" is an uninformative molecular-function term. The specific biology is better represented by the protein-membrane adaptor activity MF (GO:0043495) and the DPM synthase complex CC (GO:0033185), both already annotated.
Supporting Evidence:
PMID:10835346
via its C-terminal domain and 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 annotation from the DPM2/GPI-GnT regulation study, recording physical interaction of DPM3 with DPM1 (O60762) and DPM2 (O94777) in the shared DPM-synthase/GPI-anchor context.
Reason: The interactions are genuine, but the bare "protein binding" term is uninformative; the anchoring role is captured by the protein-membrane adaptor MF and the DPM synthase complex CC terms.
Supporting Evidence:
PMID:10944123
DPM2, but not two other components of
|
|
GO:0005515
protein binding
|
IPI
PMID:23856421 Congenital disorder of glycosylation due to DPM1 mutations p... |
MARK AS OVER ANNOTATED |
Summary: IPI protein-binding annotation supported by the DPM1-CDG study, which showed the pathogenic DPM1 variant has reduced binding to DPM3, an essential non-catalytic subunit - i.e. it documents the DPM1-DPM3 physical interaction.
Reason: The DPM1-DPM3 interaction is real and disease-relevant, but "protein binding" is uninformative; the adaptor MF and complex CC terms convey the actual biology.
Supporting Evidence:
PMID:23856421
reduced binding to DPM3, an essential,
|
|
GO:0005789
endoplasmic reticulum membrane
|
NAS
PMID:9724629 DPM2 regulates biosynthesis of dolichol phosphate-mannose in... |
ACCEPT |
Summary: ComplexPortal NAS annotation of ER membrane localization. The cited study established that the DPM complex resides and functions in the ER membrane (where DPM2 makes a complex with DPM1 essential for ER localization of DPM1).
Reason: Consistent with all other localization evidence placing DPM3 and the DPM synthase complex in the ER membrane.
Supporting Evidence:
PMID:9724629
with DPM1 that is essential for the ER localization and stable expression of
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IPI
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: ComplexPortal IPI annotation of DPM3 as part of the DPM synthase complex, based on the physical demonstration that DPM3 is the third subunit associating with DPM1 and DPM2.
Reason: Directly supported experimental complex membership; this is a defining, core annotation for DPM3.
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 ... |
MODIFY |
Summary: IDA annotation to dolichyl monophosphate (Dol-P) biosynthesis. This term denotes formation of dolichyl monophosphate, which is the SUBSTRATE of DPM synthase, not its product. DPM synthase (and thus DPM3) makes Dol-P-Man from Dol-P + GDP-mannose; it does not synthesize Dol-P itself. The evidence in PMID:10835346 concerns restoration of Dol-P-Man (DPM) biosynthesis.
Reason: The term is a misfit - DPM3 contributes to biosynthesis of dolichol phosphate mannose (Dol-P-Man), not dolichyl monophosphate. The IDA evidence supports the Dol-P-Man process term instead.
Proposed replacements:
dolichol phosphate mannose biosynthetic process
Supporting Evidence:
PMID:10835346
restored the biosynthesis of DPM with an
|
|
GO:0043495
protein-membrane adaptor activity
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: ISS annotation (from ortholog Q4LDX8) to protein-membrane adaptor activity. This is the most informative molecular-function term for DPM3, whose role is to tether the catalytic DPM1 subunit (which lacks a transmembrane domain) to the ER membrane, bridging it to DPM2. This captures DPM3's true non-catalytic anchoring/scaffolding function.
Reason: Best represents DPM3's core molecular function - anchoring the soluble catalytic DPM1 to the ER membrane. Directly consistent with the UniProt FUNCTION statement and experimental data.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
|
|
GO:0180047
dolichol phosphate mannose biosynthetic process
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA annotation to dolichol phosphate mannose (Dol-P-Man) biosynthesis. This is the core biological process of DPM3, which is required for assembly and activity of the DPM synthase that produces Dol-P-Man. Overexpression of DPM3 in DPM2-null Lec15 cells restored DPM biosynthesis.
