DOLK is dolichol kinase, a polytopic endoplasmic reticulum membrane enzyme that catalyzes the CTP-dependent phosphorylation of dolichol to dolichyl monophosphate (Dol-P), the terminal step in de novo Dol-P biosynthesis (EC 2.7.1.108). Dol-P is the essential lipid carrier that primes assembly of the dolichol-linked oligosaccharide for protein N-linked glycosylation and is also required for O-mannosylation, C-mannosylation and GPI-anchor biosynthesis, so DOLK supplies the activated lipid carrier used throughout the glycosylation system. The enzyme has a cytoplasmically oriented CTP-binding site and belongs to the polyprenol kinase family. Loss-of-function mutations cause DOLK-CDG (congenital disorder of glycosylation type Im), whose features include dilated cardiomyopathy (linked to deficient alpha-dystroglycan O-mannosylation), ichthyosis and neurological disease.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005789
endoplasmic reticulum membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred ER membrane localization, consistent with the experimentally demonstrated ER membrane localization of human dolichol kinase and its yeast ortholog SEC59.
Reason: DOLK is an experimentally validated polytopic ER membrane protein (PMID:16923818), so the IBA localization is correct and represents a core aspect of where the enzyme acts.
Supporting Evidence:
PMID:16923818
shown to be a polytopic membrane protein localized in the endoplasmic reticulum with an N terminus extended into the lumen and a cytoplasmically oriented C terminus.
|
|
GO:0004168
dolichol kinase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred dolichol kinase activity, the defining and experimentally established molecular function of DOLK.
Reason: This is the core molecular function of the gene, directly demonstrated biochemically (PMID:12213788, PMID:16923818) and by disease-variant enzyme assays (PMID:17273964, PMID:22242004). GOA carries this exact current term (GO:0004168, EC 2.7.1.108).
Supporting Evidence:
PMID:12213788
Dolichol kinase (DK) catalyzes the CTP-mediated phosphorylation of dolichol in eukaryotic cells, the terminal step in dolichyl monophosphate (Dol-P) biosynthesis de novo.
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically inferred involvement in dolichyl monophosphate (Dol-P) biosynthesis, the pathway output of the dolichol kinase reaction.
Reason: Dol-P biosynthesis is the direct biological process to which the DOLK reaction contributes; this is well supported experimentally and the IBA is at an appropriate level of specificity.
Supporting Evidence:
PMID:12213788
the terminal step in dolichyl monophosphate (Dol-P) biosynthesis de novo.
|
|
GO:0004168
dolichol kinase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Automated annotation of dolichol kinase activity from the RHEA/EC mapping (RHEA:13133, EC 2.7.1.108).
Reason: The EC/RHEA mapping is exactly correct for DOLK and matches the experimentally established catalytic activity. The reaction is documented in UniProt.
Supporting Evidence:
file:human/DOLK/DOLK-uniprot.txt
Reaction=a di-trans,poly-cis-dolichol + CTP = a di-trans,poly-cis-
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Automated ER membrane localization from the UniProt subcellular-location keyword mapping, consistent with experimental data.
Reason: DOLK is an experimentally confirmed integral ER membrane protein; the SubCell mapping is accurate.
Supporting Evidence:
file:human/DOLK/DOLK-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
|
|
GO:0005515
protein binding
|
IPI
PMID:25416956 A proteome-scale map of the human interactome network. |
MARK AS OVER ANNOTATED |
Summary: Interactor identified in a proteome-scale binary interactome map. The generic "protein binding" term is uninformative about DOLK's actual molecular function.
Reason: This annotation comes from a large-scale high-throughput interactome screen and only asserts the uninformative term GO:0005515 protein binding. Per curation guidelines this term should not be treated as core function; the physiologically meaningful function is dolichol kinase activity. Retained as an experimental IPI rather than removed.
Supporting Evidence:
PMID:25416956
A proteome-scale map of the human interactome network.
|
|
GO:0005515
protein binding
|
IPI
PMID:26871637 Widespread Expansion of Protein Interaction Capabilities by ... |
MARK AS OVER ANNOTATED |
Summary: Interactor reported in a large-scale alternative-splicing interactome study; the term is uninformative for DOLK function.
Reason: High-throughput protein-protein interaction annotation using the generic GO:0005515 term. It does not inform the molecular function of DOLK and is not a core annotation. Retained as an experimental IPI.
