Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
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PAINT phylogenetic inference places DPM1 in the Dpm1/GT2 dolichyl-phosphate mannosyltransferase clade, supporting the IBA annotations to dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582), endoplasmic reticulum membrane (GO:0005789) and dolichol-linked oligosaccharide biosynthetic process (GO:0006488).
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Human dolichol-phosphate-mannose synthase consists of three subunits, DPM1, DPM2 and DPM3.
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Human DPM synthase contains catalytic DPM1 with DPM3-mediated anchoring and DPM2-dependent stabilization and enhancement. Under DPM3 overexpression, measurable activity persists without DPM2.
"We reported previously that mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2 subunits, and that DPM1 requires DPM2 for its stable expression in the endoplasmic reticulum. Here we report that human DPM synthase consists of three subunits."
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DPM3 binds DPM1 through its C-terminal domain and DPM2 through its N-terminal portion, giving a stabilization chain in which DPM2 stabilizes DPM3 and DPM3 stabilizes DPM1 - the basis of the DPM1-DPM3 protein-binding annotation.
"The third subunit, DPM3, comprises 92 amino acids associated with DPM1 via its C-terminal domain and with DPM2 via its N-terminal portion."
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DPM2 also contributes to catalysis and not only to stability, since synthase activity is about ten-fold higher in its presence.
"DPM synthase activity was 10 times higher in the presence of DPM2, indicating that DPM2 also plays a role in the enzymatic reaction."
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The Dol-P-Man made by the DPM1-containing synthase is the mannosyl donor for GPI anchors, N-glycans, and protein O- and C-mannosylation, which is why DPM1 carries annotations across all of these downstream processes.
"Dolichol-phosphate-mannose (DPM) synthase generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation."
Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P and is regulated by DPM2.
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DPM2, a subunit of the DPM synthase that contains DPM1, also associates with and enhances GPI-N-acetylglucosaminyltransferase, implying co-regulation of GPI anchor initiation with the pathway that supplies its mannosyl donor.
"DPM2, but not two other components of dolichol-phosphate-mannose synthase, associates with GPI-GnT through interactions with PIG-A, PIG-C and GPI1."
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Figure 5A and the corresponding Results report controlled FLAG-DPM3/GST-DPM1 co-immunoprecipitation in human JY5 cells, including ALDH controls. The separate GPI-GnT association is specific to DPM2, not DPM1.
DPM1, the catalytic subunit of dolichol-phosphate mannose synthase, is tethered to and stabilized on the endoplasmic reticulum membrane by DPM3.
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The abstract reports loss of detectable microsomal synthase activity and GPI-anchored proteins in the DPM3-defective CHO context; this establishes the requirement under those cellular conditions.
"CHO2.38 cells were negative for GPI-anchored proteins, and microsomes from these cells showed no detectable DPM synthase activity, indicating that DPM3 is an essential component of this enzyme."
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A coiled-coil domain near the DPM3 C terminus tethers the catalytic DPM1 subunit to the ER membrane and is required for activity - DPM1 itself lacks a transmembrane anchor, so its ER-membrane localization is conferred in trans.
"A coiled-coil domain near the C terminus of DPM3 was important for tethering DPM1, the catalytic subunit of the enzyme, to the endoplasmic reticulum membrane and, therefore, was critical for enzyme activity."
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Free DPM1 is rapidly degraded by the proteasome in the absence of DPM3 and associates with the E3 ligase CHIP, so complex assembly also controls DPM1 steady-state level.
"DPM1 was rapidly degraded by the proteasome in the absence of DPM3. Free DPM1 was strongly associated with the C terminus of Hsc70-interacting protein (CHIP), a chaperone-dependent E3 ubiquitin ligase"
Defining the membrane proteome of NK cells.
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The curator assigns DPM1 to the membrane proteome of the YTS line. The complete abstract describes the survey, while the particular DPM1 identification row was not independently recovered.
"Mass spectrometric analysis identified 1843 proteins with high confidence scores. On the basis of the presence of transmembrane regions or evidence of posttranslational modifications and prediction algorithms, approximately 40% of the identified proteins were predicted as plausible membrane proteins."
Proteomic characterization of the human sperm nucleus.
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The article abstract reports 403 proteins identified from isolated human sperm nuclei. The DPM1-specific identification is documented separately in Table 8.1 of the registered author thesis.
"With this approach, 403 different proteins have been identified from the isolated sperm nuclei."
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The reported isolation and microscopy criteria characterize the preparation. They do not establish either a nuclear enzymatic role for DPM1 or that its detected peptides are contamination.
"sperm nuclei were obtained through CTAB treatment and isolated to over 99.9% purity without any tail fragments, acrosome or mitochondria as assessed by optical microscopy and transmission electron microscopy"
Congenital disorder of glycosylation due to DPM1 mutations presenting with dystroglycanopathy-type congenital muscular dystrophy.