Reason: Correct core process, directly supported by experimental evidence that DPM3 is required for Dol-P-Man biosynthesis.
Supporting Evidence:
PMID:10835346
restored the biosynthesis of DPM with an
|
|
GO:0035269
protein O-linked glycosylation via mannose
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: ISS annotation to protein O-mannosylation. DPM synthase supplies the Dol-P-Man donor used for O-mannosylation of alpha-dystroglycan; loss of DPM3 causes an alpha-dystroglycanopathy with reduced O-mannosylation. However, this is a downstream process that consumes DPM synthase output rather than DPM3's own direct enzymatic step.
Reason: Biologically connected (and the basis of the DPM3-CDG dystroglycanopathy), but DPM3 acts upstream by producing the mannosyl donor; O-mannosylation itself is performed by other enzymes. Retained as non-core.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
reduced O-mannosylation of alpha-dystroglycan.
|
|
GO:0008047
enzyme activator activity
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
KEEP AS NON CORE |
Summary: IDA annotation to enzyme activator activity. DPM3 increases DPM synthase output - overexpression restored DPM biosynthesis with an increase in DPM1, and DPM3 directly stabilizes DPM1. The activation, however, is achieved through stabilization/membrane anchoring of the catalytic subunit rather than classic allosteric enzyme activation.
Reason: Defensible - DPM3 raises catalytic activity of the complex - but the mechanism is structural stabilization/anchoring, which is more precisely captured by protein-membrane adaptor activity (GO:0043495). Retained as non-core rather than removed.
Supporting Evidence:
PMID:10835346
indicating that DPM3 directly stabilized DPM1.
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4719354 |
ACCEPT |
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM3 failing to form Dol-P-Man. Consistent with all other ER-membrane evidence.
Reason: Reactome curated localization agrees with experimental and phylogenetic ER-membrane annotations.
Supporting Evidence:
Reactome:R-HSA-4719354
Normally, the DPM3 subunit tethers the catalytic DPM1 subunit to the ER membrane.
|
|
GO:0016020
membrane
|
HDA
PMID:19946888 Defining the membrane proteome of NK cells. |
MARK AS OVER ANNOTATED |
Summary: High-throughput MS detection of DPM3 in an NK-cell (YTS) membrane proteome, yielding a generic "membrane" localization. DPM3 is indeed a membrane protein, but this generic term is subsumed by the specific ER-membrane annotations.
Reason: Generic "membrane" is uninformative given the well-supported ER-membrane (GO:0005789) localization; derived from a large-scale membrane-proteome screen not specific to DPM3.
Supporting Evidence:
PMID:19946888
Isolated membranes were
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-162721 |
ACCEPT |
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway for the Dol-P-Man synthesis reaction (dolichyl phosphate + GDP-mannose -> dolichyl phosphate D-mannose) catalysed by the ER-membrane DPM synthase.
Reason: Consistent with all other ER-membrane localization evidence.
Supporting Evidence:
Reactome:R-HSA-162721
a heterotrimeric protein embedded in the endoplasmic reticulum membrane
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4717406 |
ACCEPT |
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM1 failing to form Dol-P-Man; the DPM complex (including DPM3) is annotated at the ER membrane.
Reason: Consistent with the other ER-membrane localization annotations.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4719375 |
ACCEPT |
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM2 failing to form Dol-P-Man; the DPM complex (including DPM3) is annotated at the ER membrane.
Reason: Consistent with the other ER-membrane localization annotations.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0005783
endoplasmic reticulum
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA localization of DPM3 to the endoplasmic reticulum. This is the parent organelle term; the more specific and equally well-supported ER membrane term is the informative localization.
Reason: Correct localization, directly determined; retained (as the parent of the more specific ER-membrane term) but non-core relative to ER membrane.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
|
GO:0033185
dolichol-phosphate-mannose synthase complex
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA annotation (UniProt) of DPM3 as part of the DPM synthase complex, based on the direct experimental demonstration that human DPM synthase consists of DPM1, DPM2 and DPM3.