Supporting Evidence:
PMID:26871637
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: Interactors reported in a large-scale interactome map (e.g. KCNA6, LRRC4C); the generic term is uninformative for DOLK function.
Reason: High-throughput interactome annotation using the uninformative GO:0005515 term. DOLK's interactors here are largely co-resident ER membrane proteins and the binding data do not establish a specific molecular function. Retained as an experimental IPI.
Supporting Evidence:
PMID:28514442
Architecture of the human interactome defines protein communities and disease networks.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: Multiple interactors reported in the HuRI binary interactome map; the generic term is uninformative for DOLK function.
Reason: High-throughput binary interactome annotation using the uninformative GO:0005515 term. The many interactors (largely ER/membrane proteins) do not define a specific molecular function for DOLK. Retained as an experimental IPI.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: Interactors reported in a proteome-scale AP-MS network study; the generic term is uninformative for DOLK function.
Reason: High-throughput proteome-scale interaction annotation using the uninformative GO:0005515 term. Does not inform DOLK molecular function and is not core. Retained as an experimental IPI.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
TAS
Reactome:R-HSA-446199 |
ACCEPT |
Summary: Reactome-asserted involvement in dolichyl phosphate synthesis, matching the enzyme's pathway role.
Reason: DOLK catalyzes the terminal step producing Dol-P; the Reactome pathway "Synthesis of dolichyl-phosphate" correctly captures this biological process.
Supporting Evidence:
PMID:12213788
the terminal step in dolichyl monophosphate (Dol-P) biosynthesis de novo.
|
|
GO:0004168
dolichol kinase activity
|
TAS
Reactome:R-HSA-446195 |
ACCEPT |
Summary: Reactome-asserted dolichol kinase activity (DOLK phosphorylates dolichol to Dol-P), matching the core molecular function.
Reason: Correct assignment of the enzyme's defining catalytic activity, corroborated by biochemical assays.
Supporting Evidence:
PMID:16923818
Human dolichol kinase, a polytopic endoplasmic reticulum membrane protein with a cytoplasmically oriented CTP-binding site.
|
|
GO:0004168
dolichol kinase activity
|
TAS
Reactome:R-HSA-4755600 |
ACCEPT |
Summary: Reactome-asserted dolichol kinase activity (disease-annotated reaction), matching the core molecular function.
Reason: Correct assignment of the defining catalytic activity of DOLK.
Supporting Evidence:
PMID:16923818
Human dolichol kinase, a polytopic endoplasmic reticulum membrane protein with a cytoplasmically oriented CTP-binding site.
|
|
GO:0005730
nucleolus
|
IDA
GO_REF:0000052 |
MARK AS OVER ANNOTATED |
Summary: Single high-throughput immunofluorescence (HPA) annotation to the nucleolus, inconsistent with the well-established integral ER membrane localization of this polytopic membrane kinase.
Reason: DOLK is a ~15-pass integral ER membrane protein (PMID:16923818); a nucleolar localization is biologically implausible for its function and is contradicted by IDA, IBA, IEA and Reactome ER membrane annotations. This is most likely background/off-target signal in the HPA immunofluorescence screen. Not removed (single experimental IF datum) but flagged as over-annotation.
Supporting Evidence:
PMID:16923818
shown to be a polytopic membrane protein localized in the endoplasmic reticulum with an N terminus extended into the lumen and a cytoplasmically oriented C terminus.
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IGI
PMID:12213788 Expression and characterization of a human cDNA that complem... |
ACCEPT |
Summary: Genetic interaction evidence: human DOLK (hDK1) complements the yeast sec59-1 (SEC59/dolichol kinase) mutant, restoring dolichol kinase activity, Dol-P levels and N-glycosylation, establishing its role in Dol-P biosynthesis.
Reason: Cross-species complementation (with yeast SEC59, UniProtKB:P20048) demonstrates DOLK functions in de novo Dol-P biosynthesis. This is a well-supported core biological process annotation.
Supporting Evidence:
PMID:12213788
hDK1 is capable of complementing the growth defect, elevating DK activity, and consequently increasing Dol-P levels in vivo and restoring normal N-glycosylation of carboxypeptidase Y at the restrictive temperature in the temperature-sensitive mutant sec59-1.
|
|
GO:0004168
dolichol kinase activity
|
EXP
PMID:17273964 A defect in dolichol phosphate biosynthesis causes a new inh... |
ACCEPT |
Summary: Experimental demonstration of dolichol kinase activity via disease-variant characterization: CDG1M variants Cys99Ser and Tyr441Ser have only 2-4% residual DK activity.
