Ypd1 (YDL235C) is a small (167 aa), soluble, stand-alone histidine-containing phosphotransfer (HPt) protein that forms the branch point of the Sln1 multistep His-Asp phosphorelay in Saccharomyces cerevisiae. Phosphate from the autophosphorylated plasma-membrane osmosensor histidine kinase Sln1 (His576 -> receiver Asp1144) is transferred to Ypd1 His64, which in turn phosphorylates the receiver aspartates of two response regulators: cytoplasmic Ssk1 (Asp554) and nuclear Skn7 (Asp427). Transfer to Ssk1 is fast and effectively irreversible, and Ypd1 binding greatly stabilises phospho-Ssk1, keeping Ssk1 inactive and the Ssk2/Ssk22-Pbs2-Hog1 MAPK cascade off under normal osmolarity; hyperosmotic stress reduces relay flux so that unphosphorylated Ssk1 activates HOG signalling. Loss of Ypd1 is lethal because of constitutive HOG activation. Ypd1 is a four-helix-bundle protein that uses a common hydrophobic docking surface for the Sln1, Ssk1 and Skn7 receiver domains, and it is distributed in both cytoplasm and nucleus, shuttling between them so that it can deliver phosphate to Skn7 in the nucleus.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000160 phosphorelay signal transduction system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA placing the AHP1-5/YPD1 HPt family (PTN002000688) in phosphorelay signal transduction; Ypd1 is the HPt intermediate of the Sln1 phosphorelay. Reason: Ypd1 is the canonical eukaryotic HPt protein and does the work of the phosphorelay by carrying phosphate on His64 between Sln1 and the response regulators Ssk1 and Skn7. The IBA term is correct at the family level; the more specific osmosensory term GO:0007234 is separately annotated experimentally. Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. PMID:15628880 In Saccharomyces cerevisiae, the histidine-containing phosphotransfer (HPt) protein YPD1 transfers phosphoryl groups between the three different response regulator domains of SLN1, SSK1, and SKN7 (designated R1, R2, and R3, respectively). |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro (HPt domain, IPR008207/IPR036641/IPR045871) mapping to phosphorelay signal transduction system. Reason: Correct general process for an HPt-domain protein; consistent with the experimentally established role of Ypd1 in the Sln1-Ypd1-Ssk1/Skn7 phosphorelay. Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. |
| GO:0005515 protein binding | IPI PMID:14656441 The yeast YPD1/SLN1 complex: insights into molecular recogni... | MODIFY | Summary: Generic protein binding with SLN1 (P39928), from the co-crystal structure of Ypd1 with the Sln1 receiver domain (Xu et al. 2003). Reason: Generic protein binding is uninformative. The partner is the hybrid sensor histidine kinase Sln1, and the complex is the phosphodonor-HPt docking complex of the relay; the informative term SGD already uses for the Ypd1-Sln1 interaction (IPI, PMID:8808622) is GO:0043424 protein histidine kinase binding. The underlying catalytic activity is captured by GO:0009927. Proposed replacements: protein histidine kinase binding Supporting Evidence: PMID:14656441 Here we report the first crystal structure of a prototypical monomeric histidine-containing phosphotransfer (HPt) protein YPD1 in complex with its upstream phosphodonor, the response regulator domain associated with SLN1. PMID:14656441 YPD1 functions as a histidine-phosphorylated protein intermediate required for phosphoryl group transfer from a membrane-bound sensor histidine kinase (SLN1) to two distinct response regulator proteins (SSK1 and SKN7). |
| GO:0005515 protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | REMOVE | Summary: Generic protein binding with SSK1 (Q07084) from a genome-wide in vivo protein-fragment complementation screen (Tarassov et al. 2008). Reason: Generic protein binding is uninformative. The Ypd1-Ssk1 interaction is real and central (Ypd1 is the phosphodonor for the Ssk1 receiver domain), so removal does not mean the interaction is false. However Ssk1 is a response regulator, GO has no informative response-regulator-binding MF, and this high-throughput screen does not assay phosphotransfer; the functional content of the interaction is already captured by GO:0009927 histidine phosphotransfer kinase activity (with Ssk1 as downstream acceptor). Supporting Evidence: PMID:8808622 Ypd1p binds to both Sln1p and Ssk1p and mediates the multistep phosphotransfer reaction (phosphorelay). PMID:18467557 We identified 2770 interactions among 1124 endogenously expressed proteins. |