Reason: Directly supported experimental complex membership; a defining core annotation.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... |
ACCEPT |
Summary: IDA localization of DPM3 to the ER membrane, directly determined in the study that characterized the human DPM synthase complex.
Reason: Directly determined ER-membrane localization; the core, informative cellular-component annotation for DPM3.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
|
Human DPM3 = dolichol-phosphate mannosyltransferase subunit 3 (anchoring subunit).
92 aa; two predicted TM helices (aa 8-28, 37-57). Belongs to the DPM3 family.
Deep research: falcon is OUT OF CREDITS (HTTP 402); no -deep-research-falcon.md was
generated. Review grounded in UniProt (Q9P2X0), the seeded GOA, and cached publications.
DPM3 is the membrane-anchoring / stabilizer subunit of the heterotrimeric
dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex (DPM1/DPM2/DPM3). It is
non-catalytic — its function is structural/anchoring, not enzymatic.
ER membrane, multi-pass membrane protein. [file:human/DPM3/DPM3-uniprot.txt "Endoplasmic
reticulum membrane; Multi-pass"] IDA localization to ER / ER membrane from PMID:10835346.
Reactome (TAS) also places the reaction and complex in the ER membrane. The HDA "membrane"
(GO:0016020) call comes from a large-scale NK-cell membrane-proteome MS study
(PMID:19946888), a generic membrane term subsumed by the ER-membrane annotations.
DPM3-CDG (congenital disorder of glycosylation type Io) — an
alpha-dystroglycanopathy-type muscular dystrophy. UniProt records two OMIM disease entries:
- MDDGC15 (limb-girdle, MIM:612937): muscle weakness, increased serum CK, dystrophic muscle
biopsy, reduced O-mannosylation of alpha-dystroglycan. [file:human/DPM3/DPM3-uniprot.txt
"MDDGC15 patients have muscle"; "weakness, increased serum creatine kinase, dystrophic
changes on muscle"; "reduced O-mannosylation of alpha-dystroglycan."]
- MDDGB15 (congenital with impaired intellectual development, MIM:618992).
The L85S variant reduces DPM1 binding and DPM synthase activity (Lefeber et al. 2009,
PMID:19576565, characterized in UniProt VARIANT feature). DPM1-CDG patients also show reduced
DPM1-DPM3 binding as the pathogenic mechanism. [PMID:23856421 "reduced binding to DPM3, an
essential,"; "non-catalytic subunit of the DPM complex"]
id: Q9P2X0
gene_symbol: DPM3
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: DPM3 is the small (92-residue) membrane-anchoring and stabilizer subunit
of the heterotrimeric dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex,
which also comprises the catalytic subunit DPM1 and the regulatory subunit DPM2.
DPM synthase transfers mannose from cytosolic GDP-mannose to dolichyl phosphate at
the endoplasmic reticulum membrane to produce dolichol-phosphate-mannose (Dol-P-Man),
the essential lumenal mannosyl donor for GPI-anchor biosynthesis, N-glycan precursor
assembly, and protein O- and C-mannosylation. DPM3 is non-catalytic; because the
catalytic DPM1 subunit lacks a transmembrane domain, DPM3 (a multi-pass ER membrane
protein) tethers DPM1 to the ER membrane and bridges the complex, associating with
DPM1 through its C-terminal region and with DPM2 through its N-terminal region. This
scaffolding stabilizes DPM1 and is required for assembly and activity of the DPM
synthase. Loss of DPM3 function causes DPM3-CDG, an alpha-dystroglycanopathy-type
congenital muscular dystrophy (with elevated serum creatine kinase, reduced
O-mannosylation of alpha-dystroglycan, and cardiomyopathy in some patients).
alternative_products:
- name: 1 (Short)
id: Q9P2X0-1
- name: 2 (Long)
id: Q9P2X0-2
sequence_note: VSP_001308
existing_annotations:
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetic (IBA) localization of DPM3 to the ER membrane, where the
DPM synthase complex acts. This is consistent with the experimentally determined
localization and with DPM3 being a multi-pass ER membrane protein.
action: ACCEPT
reason: The ER membrane is the established site of the DPM synthase complex and
of DPM3, corroborated by IDA localization and the UniProt subcellular location.
supported_by:
- reference_id: file:human/DPM3/DPM3-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) involvement in dolichol-linked oligosaccharide biosynthesis.