Reason: Direct experimental measurement of the enzyme's catalytic activity in patient cells and by yeast complementation; core molecular function.
Supporting Evidence:
PMID:17273964
The residual activity of mutant DK1 was 2%-4% when compared with control cells.
|
|
GO:0004168
dolichol kinase activity
|
IMP
PMID:22242004 Autosomal recessive dilated cardiomyopathy due to DOLK mutat... |
ACCEPT |
Summary: Mutant-phenotype evidence: pathogenic DOLK mutations cause a dolichol kinase deficiency confirmed by enzyme analysis in patient fibroblasts.
Reason: Loss of catalytic activity upon mutation directly supports the dolichol kinase molecular function of DOLK; core.
Supporting Evidence:
PMID:22242004
Enzyme analysis in patients' fibroblasts confirmed a dolichol kinase deficiency in all families.
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IMP
PMID:22242004 Autosomal recessive dilated cardiomyopathy due to DOLK mutat... |
ACCEPT |
Summary: Mutant-phenotype evidence that DOLK is required for dolichol-phosphate formation; DOLK mutations abolish dolichol kinase activity and downstream glycosylation.
Reason: DOLK mutations cause deficient formation of dolichol-phosphate and impaired N-glycosylation / O-mannosylation, supporting its role in Dol-P biosynthesis. Core biological process.
Supporting Evidence:
PMID:22242004
pathogenic mutations were identified in DOLK, encoding the dolichol kinase responsible for formation of dolichol-phosphate.
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-4755600 |
ACCEPT |
Summary: Reactome-asserted ER membrane localization, consistent with experimental data.
Reason: Correct; matches the experimentally established ER membrane localization of DOLK.
Supporting Evidence:
PMID:16923818
localized in the endoplasmic reticulum
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-446195 |
ACCEPT |
Summary: Reactome-asserted ER membrane localization, consistent with experimental data.
Reason: Correct; matches the experimentally established ER membrane localization of DOLK.
Supporting Evidence:
PMID:16923818
localized in the endoplasmic reticulum
|
|
GO:0004168
dolichol kinase activity
|
IDA
PMID:12213788 Expression and characterization of a human cDNA that complem... |
ACCEPT |
Summary: Direct assay evidence: overexpression of human DOLK (hDK1) increased dolichol kinase activity ~15-fold in microsomes and complemented the yeast DK-deficient mutant.
Reason: Biochemical demonstration of the enzyme's catalytic activity; the defining and core molecular function.
Supporting Evidence:
PMID:12213788
overexpression of hDK1p in Sf-9 cells resulted in a 15-fold increase in DK activity but not DAG kinase activity in crude microsomal fractions.
|
|
GO:0004168
dolichol kinase activity
|
IDA
PMID:16923818 Human dolichol kinase, a polytopic endoplasmic reticulum mem... |
ACCEPT |
Summary: Direct assay evidence with mapping of the CTP-binding site and kinetics (KM 22.8 uM dolichol; 3.5 uM CTP); G443D abolishes activity.
Reason: Detailed biochemical characterization of DOLK's dolichol kinase activity; core molecular function.
Supporting Evidence:
file:human/DOLK/DOLK-uniprot.txt
KM=22.8 uM for dolichol {ECO:0000269|PubMed:16923818};
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IDA
PMID:12213788 Expression and characterization of a human cDNA that complem... |
ACCEPT |
Summary: Direct evidence that DOLK produces Dol-P: expression elevates DK activity and increases in vivo Dol-P levels, restoring N-glycosylation.
Reason: DOLK catalyzes the terminal step of Dol-P biosynthesis; increased Dol-P upon expression directly supports this process. Core.
Supporting Evidence:
PMID:12213788
elevating DK activity, and consequently increasing Dol-P levels in vivo
|
|
GO:0043048
dolichyl monophosphate biosynthetic process
|
IDA
PMID:16923818 Human dolichol kinase, a polytopic endoplasmic reticulum mem... |
ACCEPT |
Summary: Direct evidence linking DOLK catalytic activity to dolichyl monophosphate biosynthesis, with functional mapping of catalytic residues.
Reason: DOLK catalyzes CTP-dependent dolichol phosphorylation, the terminal step of Dol-P biosynthesis; mutations abolishing activity confirm the requirement. Core.
