DPH1

Summary: Binary binding to the DNA-binding transcription factor TFCP2.

Reason: GO:0140297 specifies binding to a DNA-binding transcription factor; it does not require DPH1 to regulate transcription. TFCP2/Q12800 is independently established as such a partner. In PMID:25416956 the human DPH1–TFCP2 pair is recorded in yeast by two-hybrid array (EBI-10456463), validated two-hybrid (EBI-10545280) and prey pooling (EBI-10303209). These are three records from one study, without complex expansion or negative flags. The original pipeline retained identity-confirmed pairs positive in at least three of four retests; pair-specific orthogonal validation is not established. This supports the narrower binding capability under the assay conditions. IntAct participant checksums match Q9BZG8-4 (438 residues) and Q12800 (502 residues), identifying reference sequences rather than independently authenticating experimental inserts. Endogenous association and downstream effects remain open questions, distinct from the measured binding capability. No transcriptional regulatory process or separate core is inferred, and other DPH1 products are not assigned this activity.

Proposed replacements: DNA-binding transcription factor binding

Summary: Refine the positive nuclear pool to nucleoplasm.

Reason: The original PMID:10519411 fractionation study detects the approximately 50-kDa OVCA1 species in nuclear and cytoplasmic fractions of human ovarian surface epithelial cells; tagged-cell imaging also shows diffuse and perinuclear punctate staining. Independently, current HPA ICC/IF with HPA069750 reports nucleoplasmic staining in A-549 and U2OS at approved reliability (supported subassay). Nucleoplasm is a verified part-of descendant of nucleus. Refine the established nuclear pool at gene level without attributing subnuclear resolution to the 1999 experiment, excluding other pools, or assigning the diphthamide reaction to the nucleus.

Proposed replacements: nucleoplasm

Summary: Refine the mapped nuclear pool to nucleoplasm.

Reason: The original PMID:10519411 fractionation study detects the approximately 50-kDa OVCA1 species in nuclear and cytoplasmic fractions of human ovarian surface epithelial cells; tagged-cell imaging also shows diffuse and perinuclear punctate staining. Independently, current HPA ICC/IF with HPA069750 reports nucleoplasmic staining in A-549 and U2OS at approved reliability (supported subassay). Nucleoplasm is a verified part-of descendant of nucleus. Refine the established nuclear pool at gene level without attributing subnuclear resolution to the 1999 experiment, excluding other pools, or assigning the diphthamide reaction to the nucleus.

Proposed replacements: nucleoplasm

Summary: Positive nucleoplasmic localization in human cell lines.

Reason: HPA069750 ICC/IF reports nucleoplasm in A-549 and U2OS, with approved overall reliability and supported subassay validation. Retain this positive, nonexclusive localization. These antibody observations do not resolve a natural product or demonstrate that the DPH1–DPH2 catalytic reaction occurs in this compartment. Additional cell-junction staining is recorded by HPA but does not require a new assertion here.

Summary: Refine the positive cytoplasmic pool to cytosol.

Reason: The original PMID:10519411 Methods explicitly prepare a cytosolic supernatant after removing nuclei and insoluble material, and Figure 4C/Results detect the approximately 50-kDa OVCA1 species in both cytoplasmic and nuclear fractions. The Reactome model independently places the human DPH1-containing complex in cytosol. Refine the positive cytoplasmic pool to cytosol, a typed descendant, without excluding the observed perinuclear puncta or nuclear pool. The source does not establish the identity of every immunoreactive band or localization of every natural splice product.

Proposed replacements: cytosol

Summary: Refine the mapped cytoplasmic pool to cytosol.

Reason: The original PMID:10519411 Methods explicitly prepare a cytosolic supernatant after removing nuclei and insoluble material, and Figure 4C/Results detect the approximately 50-kDa OVCA1 species in both cytoplasmic and nuclear fractions. The Reactome model independently places the human DPH1-containing complex in cytosol. Refine the positive cytoplasmic pool to cytosol, a typed descendant, without excluding the observed perinuclear puncta or nuclear pool. The source does not establish the identity of every immunoreactive band or localization of every natural splice product.