DPM synthase produces Dol-P-Man, the mannosyl donor consumed during assembly
of the dolichol-linked oligosaccharide (N-glycan precursor), so DPM3 contributes
to this process as part of the complex.
action: ACCEPT
reason: DPM3 is required for DPM synthase activity, which supplies the Dol-P-Man
mannosyl donor used in dolichol-linked oligosaccharide (LLO) assembly and
downstream glycosylation.
supported_by:
- reference_id: PMID:10835346
supporting_text: N-glycan and protein O- and C-mannosylation.
- 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 DPM3 as part of the dolichol-phosphate-mannose
synthase complex. This is the defining complex membership of DPM3 and is
strongly supported experimentally.
action: ACCEPT
reason: DPM3 is one of the three subunits (DPM1/DPM2/DPM3) of the human DPM
synthase complex; complex membership is directly established experimentally.
supported_by:
- reference_id: PMID:10835346
supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
with DPM1
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Electronic annotation of ER membrane localization from the UniProt
subcellular-location vocabulary mapping. Matches the curated UniProt location
and the experimental IDA evidence.
action: ACCEPT
reason: The IEA ER-membrane localization agrees with the UniProt subcellular
location and with experimental evidence; correctly mapped.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
id: GO:0009101
label: glycoprotein biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: InterPro2GO (IEA) mapping to glycoprotein biosynthesis. This is a broad
downstream process term - DPM synthase supplies the Dol-P-Man donor for protein
glycosylation, so DPM3 contributes indirectly, but glycoprotein biosynthesis
is a general consequence rather than DPM3's direct/core role.
action: KEEP_AS_NON_CORE
reason: Correct in direction (DPM synthase output feeds glycoprotein biosynthesis)
but broad and downstream; retained as a non-core process. The core BP is the
biosynthesis of the Dol-P-Man donor itself.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: 'Protein modification; protein glycosylation.'
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:10835346
qualifier: enables
review:
summary: IPI protein-binding annotation capturing physical interaction of DPM3
with DPM1 (O60762), DPM2 (O94777), and Xenopus Dpm2 (Q9Z325). These are the
functionally central interactions of DPM3, but the bare "protein binding" term
is uninformative about the anchoring/adaptor role.
action: MARK_AS_OVER_ANNOTATED
reason: The DPM1/DPM2 interactions are real and central, but "protein binding"
is an uninformative molecular-function term. The specific biology is better
represented by the protein-membrane adaptor activity MF (GO:0043495) and the
DPM synthase complex CC (GO:0033185), both already annotated.
supported_by:
- reference_id: PMID:10835346
supporting_text: via its C-terminal domain and 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 annotation from the DPM2/GPI-GnT regulation study,
recording physical interaction of DPM3 with DPM1 (O60762) and DPM2 (O94777)
in the shared DPM-synthase/GPI-anchor context.
action: MARK_AS_OVER_ANNOTATED
reason: The interactions are genuine, but the bare "protein binding" term is
uninformative; the anchoring role is captured by the protein-membrane adaptor
MF and the DPM synthase complex CC terms.
supported_by:
- reference_id: PMID:10944123
supporting_text: DPM2, but not two other components of
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:23856421
qualifier: enables
review:
summary: IPI protein-binding annotation supported by the DPM1-CDG study, which
showed the pathogenic DPM1 variant has reduced binding to DPM3, an essential
non-catalytic subunit - i.e. it documents the DPM1-DPM3 physical interaction.
action: MARK_AS_OVER_ANNOTATED
reason: The DPM1-DPM3 interaction is real and disease-relevant, but "protein
binding" is uninformative; the adaptor MF and complex CC terms convey the
actual biology.