Supporting Evidence:
PMID:16923818
Dolichol kinase (DK) catalyzes the CTP-dependent phosphorylation of dolichol in the biosynthesis de novo and possibly the recycling of dolichyl monophosphate
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:16923818 Human dolichol kinase, a polytopic endoplasmic reticulum mem... |
ACCEPT |
Summary: Direct assay evidence that human DOLK is a polytopic ER membrane protein, from overexpression and topology mapping in CHO cells.
Reason: Experimentally demonstrated ER membrane localization by the primary characterization paper; this is the core location where DOLK acts.
Supporting Evidence:
PMID:16923818
shown to be a polytopic membrane protein localized in the endoplasmic reticulum with an N terminus extended into the lumen and a cytoplasmically oriented C terminus.
|
|
GO:0006488
dolichol-linked oligosaccharide biosynthetic process
|
IGI
PMID:12213788 Expression and characterization of a human cDNA that complem... |
NEW |
Summary: Proposed annotation capturing DOLK's role in supplying Dol-P for assembly of the dolichol-linked oligosaccharide (LLO) used in N-glycosylation. DOLK complementation of the yeast dolichol kinase mutant restores N-glycosylation, demonstrating this downstream involvement.
Reason: The existing GOA BP annotations stop at dolichyl monophosphate biosynthesis (GO:0043048). DOLK is upstream of, and required for, LLO assembly for protein N-linked glycosylation; adding GO:0006488 records this downstream biological role explicitly, supported by rescue of N-glycosylation in the yeast complementation assay.
Supporting Evidence:
PMID:12213788
restoring normal N-glycosylation of carboxypeptidase Y at the restrictive temperature in the temperature-sensitive mutant sec59-1.
|
Q: Does DOLK activity contribute to Dol-P recycling in addition to de novo synthesis, and how is this partitioned in vivo?
Q: Why do some DOLK-CDG patients present predominantly with dilated cardiomyopathy (via alpha-dystroglycan O-mannosylation) while others show multisystem or purely neurological disease?
Experiment: Tissue-specific conditional Dolk knockout in mouse heart to test whether dilated cardiomyopathy arises specifically from reduced alpha-dystroglycan O-mannosylation.
Experiment: Structure determination (cryo-EM) of human DOLK to define the dolichol- and CTP-binding pockets and rationalize CDG1M variant effects.
DOLK catalyses the CTP-dependent phosphorylation of dolichol to dolichyl monophosphate
(Dol-P), the terminal step of de novo Dol-P biosynthesis at the ER membrane. Dol-P is the
essential lipid carrier that primes dolichol-linked oligosaccharide (LLO) assembly for
protein N-glycosylation and is also required for O-mannosylation, C-mannosylation and
GPI-anchor biosynthesis.
IntAct GO:0005515 protein binding annotations derive from large-scale binary interactome /
AP-MS maps (PMID:25416956, 26871637, 28514442, 32296183, 33961781). Interactors are largely
co-ER membrane proteins (ion channels KCNA1/3/6/10, CD79A, GPX8, EDA, etc.). None establish a
specific molecular function for DOLK; per curation policy protein binding is uninformative
and these are MARK_AS_OVER_ANNOTATED (not REMOVE — experimental IPIs).
id: Q9UPQ8
gene_symbol: DOLK
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
DOLK is dolichol kinase, a polytopic endoplasmic reticulum membrane enzyme that
catalyzes the CTP-dependent phosphorylation of dolichol to dolichyl monophosphate
(Dol-P), the terminal step in de novo Dol-P biosynthesis (EC 2.7.1.108). Dol-P is
the essential lipid carrier that primes assembly of the dolichol-linked
oligosaccharide for protein N-linked glycosylation and is also required for
O-mannosylation, C-mannosylation and GPI-anchor biosynthesis, so DOLK supplies the
activated lipid carrier used throughout the glycosylation system. The enzyme has a
cytoplasmically oriented CTP-binding site and belongs to the polyprenol kinase
family. Loss-of-function mutations cause DOLK-CDG (congenital disorder of
glycosylation type Im), whose features include dilated cardiomyopathy (linked to
deficient alpha-dystroglycan O-mannosylation), ichthyosis and neurological disease.