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The patient-membrane assays report strongly reduced synthase activity without depressed apparent substrate affinity; altered abundance or assembly of active enzyme is a proposed explanation, not a direct enzyme-count measurement.
"DPM1 activity in fibroblasts was reduced by 80%, while affinity for the substrate was not depressed, suggesting a decrease in the amount of active enzyme."
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The p.Gly152Val substitution reduces DPM1 binding to DPM3, giving a mechanistic link between the DPM1-DPM3 interaction and disease and supporting the functional relevance of that protein-binding annotation.
"Transfected cells expressing tagged versions of wild type and the p.Gly152Val mutant displayed reduced binding to DPM3, an essential, non-catalytic subunit of the DPM complex, suggesting a mechanism for pathogenicity."
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Loss of DPM1 function produces a dystroglycanopathy phenotype with reduced alpha-dystroglycan glycoepitope staining, in vivo evidence that DPM1-derived Dol-P-Man feeds protein O-mannosylation and not only N-glycosylation.
"Muscle biopsy showed muscular dystrophy and reduced α-dystroglycan immunostaining with glycoepitope-specific antibodies in a pattern diagnostic of dystroglycanopathy."
A proteome-scale map of the human interactome network.
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The systematic binary map contains sequence-confirmed, validated DPM1–TDO2 binding records. Enzyme-partner binding is supported without assigning a native metabolic regulatory function.
"Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions."
Widespread macromolecular interaction perturbations in human genetic disorders.
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The interaction-perturbation study includes DPM1–TDO2 binary records, with source variant features preserved; binding class and native physiological consequence are separate questions.
"Here we functionally profile several thousand missense mutations across a spectrum of Mendelian disorders using various interaction assays."
A reference map of the human binary protein interactome.
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HuRI contains positive, validated DPM1–MEOX2 clone records. Independent sequence and partner-function evidence supports DNA-binding transcription-factor binding, without transferring MEOX2 transcriptional activity to DPM1.
"Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies."
A homologue of Saccharomyces cerevisiae Dpm1p is not sufficient for synthesis of dolichol-phosphate-mannose in mammalian cells.
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Human and mouse DPM1 encode 260-residue proteins that are ~30% identical to yeast Dpm1p but, unlike the yeast synthase, lack a hydrophobic transmembrane domain - the structural reason DPM1 must be tethered to the ER membrane by a partner subunit.
"We cloned human and mouse homologues of DPM1, termed hDPM1 and mDPM1, respectively, both of which encode proteins of 260 amino acids, having 30% amino acid identity with yeast Dpm1 protein but lacking a hydrophobic transmembrane domain, which exists in the yeast synthase."
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Human DPM1 cDNA restores Dol-P-Man synthesis and GPI-anchored Thy-1 expression in DPM1-deficient class E mutant cells, direct functional evidence for DPM1 in Dol-P-Man synthesis and GPI anchor biosynthesis.
"Human and mouse DPM1 cDNA restored Dol-P-Man synthesis in mouse Thy-1-deficient mutant class E cells."
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Human and mouse DPM1 fail to rescue hamster Lec15 under the reported conditions, although they rescue mouse class E cells. This points to an additional membrane-associated requirement rather than disproving catalytic DPM1 identity.
"In contrast, hDPM1 and mDPM1 cDNA did not complement another Dol-P-Man synthesis mutant, hamster Lec15 cells, whereas yeast DPM1 restored both mutants."
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The paper describes Dol-P-Man supply to N-glycan and GPI synthesis and explicitly gives yeast as its O-linked-glycan example. Human O-mannosylation context has independent disease support.
"It donates four mannosyl residues in the N-linked oligosaccharide precursor and all three mannosyl residues in the core of the glycosylphosphatidylinositol anchor. In yeasts it also donates one mannose to the O-linked oligosaccharide."
DPM2 regulates biosynthesis of dolichol phosphate-mannose in mammalian cells: correct subcellular localization and stabilization of DPM1, and binding of dolichol phosphate.
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The original experiments show DPM2-dependent localization/stability and enhanced Dol-P association in their cellular system; later work identifies DPM3 as the DPM1 anchoring partner and demonstrates DPM2-independent activity under DPM3 overexpression.
"DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localization and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase."
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An engineered ER-anchored DPM1 fusion forms Dol-P-Man without DPM2. DPM3 was not removed in that experiment, so it does not establish isolated unanchored human DPM1 catalysis.
"Mammalian DPM1 is catalytic because a fusion protein of DPM1 that was stably expressed in the ER synthesized DPM without DPM2."
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Dol-P-Man is the required mannosyl donor for GPI and N-glycan precursor biosynthesis, linking DPM1 activity to both downstream pathways.
"Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM)."
Synthesis of dolichyl-phosphate mannose
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Dol-P-Man is the mannose donor for N-linked glycosylation, GPI anchor precursor synthesis, and protein O- and C-mannosylation, which is why DPM1 sits upstream of all four processes.