supported_by:
- reference_id: PMID:23856421
supporting_text: reduced binding to DPM3, an essential,
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: NAS
original_reference_id: PMID:9724629
qualifier: located_in
review:
summary: ComplexPortal NAS annotation of ER membrane localization. The cited
study established that the DPM complex resides and functions in the ER membrane
(where DPM2 makes a complex with DPM1 essential for ER localization of DPM1).
action: ACCEPT
reason: Consistent with all other localization evidence placing DPM3 and the DPM
synthase complex in the ER membrane.
supported_by:
- reference_id: PMID:9724629
supporting_text: with DPM1 that is essential for the ER localization and stable
expression of
- term:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
evidence_type: IPI
original_reference_id: PMID:10835346
qualifier: part_of
review:
summary: ComplexPortal IPI annotation of DPM3 as part of the DPM synthase complex,
based on the physical demonstration that DPM3 is the third subunit associating
with DPM1 and DPM2.
action: ACCEPT
reason: Directly supported experimental complex membership; this is a defining,
core annotation for DPM3.
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 (Dol-P) biosynthesis. This term
denotes formation of dolichyl monophosphate, which is the SUBSTRATE of DPM
synthase, not its product. DPM synthase (and thus DPM3) makes Dol-P-Man from
Dol-P + GDP-mannose; it does not synthesize Dol-P itself. The evidence in
PMID:10835346 concerns restoration of Dol-P-Man (DPM) biosynthesis.
action: MODIFY
reason: The term is a misfit - DPM3 contributes to biosynthesis of dolichol
phosphate mannose (Dol-P-Man), not dolichyl monophosphate. The IDA evidence
supports the Dol-P-Man process term instead.
proposed_replacement_terms:
- id: GO:0180047
label: dolichol phosphate mannose biosynthetic process
supported_by:
- reference_id: PMID:10835346
supporting_text: restored the biosynthesis of DPM with an
- term:
id: GO:0043495
label: protein-membrane adaptor activity
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: enables
review:
summary: ISS annotation (from ortholog Q4LDX8) to protein-membrane adaptor
activity. This is the most informative molecular-function term for DPM3, whose
role is to tether the catalytic DPM1 subunit (which lacks a transmembrane
domain) to the ER membrane, bridging it to DPM2. This captures DPM3's true
non-catalytic anchoring/scaffolding function.
action: ACCEPT
reason: Best represents DPM3's core molecular function - anchoring the soluble
catalytic DPM1 to the ER membrane. Directly consistent with the UniProt FUNCTION
statement and experimental data.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
- 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 dolichol phosphate mannose (Dol-P-Man) biosynthesis.
This is the core biological process of DPM3, which is required for assembly and
activity of the DPM synthase that produces Dol-P-Man. Overexpression of DPM3
in DPM2-null Lec15 cells restored DPM biosynthesis.
action: ACCEPT
reason: Correct core process, directly supported by experimental evidence that
DPM3 is required for Dol-P-Man biosynthesis.
supported_by:
- reference_id: PMID:10835346
supporting_text: restored the biosynthesis of DPM with an
- term:
id: GO:0035269
label: protein O-linked glycosylation via mannose
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: involved_in
review:
summary: ISS annotation to protein O-mannosylation. DPM synthase supplies the
Dol-P-Man donor used for O-mannosylation of alpha-dystroglycan; loss of DPM3
causes an alpha-dystroglycanopathy with reduced O-mannosylation. However, this
is a downstream process that consumes DPM synthase output rather than DPM3's
own direct enzymatic step.
action: KEEP_AS_NON_CORE
reason: Biologically connected (and the basis of the DPM3-CDG dystroglycanopathy),
but DPM3 acts upstream by producing the mannosyl donor; O-mannosylation itself
is performed by other enzymes. Retained as non-core.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: reduced O-mannosylation of alpha-dystroglycan.