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: >-
Phylogenetically inferred ER membrane localization, consistent with the
experimentally demonstrated ER membrane localization of human dolichol kinase
and its yeast ortholog SEC59.
action: ACCEPT
reason: >-
DOLK is an experimentally validated polytopic ER membrane protein (PMID:16923818),
so the IBA localization is correct and represents a core aspect of where the
enzyme acts.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
shown to be a polytopic membrane protein localized in the endoplasmic
reticulum with an N terminus extended into the lumen and a cytoplasmically
oriented C terminus.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetically inferred dolichol kinase activity, the defining and
experimentally established molecular function of DOLK.
action: ACCEPT
reason: >-
This is the core molecular function of the gene, directly demonstrated
biochemically (PMID:12213788, PMID:16923818) and by disease-variant enzyme
assays (PMID:17273964, PMID:22242004). GOA carries this exact current term
(GO:0004168, EC 2.7.1.108).
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
Dolichol kinase (DK) catalyzes the CTP-mediated phosphorylation of dolichol
in eukaryotic cells, the terminal step in dolichyl monophosphate (Dol-P)
biosynthesis de novo.
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetically inferred involvement in dolichyl monophosphate (Dol-P)
biosynthesis, the pathway output of the dolichol kinase reaction.
action: ACCEPT
reason: >-
Dol-P biosynthesis is the direct biological process to which the DOLK reaction
contributes; this is well supported experimentally and the IBA is at an
appropriate level of specificity.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
the terminal step in dolichyl monophosphate (Dol-P) biosynthesis de novo.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Automated annotation of dolichol kinase activity from the RHEA/EC mapping
(RHEA:13133, EC 2.7.1.108).
action: ACCEPT
reason: >-
The EC/RHEA mapping is exactly correct for DOLK and matches the experimentally
established catalytic activity. The reaction is documented in UniProt.
supported_by:
- reference_id: file:human/DOLK/DOLK-uniprot.txt
supporting_text: >-
Reaction=a di-trans,poly-cis-dolichol + CTP = a di-trans,poly-cis-
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Automated ER membrane localization from the UniProt subcellular-location
keyword mapping, consistent with experimental data.
action: ACCEPT
reason: >-
DOLK is an experimentally confirmed integral ER membrane protein; the SubCell
mapping is accurate.
supported_by:
- reference_id: file:human/DOLK/DOLK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:25416956
qualifier: enables
review:
summary: >-
Interactor identified in a proteome-scale binary interactome map. The generic
"protein binding" term is uninformative about DOLK's actual molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This annotation comes from a large-scale high-throughput interactome screen and
only asserts the uninformative term GO:0005515 protein binding. Per curation
guidelines this term should not be treated as core function; the physiologically
meaningful function is dolichol kinase activity. Retained as an experimental IPI
rather than removed.
supported_by:
- reference_id: PMID:25416956
supporting_text: A proteome-scale map of the human interactome network.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:26871637
qualifier: enables
review:
summary: >-
Interactor reported in a large-scale alternative-splicing interactome study;
the term is uninformative for DOLK function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
High-throughput protein-protein interaction annotation using the generic
GO:0005515 term. It does not inform the molecular function of DOLK and is not a
core annotation. Retained as an experimental IPI.
supported_by:
- reference_id: PMID:26871637
supporting_text: >-
Widespread Expansion of Protein Interaction Capabilities by Alternative
Splicing.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
qualifier: enables
review:
summary: >-
Interactors reported in a large-scale interactome map (e.g. KCNA6, LRRC4C);
the generic term is uninformative for DOLK function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
High-throughput interactome annotation using the uninformative GO:0005515 term.
DOLK's interactors here are largely co-resident ER membrane proteins and the
binding data do not establish a specific molecular function. Retained as an
experimental IPI.
supported_by:
- reference_id: PMID:28514442
supporting_text: >-
Architecture of the human interactome defines protein communities and disease
networks.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: >-
Multiple interactors reported in the HuRI binary interactome map; the generic
term is uninformative for DOLK function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
High-throughput binary interactome annotation using the uninformative GO:0005515
term. The many interactors (largely ER/membrane proteins) do not define a
specific molecular function for DOLK. Retained as an experimental IPI.
supported_by:
- reference_id: PMID:32296183
supporting_text: A reference map of the human binary protein interactome.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: >-
Interactors reported in a proteome-scale AP-MS network study; the generic term
is uninformative for DOLK function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
High-throughput proteome-scale interaction annotation using the uninformative
GO:0005515 term. Does not inform DOLK molecular function and is not core.