"Dolichyl-phosphate-mannose (DPM, DOLPman) is the donor of mannose groups in the synthesis of the dolichyl pyrophosphate-linked precursor oligosaccharide in asparagine-linked glycosylation, in the synthesis of the glycosyl phosphatidylinositol (GPI) anchor precursor, in protein O-mannosylation and in protein C-mannosylation."
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DPM is made on the cytosolic face of the ER membrane and then flips so its mannose faces the ER lumen, placing the DPM1-catalysed step on the cytosolic side of the ER membrane.
"First, cytosolic GDP-mannose reacts with dolichyl phosphate exposed on the cytosolic face of the endoplasmic reticulum membrane to form DPM with its mannose moiety oriented toward the cytosol."
dolichyl phosphate + GDP-alpha-D-mannose -> dolichyl phosphate D-mannose
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Reactome models the reaction as catalysed by a heterotrimeric ER-membrane dolichyl-phosphate mannosyltransferase in which DPM1 is the catalyst and the other two subunits are stabilizers, matching the review's core-function model.
"The reaction is catalysed by dolichyl-phosphate mannosyltransferase, a heterotrimeric protein embedded in the endoplasmic reticulum membrane. The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits appear to stabilise it"
Defective DPM1 does not transfer mannose to DOLP to form DOLPman
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Loss-of-function variants in DPM1 cause congenital disorder of glycosylation type 1e, confirming that the mannosyltransferase step DPM1 catalyses is required for normal glycoprotein biosynthesis in humans.
"Defects in DPM1 can cause congenital disorder of glycosylation 1e (DPM1-CDG, CDG-1e; MIM:608799), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins"
Defective DPM3 does not transfer mannose to DOLP to form DOLPman
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The DPM3 L85S disease context reduces DPM1 binding and strongly reduces synthase activity, consistent with defective anchoring; it is not evidence that every DPM3 variant abolishes activity.
"Normally, the DPM3 subunit tethers the catalytic DPM1 subunit to the ER membrane. A homozygous 254T-C transition in the DPM3 gene results in a leu85-to-ser (L85S) substitution in a highly conserved residue in the coiled-coil domain. This mutant shows a reduced binding capacity to DPM1 which vastly reduces dolichyl-phosphate mannosyltransferase activity"
Defective DPM2 does not transfer mannose to DOLP to form DOLPman
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This failed-reaction context concerns a DPM2 variant in the DPM synthase complex. The normal stabilization and substrate-binding roles are interpreted alongside the experimentally demonstrated DPM2-independent activity under DPM3 overexpression.
"DPM2 is essential for the ER localisation and stable expression of DPM1 and it enhances binding of the substrate dolichyl phosphate (Maeda et al. 1998)."
UniProtKB entry O60762 (DPM1_HUMAN)
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UniProt records DPM1 as the catalytic subunit of the DPM synthase complex, transferring mannose from GDP-mannose to dolichol monophosphate to make the Dol-P-Man donor used in N-glycosylation, GPI anchoring and O-mannosylation.
"FUNCTION: Transfers mannose from GDP-mannose to dolichol monophosphate"
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UniProt assigns EC 2.4.1.83 and the Rhea reaction dolichyl phosphate + GDP-alpha-D-mannose = dolichyl beta-D-mannosyl phosphate + GDP to DPM1.
"Reaction=a di-trans,poly-cis-dolichyl phosphate + GDP-alpha-D-mannose ="
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UniProt places DPM1 in a three-subunit complex with DPM2 and DPM3, with a direct DPM1-DPM3 interaction that stabilizes DPM1.
"SUBUNIT: Component of the dolichol-phosphate mannose (DPM) synthase"
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UniProt records DPM1 deficiency as congenital disorder of glycosylation 1E, with some patients showing O-mannosylation defects and dystroglycanopathy features.
"DISEASE: Congenital disorder of glycosylation 1E (CDG1E) [MIM:608799]:"
Structural basis for dolichylphosphate mannose biosynthesis.
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Purified Pyrococcus furiosus dolichol-phosphate mannose synthase provides direct structural, metal-dependent and biochemical grounding for the archaeal ISS donor. This does not establish the same topology, temperature optimum or a human metal-binding structure.
DPM1 interaction source and participant-sequence audit
Caracterització del contingut proteic del nucli de l’espermatozoïde humà i el seu potencial epigenètic
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Table 8.1, printed page 193 (physical PDF page 194), reports DPM1/O60762 with 13.1% sequence coverage and two peptides in isolated human sperm nuclei.
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The thesis describes CTAB/digitonin isolation, washing and microscopy assessment; LC-MS/MS identification used FDR 0.05 and at least two peptides, including one unique peptide. These are preparation and identification controls, not DPM1-specific nuclear imaging or a nuclear catalytic assay.