Proposed replacements: cytosol

Summary: Retain the cytosolic DPH1 pool.

Reason: The literal mouse Q5NCQ5 donor record carries cytosol, and independent human OVCA1 fractionation in PMID:10519411 and the target-specific Reactome complex support this localization. Preserve the imported ortholog assertion and source relationship. The positive nuclear and perinuclear pools are nonexclusive; the electronic transfer is not represented as a direct human imaging experiment.

Summary: Retain target-specific curated cytosolic complex localization.

Reason: The checked Reactome chain is reaction 5358494 → catalyst 5358378 → complex 5358365 → human DPH1 component 5358384 (residues 1–438), with cytosol assigned to the complex. Human OVCA1 fractionation corroborates this location. The same model identifies DPH2 as activeUnit by archaeal homology; that mechanistic attribution must be distinguished from the independently supported location and from the eukaryotic DPH1/DPH2 division of labor.

Summary: Conserved participation in diphthamide biosynthesis.

Reason: The literal PAINT IBD assigns GO:0017183 to PTN000079945, and the current family tree places human Q9BZG8 below that node through 22 recorded nodes. The target participates in the first chemical step on EEF2 rather than merely being a substrate of the pathway. The IBD is a phylogenetic judgment supported by yeast, mouse and human descendant evidence; its donor count and inclusion of another pathway subunit do not invalidate the inherited process assertion.

Summary: Retain the convergent electronic diphthamide-process assignment.

Reason: The exact IPR016435 mapping includes GO:0017183 and the target has a verified family match at residues 25–401 of the displayed 438-aa sequence. The mouse Dph1 record and UniPathway source converge on the same first-step role. Human functional evidence and the eukaryotic heterodimer mechanism support participation; a broad DPH1/DPH2 family label is not itself proof that either human subunit acts alone.

Summary: Retain curator-transferred participation from yeast Dph1.

Reason: The literal donor P40487 is Saccharomyces cerevisiae Dph1 and carries experimental GO:0017183 evidence, including PMID:31463593. Transfer is consistent with the human functional evidence. The protein performs the first biosynthetic step as part of the DPH1–DPH2 machinery; EEF2, not DPH1, is the modified substrate.

Summary: Retain human DPH1 involvement in the first diphthamide step.

Reason: The clinical and functional study PMID:30877278 supports the DPH1-dependent formation of diphthamide on EEF2. This is direct pathway participation by the biosynthetic machinery, not a process inferred merely from developmental consequences. Retain the existing NAS assertion while separating human functional assays from mechanistic details established in yeast biochemical work.

Summary: Specify the DPH1–DPH2 synthase complex.

Reason: The specific DPH1–DPH2 synthase complex captures the supported first-step machinery more precisely than a generic complex term. The current GO:0120513 definition explicitly describes the eukaryotic heterodimer and is a typed descendant of both protein-containing complex and catalytic complex. Preserve the distinction between this defined synthase and accessory reducing-system factors; the term does not assert a permanently assembled human DPH1–DPH2–DPH3 stoichiometry or equivalent complex formation by all natural products.

Proposed replacements: 2-(3-amino-3-carboxypropyl)histidine synthase complex

Summary: Retain positive perinuclear cytoplasmic localization.

Reason: The mouse Q5NCQ5 donor carries an experimental perinuclear assertion. Independently, the actual human OVCA1 study PMID:10519411 reports perinuclear enrichment of punctate tagged-protein staining in COS-1 and immortalized human ovarian surface epithelial cells, alongside diffuse staining. This positively supports a nonexclusive perinuclear pool; it does not identify an organelle, demonstrate local catalysis, or prove that every natural product shares the pattern.

Summary: Retain the conserved catalytic iron–sulfur cofactor assignment.

Reason: The literal yeast Dph1 donor P40487 has experimental 4Fe–4S binding evidence, including the subunit-resolved study PMID:31463593. Retain the curator-supported transfer to human DPH1 as a cofactor requirement of the first-step enzyme. This is not a claim that purified human DPH1 or each natural splice product was directly measured for cluster occupancy, nor a transfer of the archaeal Dph2 name onto human DPH2.

