title: DPM1 source and assay guide
gene: DPM1
annotation_scope:
imported_annotations: 43
new_annotations: 0
DPM1 supplies the catalytic component of Dol-P-Man synthesis at the ER membrane. The single core distinguishes that reaction from production of its Dol-P substrate, downstream glycosylation and the separate flipping step. All 43 historical source assertions remain intact; current raw provenance contains 44 contexts because one term/evidence/reference assertion has two provider/date contexts. Newly fetched metadata is retained separately from the historical source dictionaries.
| Source | Actual evidence and limits |
|---|---|
| PMID:9535917(https://pubmed.ncbi.nlm.nih.gov/9535917/) — indexed author original | Human and mouse DPM1 constructs rescue mouse class E cells but fail in hamster Lec15 cells under the reported conditions. Microsomal GDP-mannose/Dol-P assays measure Dol-P-Man, and human GST-DPM1 membrane fractionation is described. Original Methods, Results and Discussion were read; the normal cache remains abstract-only. Its O-linked-glycan example explicitly concerns yeast. |
| PMID:9724629(https://pubmed.ncbi.nlm.nih.gov/9724629/) — indexed author original | Human DPM1 and rat DPM2 in hamster-host co-immunoprecipitation/fractionation are distinguished from the engineered human DPM1–rat microsomal ALDH anchor. The fusion forms Dol-P-Man without DPM2. DPM3 was not removed, and this was not purified unanchored human DPM1. The continuation around Figure 9 describes lipid association without proving zero DPM1 substrate binding. |
| PMID:10835346, original | Human DPM1-containing complexes purified from JY25 cells were reconstituted in PC/PE liposomes; GDP-[3H]mannose incorporation and lipid TLC establish product formation. The synthase assay was performed without exogenous Dol-P. Separate hamster Lec15 experiments used human DPM1/DPM3 and rat DPM2. DPM3 overexpression permits activity without DPM2, with lower specific activity. Results, Methods and figure captions were read; image pixels were not independently scored. |
| PMID:10944123, original | Figure 5A and its Results report FLAG-DPM3/GST-DPM1 co-immunoprecipitation in human JY5 cells with GST-ALDH and FLAG-ALDH controls. The separate GPI-GnT association is specific to DPM2, not DPM1 or DPM3. |
| PMID:16280320(https://pubmed.ncbi.nlm.nih.gov/16280320/) | The complete abstract positively reports DPM3-mediated anchoring, DPM1 degradation without DPM3 and association of free DPM1 with CHIP. Full-body access attempts were unsuccessful; exact CHIP construct/tag/panel details are not claimed. The current IntAct participant record is human DPM1 with hamster DPM3, not a STUB1 record. |
| PMID:23856421, original | Human WT/G152V DPM1–DPM3 co-immunoprecipitation includes expression controls. Reduced binding and patient-membrane synthase activity are positive findings, not proof of complete binding loss. Muscle glycoepitope changes support human O-mannosylation context. Patient-cell labels vary within the paper; the activity preparation is described conservatively as patient membranes. |
| PMID:28743912, original | Purified Pyrococcus furiosus Q8U4M3 expressed in E. coli provides substrate/product structures, metal dependence and biochemical activity. The high-temperature assay and membrane topology are not human measurements. The GDP–Mg2+ and GDP-mannose–Mn2+ structures and divalent-ion-dependent transfer assay directly ground the archaeal ISS donor; they do not measure human DPM1 metal occupancy. |
The official human O60762 record and FASTA establish one 260-residue primary sequence without an alternative-products block. Initiator-methionine removal produces the annotated chain 2–260, PRO_0000059170, with acetylated Ala2. Processing does not create a separate splice product or establish another function.
The core uses molecular_function for GO:0004582: DPM1 supplies the catalytic chemistry, while anchoring and regulatory subunits support its native activity. The physiological complex remains in in_complex. This does not claim activity of isolated unanchored human DPM1, DPM3 absence in the anchor-fusion experiment, or indispensable DPM2 dependence under every assay condition. Imported source qualifiers remain unchanged. GO:0180047 describes Dol-P-Man formation; GO:0043048 describes Dol-P formation and is not the measured DPM1 reaction. The replacement is a chemistry correction, not an asserted ontology ancestor relation.
The portable interaction audit includes exact raw query bytes, public URLs and hashes, all 42 MITAB fields, participant-sequence calculations and executed outputs. Ten selected records represent repeated source/assay contexts for DPM3, TDO2 and a MEOX2 clone, not ten independent partners. Source records absent from that snapshot are assessed from their original experiments.
| Source | Target evidence |
|---|---|
| PMID:25416956, original | Three DPM1–TDO2 records include validated two-hybrid retesting. Original Methods describe fresh-colony quadruplicate tests, at least three positive attempts and confirmed identities. Dataset-level orthogonal tests are not assigned to the DPM1 pair without pair-specific evidence. |
| PMID:25910212, original | Three DPM1–TDO2 records retain variant features and repeat-assay contexts. Original Methods distinguish Y2H from separately used LUMIER assays. Normal cached text omits some operative Methods that were read in the indexed original. |
| PMID:32296183, original | Three DPM1–Q6FHY5 records include validated two-hybrid retesting. HuRI reports quadruplicate retests and sequence confirmation; the earlier 2014 three-of-four threshold is not transferred. Q6FHY5 reproduces its recorded checksum. It differs from canonical MEOX2 P50222 by one glutamine within positions 81–84, outside the homeobox. The repeated sequence prevents assigning a unique deletion position. |
TDO2 P48775 is an enzyme, supporting GO:0019899 enzyme binding. MEOX2 P50222 has curated DNA-dependent transcriptional activity, supporting GO:0140297 for the verified clone. The positive CHIP association supports GO:0031625 ubiquitin protein ligase binding. These are partner-class statements, not assertions that DPM1 catalyzes TDO2 chemistry, regulates transcription or performs ubiquitination.