Retained as an experimental IPI.
supported_by:
- reference_id: PMID:33961781
supporting_text: >-
Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-446199
qualifier: involved_in
review:
summary: >-
Reactome-asserted involvement in dolichyl phosphate synthesis, matching the
enzyme's pathway role.
action: ACCEPT
reason: >-
DOLK catalyzes the terminal step producing Dol-P; the Reactome pathway
"Synthesis of dolichyl-phosphate" correctly captures this biological process.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
the terminal step in dolichyl monophosphate (Dol-P) biosynthesis de novo.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-446195
qualifier: enables
review:
summary: >-
Reactome-asserted dolichol kinase activity (DOLK phosphorylates dolichol to
Dol-P), matching the core molecular function.
action: ACCEPT
reason: >-
Correct assignment of the enzyme's defining catalytic activity, corroborated by
biochemical assays.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
Human dolichol kinase, a polytopic endoplasmic reticulum membrane protein with
a cytoplasmically oriented CTP-binding site.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4755600
qualifier: enables
review:
summary: >-
Reactome-asserted dolichol kinase activity (disease-annotated reaction),
matching the core molecular function.
action: ACCEPT
reason: >-
Correct assignment of the defining catalytic activity of DOLK.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
Human dolichol kinase, a polytopic endoplasmic reticulum membrane protein with
a cytoplasmically oriented CTP-binding site.
- term:
id: GO:0005730
label: nucleolus
evidence_type: IDA
original_reference_id: GO_REF:0000052
qualifier: located_in
review:
summary: >-
Single high-throughput immunofluorescence (HPA) annotation to the nucleolus,
inconsistent with the well-established integral ER membrane localization of this
polytopic membrane kinase.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DOLK is a ~15-pass integral ER membrane protein (PMID:16923818); a nucleolar
localization is biologically implausible for its function and is contradicted by
IDA, IBA, IEA and Reactome ER membrane annotations. This is most likely
background/off-target signal in the HPA immunofluorescence screen. Not removed
(single experimental IF datum) but flagged as over-annotation.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
shown to be a polytopic membrane protein localized in the endoplasmic
reticulum with an N terminus extended into the lumen and a cytoplasmically
oriented C terminus.
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IGI
original_reference_id: PMID:12213788
qualifier: involved_in
review:
summary: >-
Genetic interaction evidence: human DOLK (hDK1) complements the yeast sec59-1
(SEC59/dolichol kinase) mutant, restoring dolichol kinase activity, Dol-P levels
and N-glycosylation, establishing its role in Dol-P biosynthesis.
action: ACCEPT
reason: >-
Cross-species complementation (with yeast SEC59, UniProtKB:P20048) demonstrates
DOLK functions in de novo Dol-P biosynthesis. This is a well-supported core
biological process annotation.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
hDK1 is capable of complementing the growth defect, elevating DK activity, and
consequently increasing Dol-P levels in vivo and restoring normal
N-glycosylation of carboxypeptidase Y at the restrictive temperature in the
temperature-sensitive mutant sec59-1.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: EXP
original_reference_id: PMID:17273964
qualifier: enables
review:
summary: >-
Experimental demonstration of dolichol kinase activity via disease-variant
characterization: CDG1M variants Cys99Ser and Tyr441Ser have only 2-4% residual
DK activity.
action: ACCEPT
reason: >-
Direct experimental measurement of the enzyme's catalytic activity in patient
cells and by yeast complementation; core molecular function.
supported_by:
- reference_id: PMID:17273964
supporting_text: >-
The residual activity of mutant DK1 was 2%-4% when compared with control cells.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: IMP
original_reference_id: PMID:22242004
qualifier: enables
review:
summary: >-
Mutant-phenotype evidence: pathogenic DOLK mutations cause a dolichol kinase
deficiency confirmed by enzyme analysis in patient fibroblasts.
action: ACCEPT
reason: >-
Loss of catalytic activity upon mutation directly supports the dolichol kinase
molecular function of DOLK; core.
supported_by:
- reference_id: PMID:22242004
supporting_text: >-
Enzyme analysis in patients' fibroblasts confirmed a dolichol kinase
deficiency in all families.
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IMP
original_reference_id: PMID:22242004
qualifier: involved_in
review:
summary: >-
Mutant-phenotype evidence that DOLK is required for dolichol-phosphate formation;
DOLK mutations abolish dolichol kinase activity and downstream glycosylation.
action: ACCEPT
reason: >-
DOLK mutations cause deficient formation of dolichol-phosphate and impaired
N-glycosylation / O-mannosylation, supporting its role in Dol-P biosynthesis.