Summary: Retain the first-step synthase activity mapping.

Reason: The current GO:0090560 definition specifies transfer of the SAM-derived 3-amino-3-carboxypropyl group to EEF2 histidine, not a later methylation or amidation step. Human DPH1 complementation of deficient MCF7 cells restores a toxin-reactive diphthamide endpoint; the subunit-resolved yeast Dph1–Dph2 study uses reconstituted SAM transfer and distinguishes catalytic Dph1 cluster function from Dph2-dependent use of the physiological reducing system. Together they support DPH1 as the catalytic component of this machinery. Retain the activity in its complex-dependent context; this does not claim autonomous purified human catalysis, identify all natural products as active, or make human DPH2 catalytic merely because an archaeal enzyme is called Dph2.

Summary: Retain the explicitly complex-contributing synthase assertion.

Reason: The current GO:0090560 definition specifies transfer of the SAM-derived 3-amino-3-carboxypropyl group to EEF2 histidine, not a later methylation or amidation step. Human DPH1 complementation of deficient MCF7 cells restores a toxin-reactive diphthamide endpoint; the subunit-resolved yeast Dph1–Dph2 study uses reconstituted SAM transfer and distinguishes catalytic Dph1 cluster function from Dph2-dependent use of the physiological reducing system. Together they support DPH1 as the catalytic component of this machinery. Retain the activity in its complex-dependent context; this does not claim autonomous purified human catalysis, identify all natural products as active, or make human DPH2 catalytic merely because an archaeal enzyme is called Dph2. The original contributes_to qualifier is preserved and evaluated as contribution to the heterodimeric activity, not independent possession by an isolated subunit.

Summary: Retain curator-transferred first-step synthase activity.

Reason: The current GO:0090560 definition specifies transfer of the SAM-derived 3-amino-3-carboxypropyl group to EEF2 histidine, not a later methylation or amidation step. Human DPH1 complementation of deficient MCF7 cells restores a toxin-reactive diphthamide endpoint; the subunit-resolved yeast Dph1–Dph2 study uses reconstituted SAM transfer and distinguishes catalytic Dph1 cluster function from Dph2-dependent use of the physiological reducing system. Together they support DPH1 as the catalytic component of this machinery. Retain the activity in its complex-dependent context; this does not claim autonomous purified human catalysis, identify all natural products as active, or make human DPH2 catalytic merely because an archaeal enzyme is called Dph2. The source enables relationship remains unchanged; the biological reason makes the complex requirement explicit.

Summary: Retain membership in the DPH1–DPH2 synthase complex.

Reason: The exact ortholog donor carries GO:0120513. Its definition identifies the conserved eukaryotic Dph1–Dph2 heterodimer, consistent with human functional evidence and the yeast biochemical work. Preserve this specific complex assignment without treating all reducing-system partners as fixed stoichiometric subunits or claiming that each natural human product was tested.

Summary: Retain membership in the DPH1–DPH2 synthase complex.

Reason: The exact ortholog donor carries GO:0120513. Its definition identifies the conserved eukaryotic Dph1–Dph2 heterodimer, consistent with human functional evidence and the yeast biochemical work. Preserve this specific complex assignment without treating all reducing-system partners as fixed stoichiometric subunits or claiming that each natural human product was tested.

Summary: Specify the catalytic complex as the DPH1–DPH2 synthase.

Reason: The specific DPH1–DPH2 synthase complex captures the supported first-step machinery more precisely than a generic complex term. The current GO:0120513 definition explicitly describes the eukaryotic heterodimer and is a typed descendant of both protein-containing complex and catalytic complex. Preserve the distinction between this defined synthase and accessory reducing-system factors; the term does not assert a permanently assembled human DPH1–DPH2–DPH3 stoichiometry or equivalent complex formation by all natural products.

Proposed replacements: 2-(3-amino-3-carboxypropyl)histidine synthase complex