- term:
id: GO:0008047
label: enzyme activator activity
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: enables
review:
summary: IDA annotation to enzyme activator activity. DPM3 increases DPM synthase
output - overexpression restored DPM biosynthesis with an increase in DPM1,
and DPM3 directly stabilizes DPM1. The activation, however, is achieved through
stabilization/membrane anchoring of the catalytic subunit rather than classic
allosteric enzyme activation.
action: KEEP_AS_NON_CORE
reason: Defensible - DPM3 raises catalytic activity of the complex - but the
mechanism is structural stabilization/anchoring, which is more precisely
captured by protein-membrane adaptor activity (GO:0043495). Retained as
non-core rather than removed.
supported_by:
- reference_id: PMID:10835346
supporting_text: indicating that DPM3 directly stabilized DPM1.
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4719354
qualifier: located_in
review:
summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
describing defective DPM3 failing to form Dol-P-Man. Consistent with all other
ER-membrane evidence.
action: ACCEPT
reason: Reactome curated localization agrees with experimental and phylogenetic
ER-membrane annotations.
supported_by:
- reference_id: Reactome:R-HSA-4719354
supporting_text: Normally, the DPM3 subunit tethers the catalytic DPM1 subunit
to the ER membrane.
- term:
id: GO:0016020
label: membrane
evidence_type: HDA
original_reference_id: PMID:19946888
qualifier: located_in
review:
summary: High-throughput MS detection of DPM3 in an NK-cell (YTS) membrane
proteome, yielding a generic "membrane" localization. DPM3 is indeed a
membrane protein, but this generic term is subsumed by the specific ER-membrane
annotations.
action: MARK_AS_OVER_ANNOTATED
reason: Generic "membrane" is uninformative given the well-supported ER-membrane
(GO:0005789) localization; derived from a large-scale membrane-proteome screen
not specific to DPM3.
supported_by:
- reference_id: PMID:19946888
supporting_text: Isolated membranes were
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-162721
qualifier: located_in
review:
summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
for the Dol-P-Man synthesis reaction (dolichyl phosphate + GDP-mannose ->
dolichyl phosphate D-mannose) catalysed by the ER-membrane DPM synthase.
action: ACCEPT
reason: Consistent with all other ER-membrane localization evidence.
supported_by:
- reference_id: Reactome:R-HSA-162721
supporting_text: a heterotrimeric protein embedded in the endoplasmic reticulum
membrane
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4717406
qualifier: located_in
review:
summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
describing defective DPM1 failing to form Dol-P-Man; the DPM complex (including
DPM3) is annotated at the ER membrane.
action: ACCEPT
reason: Consistent with the other ER-membrane localization annotations.
supported_by:
- reference_id: file:human/DPM3/DPM3-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-4719375
qualifier: located_in
review:
summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
describing defective DPM2 failing to form Dol-P-Man; the DPM complex (including
DPM3) is annotated at the ER membrane.
action: ACCEPT
reason: Consistent with the other ER-membrane localization annotations.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: located_in
review:
summary: IDA localization of DPM3 to the endoplasmic reticulum. This is the
parent organelle term; the more specific and equally well-supported ER membrane
term is the informative localization.
action: ACCEPT
reason: Correct localization, directly determined; retained (as the parent of
the more specific ER-membrane term) but non-core relative to ER membrane.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: part_of
review:
summary: IDA annotation (UniProt) of DPM3 as part of the DPM synthase complex,
based on the direct experimental demonstration that human DPM synthase consists
of DPM1, DPM2 and DPM3.
action: ACCEPT
reason: Directly supported experimental complex membership; a defining core
annotation.
supported_by:
- reference_id: PMID:10835346
supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
with DPM1
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:10835346
qualifier: located_in
review:
summary: IDA localization of DPM3 to the ER membrane, directly determined in the
study that characterized the human DPM synthase complex.
action: ACCEPT
reason: Directly determined ER-membrane localization; the core, informative
cellular-component annotation for DPM3.