Core biological process.
supported_by:
- reference_id: PMID:22242004
supporting_text: >-
pathogenic mutations were identified in DOLK, encoding the dolichol kinase
responsible for formation of dolichol-phosphate.
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-4755600
qualifier: located_in
review:
summary: >-
Reactome-asserted ER membrane localization, consistent with experimental data.
action: ACCEPT
reason: >-
Correct; matches the experimentally established ER membrane localization of DOLK.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
localized in the endoplasmic reticulum
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-446195
qualifier: located_in
review:
summary: >-
Reactome-asserted ER membrane localization, consistent with experimental data.
action: ACCEPT
reason: >-
Correct; matches the experimentally established ER membrane localization of DOLK.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
localized in the endoplasmic reticulum
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: IDA
original_reference_id: PMID:12213788
qualifier: enables
review:
summary: >-
Direct assay evidence: overexpression of human DOLK (hDK1) increased dolichol
kinase activity ~15-fold in microsomes and complemented the yeast DK-deficient
mutant.
action: ACCEPT
reason: >-
Biochemical demonstration of the enzyme's catalytic activity; the defining and
core molecular function.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
overexpression of hDK1p in Sf-9 cells resulted in a 15-fold increase in DK
activity but not DAG kinase activity in crude microsomal fractions.
- term:
id: GO:0004168
label: dolichol kinase activity
evidence_type: IDA
original_reference_id: PMID:16923818
qualifier: enables
review:
summary: >-
Direct assay evidence with mapping of the CTP-binding site and kinetics
(KM 22.8 uM dolichol; 3.5 uM CTP); G443D abolishes activity.
action: ACCEPT
reason: >-
Detailed biochemical characterization of DOLK's dolichol kinase activity; core
molecular function.
supported_by:
- reference_id: file:human/DOLK/DOLK-uniprot.txt
supporting_text: >-
KM=22.8 uM for dolichol {ECO:0000269|PubMed:16923818};
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:12213788
qualifier: involved_in
review:
summary: >-
Direct evidence that DOLK produces Dol-P: expression elevates DK activity and
increases in vivo Dol-P levels, restoring N-glycosylation.
action: ACCEPT
reason: >-
DOLK catalyzes the terminal step of Dol-P biosynthesis; increased Dol-P upon
expression directly supports this process. Core.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
elevating DK activity, and consequently increasing Dol-P levels in vivo
- term:
id: GO:0043048
label: dolichyl monophosphate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:16923818
qualifier: involved_in
review:
summary: >-
Direct evidence linking DOLK catalytic activity to dolichyl monophosphate
biosynthesis, with functional mapping of catalytic residues.
action: ACCEPT
reason: >-
DOLK catalyzes CTP-dependent dolichol phosphorylation, the terminal step of
Dol-P biosynthesis; mutations abolishing activity confirm the requirement. Core.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
Dolichol kinase (DK) catalyzes the CTP-dependent phosphorylation of dolichol
in the biosynthesis de novo and possibly the recycling of dolichyl
monophosphate
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:16923818
qualifier: located_in
review:
summary: >-
Direct assay evidence that human DOLK is a polytopic ER membrane protein, from
overexpression and topology mapping in CHO cells.
action: ACCEPT
reason: >-
Experimentally demonstrated ER membrane localization by the primary
characterization paper; this is the core location where DOLK acts.
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
shown to be a polytopic membrane protein localized in the endoplasmic
reticulum with an N terminus extended into the lumen and a cytoplasmically
oriented C terminus.
- term:
id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
evidence_type: IGI
original_reference_id: PMID:12213788
qualifier: involved_in
review:
summary: >-
Proposed annotation capturing DOLK's role in supplying Dol-P for assembly of
the dolichol-linked oligosaccharide (LLO) used in N-glycosylation. DOLK
complementation of the yeast dolichol kinase mutant restores N-glycosylation,
demonstrating this downstream involvement.
action: NEW
reason: >-
The existing GOA BP annotations stop at dolichyl monophosphate biosynthesis
(GO:0043048). DOLK is upstream of, and required for, LLO assembly for protein
N-linked glycosylation; adding GO:0006488 records this downstream biological
role explicitly, supported by rescue of N-glycosylation in the yeast
complementation assay.