DPM3 Q9P2X0 is an anchoring/stabilizing subunit, not an independently demonstrated enzyme. Its supported contacts remain non-core protein binding under the ClinGen project instruction. Controlled association does not automatically establish a purified interface or an additional native pathway, and lack of the latter does not invalidate a literal binding class.
PMID:21630459(https://pubmed.ncbi.nlm.nih.gov/21630459/) is linked explicitly in Annex 8.2 of Judit Castillo Corullón’s doctoral thesis catalogue record (issued 2014-09-19; the PDF prints July 2014). The portable target-data and provenance record preserves the catalogue-to-PDF mapping, direct PDF URL, checksum, table headings and source locators. Table 8.1, physical PDF page 194 (printed page 193), lists DPM1/O60762 with 13.1% sequence coverage and two peptides. The Methods describe CTAB/digitonin isolation, repeated washing and microscopy assessment, followed by LC-MS/MS with FDR 0.05 and at least two peptides including one unique peptide. The thesis procedure-efficiency estimate (~99%) and the article abstract’s 99.9% purity claim are distinct. These positive target data support contextual nuclear-fraction localization, without establishing stable residency, an entry route or a nuclear catalytic role. DPM1-specific spectra and orthogonal imaging were not independently inspected. The preparation is not rejected as crude or contaminated solely from DPM1’s established ER role.
PMID:19946888(https://pubmed.ncbi.nlm.nih.gov/19946888/) describes the YTS membrane-proteome survey. The particular DPM1 table row remained unverified, so ER-membrane refinement is grounded in the independent DPM1 fractionation/anchoring studies, not represented as organelle resolution by that survey. HPA's downloadable target XML contains tissue staining but no target ICC/IF subcellular-assay records in the inspected snapshot. It is not used as direct ER imaging.
The PANTHER family PTHR43398 tree contains the exact human O60762 leaf PTN002535381. Its ungapped alignment matches all 260 residues. The 22-node ancestor path joins the literal PAINT IBDs: PTN000092441 for ER membrane, PTN000092440 for dolichol-linked oligosaccharide biosynthesis and PTN002459128 for mannosyltransferase activity. Human target evidence among descendant sources is legitimate, not circular. The broader oligosaccharide process is retained as non-core donor-supply context rather than denied solely because its direct polymerization is performed downstream.
The normal Reactome chain is pathway R-HSA-162699 → reaction R-HSA-162721 → catalyst 162705 → complex 162692 → DPM1 entity 162865 → O60762 reference 53836. The target chain is residues 2–260 in ER membrane. The separate flipping reaction R-HSA-162715 is not assigned to DPM1.
Disease contexts are separately resolved: DPM1 failed reaction R-HSA-4717406 uses catalyst 9631868, complex 9631831 and variant set 4717364; DPM3 failed reaction R-HSA-4719354 uses catalyst 9631797 and complex 9631746, retaining normal DPM1 with DPM3 L85S; DPM2 failed reaction R-HSA-4719375 uses catalyst 9631985 and complex 9631812, retaining normal DPM1 with DPM2 Y23C. These records do not establish normal activity for every pathogenic variant.
The inspected GO-CAM target index has no O60762 activity. The cached dolichol-phosphate sugar-donor module supplies pathway context, not evidence for a new annotation. No absence-based process expansion is made.
| PMID | Effective normal cache | Actual read scope |
|---|---|---|
| 9535917 | Abstract only | Indexed author original Methods, functional rescue, fractionation and Discussion. |
| 9724629 | Abstract only | Indexed author original Methods/Results and fusion/lipid-association continuation. |
| 10835346 | Abstract only | Indexed PMC original Results, Discussion, Methods and relevant captions. |
| 10944123 | Abstract only | Separately recovered original target co-immunoprecipitation, GPI-GnT results and Methods. |
| 16280320 | Abstract only | Complete abstract; original-body attempts failed. |
| 19946888 | Abstract only | Complete abstract; target identification table not recovered. |
| 21630459 | Abstract only | Complete abstract plus authenticated author-thesis target table and isolation/MS Methods. |
| 23856421 | Abstract only | Separately recovered PMC original target assays, controls and Methods. |
| 25416956 | Full text | Authenticated original retesting Methods and exact target pair records. |
| 25910212 | Full-text flag, partial Methods | Indexed original repeat-assay/sequence Methods and exact target records. |
| 32296183 | Full text | Original platform/retesting Methods and exact target records. |
| 28743912 | New genuine full XML cache | Archaeal Methods, substrate/product structures and activity Results. |
Existing source/cache bytes and flags, provider files and historical notes are preserved. Failed routes, challenge pages and superseded parsing attempts are not treated as biological evidence. The follow-up removes six explicitly identified misleading or non-target excerpt occurrences while preserving other inherited excerpts and the complete old notes prefix. It adds no quoted source text. The public audit is a reproducible analysis of machine-source records, not an independent primary experiment.