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
core_functions:
- description: DPM3 is the membrane-anchoring/adaptor subunit that tethers the
catalytic DPM1 subunit (which has no transmembrane domain) to the endoplasmic
reticulum membrane and bridges it to DPM2, as part of the dolichol-phosphate
mannose (DPM) synthase complex.
molecular_function:
id: GO:0043495
label: protein-membrane adaptor activity
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
in_complex:
id: GO:0033185
label: dolichol-phosphate-mannose synthase complex
directly_involved_in:
- id: GO:0180047
label: dolichol phosphate mannose biosynthetic process
supported_by:
- reference_id: file:human/DPM3/DPM3-uniprot.txt
supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
- reference_id: PMID:10835346
supporting_text: via its C-terminal domain and with DPM2 via its N-terminal portion.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: PMID:10835346
title: Human dolichol-phosphate-mannose synthase consists of three subunits, DPM1,
DPM2 and DPM3.
findings:
- statement: DPM3 is a 92-amino-acid third subunit of the human DPM synthase complex
that associates with DPM1 via its C-terminal domain and with DPM2 via its
N-terminal portion; DPM3 directly stabilizes DPM1 and is required for DPM
biosynthesis.
supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
with DPM1
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Primary paper defining the three-subunit human DPM synthase and
DPM3's anchoring/stabilizing role; abstract-only cache but directly supports
all core claims.
- id: PMID:10944123
title: Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P
and is regulated by DPM2.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Focuses on GPI-GnT and DPM2 regulation; used by IntAct as a
protein-interaction source for DPM3. Supporting/corroborating for DPM3's
interaction context.
- id: PMID:19946888
title: Defining the membrane proteome of NK cells.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Large-scale NK-cell membrane-proteome MS study; source of the
generic HDA "membrane" localization, not specific to DPM3.
- id: PMID:23856421
title: Congenital disorder of glycosylation due to DPM1 mutations presenting with
dystroglycanopathy-type congenital muscular dystrophy.
findings:
- statement: DPM3 is described as an essential, non-catalytic subunit of the DPM
complex; a pathogenic DPM1 variant showed reduced binding to DPM3, indicating
a disease mechanism via impaired DPM1-DPM3 interaction.
supporting_text: non-catalytic subunit of the DPM complex
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: DPM1-CDG study; explicitly characterizes DPM3 as an essential
non-catalytic subunit and documents the DPM1-DPM3 interaction relevant to
disease.
- 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: MEDIUM
correctness: VERIFIED
review_notes: Establishes the ER-membrane DPM synthase and DPM2-dependent
stabilization/ER-localization of DPM1; ComplexPortal NAS source for DPM3
ER-membrane localization.
- id: Reactome:R-HSA-162721
title: dolichyl phosphate + GDP-alpha-D-mannose -> dolichyl phosphate D-mannose
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Reactome reaction for Dol-P-Man synthesis by the ER-membrane DPM
synthase; source of a TAS ER-membrane localization for DPM3.
- id: Reactome:R-HSA-4717406
title: Defective DPM1 does not transfer mannose to DOLP to form DOLPman
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Reactome disease reaction (defective DPM1); source of a TAS
ER-membrane localization for DPM3.
- id: Reactome:R-HSA-4719354
title: Defective DPM3 does not transfer mannose to DOLP to form DOLPman
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Reactome disease reaction (defective DPM3); states DPM3 tethers the
catalytic DPM1 subunit to the ER membrane and links DPM3 loss to DPM3-CDG.
- id: Reactome:R-HSA-4719375
title: Defective DPM2 does not transfer mannose to DOLP to form DOLPman
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Reactome disease reaction (defective DPM2); source of a TAS
ER-membrane localization for DPM3.
- id: file:human/DPM3/DPM3-uniprot.txt
title: UniProtKB entry Q9P2X0 (DPM3_HUMAN)
findings:
- statement: DPM3 is the stabilizer subunit of the DPM synthase complex that
tethers the catalytic DPM1 subunit to the ER membrane; it is a multi-pass ER
membrane protein and its loss causes DPM3-CDG dystroglycanopathy.
supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Curated UniProt record; source of FUNCTION, SUBUNIT, subcellular
location, and disease statements used in this review.