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
restoring normal N-glycosylation of carboxypeptidase Y at the restrictive
temperature in the temperature-sensitive mutant sec59-1.
core_functions:
- description: >-
CTP-dependent dolichol kinase activity: phosphorylates dolichol to dolichyl
monophosphate (Dol-P) at the ER membrane, the terminal step of de novo Dol-P
biosynthesis (EC 2.7.1.108).
molecular_function:
id: GO:0004168
label: dolichol kinase activity
directly_involved_in:
- id: GO:0043048
label: dolichyl monophosphate biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:16923818
supporting_text: >-
Dolichol kinase (DK) catalyzes the CTP-dependent phosphorylation of dolichol
in the biosynthesis de novo and possibly the recycling of dolichyl
monophosphate
- description: >-
Supplies dolichyl monophosphate, the activated lipid carrier that primes assembly
of the dolichol-linked oligosaccharide for protein N-linked glycosylation (and is
also required for O-/C-mannosylation and GPI-anchor biosynthesis).
molecular_function:
id: GO:0004168
label: dolichol kinase activity
directly_involved_in:
- id: GO:0006488
label: dolichol-linked oligosaccharide biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:12213788
supporting_text: >-
restoring normal N-glycosylation of carboxypeptidase Y at the restrictive
temperature in the temperature-sensitive mutant sec59-1.
proposed_new_terms: []
suggested_questions:
- question: >-
Does DOLK activity contribute to Dol-P recycling in addition to de novo synthesis,
and how is this partitioned in vivo?
- question: >-
Why do some DOLK-CDG patients present predominantly with dilated cardiomyopathy
(via alpha-dystroglycan O-mannosylation) while others show multisystem or purely
neurological disease?
suggested_experiments:
- description: >-
Tissue-specific conditional Dolk knockout in mouse heart to test whether dilated
cardiomyopathy arises specifically from reduced alpha-dystroglycan O-mannosylation.
- description: >-
Structure determination (cryo-EM) of human DOLK to define the dolichol- and
CTP-binding pockets and rationalize CDG1M variant effects.
references:
- 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:0000052
title: Gene Ontology annotation based on curation of immunofluorescence data
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:human/DOLK/DOLK-uniprot.txt
title: UniProtKB entry DOLK_HUMAN (Q9UPQ8)
findings: []
- id: PMID:12213788
title: 'Expression and characterization of a human cDNA that complements the temperature-sensitive
defect in dolichol kinase activity in the yeast sec59-1 mutant: the enzymatic
phosphorylation of dolichol and diacylglycerol are catalyzed by separate CTP-mediated
kinase activities in Saccharomyces cerevisiae.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Primary paper establishing human DOLK/hDK1 as dolichol kinase via yeast sec59-1
complementation; supports MF and Dol-P biosynthesis annotations. Abstract-only in
cache but title/abstract fully support the cited claims.
- id: PMID:16923818
title: Human dolichol kinase, a polytopic endoplasmic reticulum membrane protein
with a cytoplasmically oriented CTP-binding site.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Biochemical characterization of human DOLK: ER membrane topology, CTP-binding
site, kinetics, inactivating mutations. Supports MF and ER membrane annotations.
- id: PMID:17273964
title: A defect in dolichol phosphate biosynthesis causes a new inherited disorder
with death in early infancy.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Identifies DOLK/DK1 deficiency (DOLK-CDG); characterizes variants with 2-4%
residual activity. Full text available; supports EXP MF annotation and disease role.
- id: PMID:22242004
title: Autosomal recessive dilated cardiomyopathy due to DOLK mutations results
from abnormal dystroglycan O-mannosylation.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
DOLK mutations cause dilated cardiomyopathy via deficient alpha-dystroglycan
O-mannosylation; enzyme deficiency confirmed in fibroblasts. Supports IMP MF/BP.
- id: PMID:25416956
title: A proteome-scale map of the human interactome network.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Large-scale binary interactome map; source of a generic protein-binding IPI that
does not inform DOLK molecular function.
- id: PMID:26871637
title: Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
High-throughput interactome study; source of an uninformative protein-binding IPI.
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
High-throughput interactome study; source of uninformative protein-binding IPIs.
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
HuRI binary interactome map; source of multiple uninformative protein-binding IPIs.
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Proteome-scale AP-MS network study; source of uninformative protein-binding IPIs.
- id: Reactome:R-HSA-446195
title: DOLK phosphorylates DCHOL to DOLP
findings: []
- id: Reactome:R-HSA-446199
title: Synthesis of dolichyl-phosphate
findings: []
- id: Reactome:R-HSA-4755600
title: Defective DOLK does not phosphorylate DCHOL
findings: []