| GO:0005515 protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | REMOVE | Summary: Generic protein binding with SSK1 (Q07084) from a high-throughput yeast two-hybrid binary interactome map (Yu et al. 2008). Reason: Generic protein binding is uninformative. The Ypd1-Ssk1 interaction is genuine and is the phosphotransfer docking interaction of the relay, so removal does not question the interaction. Ssk1 is a response regulator (not a kinase), no informative binding MF applies, and the Y2H screen does not measure activity; the functional content is represented by GO:0009927. Supporting Evidence: PMID:8808622 Ypd1p binds to both Sln1p and Ssk1p and mediates the multistep phosphotransfer reaction (phosphorelay). PMID:18719252 this binary map is enriched for transient signaling interactions |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for nuclear activity of the AHP/YPD1 HPt family. Reason: Consistent with direct evidence: Ypd1 is present in the nucleus and nuclear Ypd1 is required for phosphotransfer to the nuclear response regulator Skn7. Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. PMID:14665464 These results indicate that nuclear localization of Ypd1p is necessary for signaling to Skn7p. |
| GO:0005634 nucleus | IDA PMID:14665464 Saccharomyces cerevisiae histidine phosphotransferase Ypd1p ... | ACCEPT | Summary: GFPx2-Ypd1 localises to both nucleus and cytoplasm (DAPI co-staining, confocal), with nuclear export shown by heterokaryon assay (Lu et al. 2003). Reason: Direct localization evidence from full-text paper; nuclear Ypd1 is functionally required for Sln1-Skn7 signalling. Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. PMID:14665464 These results indicate that nuclear localization of Ypd1p is necessary for signaling to Skn7p. PMID:14665464 These data strongly support the conclusion that Ypd1p moves between the nucleus and the cytoplasm. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/UniProt subcellular location mapping to nucleus. Reason: Agrees with experimental localization (PMID:14665464). Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for cytoplasmic activity of the AHP/YPD1 HPt family. Reason: Ypd1 receives phosphate from membrane-bound Sln1 at the cytoplasmic face and phosphorylates cytosolic Ssk1; directly supported by localization data. Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. PMID:14665464 indicating that nuclear Ypd1p is not required for Ssk1p signaling |
| GO:0005737 cytoplasm | IDA PMID:14665464 Saccharomyces cerevisiae histidine phosphotransferase Ypd1p ... | ACCEPT | Summary: GFPx2-Ypd1 distributed throughout the cytoplasm as well as the nucleus (Lu et al. 2003). Reason: Direct localization evidence; cytoplasmic Ypd1 mediates Ssk1 phosphorylation. Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/UniProt subcellular location mapping to cytoplasm. Reason: Agrees with experimental localization (PMID:14665464). Supporting Evidence: PMID:14665464 Analysis of GFP x2 -Ypd1p revealed that the Ypd1p protein is distributed throughout the cytoplasm and in the nucleus under normal growth conditions. |
| GO:0007234 osmosensory signaling via phosphorelay pathway | IDA PMID:8808622 Yeast HOG1 MAP kinase cascade is regulated by a multistep ph... | ACCEPT | Summary: Posas et al. 1996 demonstrated in vitro the His-Asp-His-Asp phosphorelay Sln1 -> Ypd1-His64 -> Ssk1 that regulates the HOG1 osmosensing cascade. Reason: Exact and core process; the term definition names the Sln1 osmosensor. Ypd1 performs a step of the pathway (His64 phosphotransfer). Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. PMID:8808622 An osmosensing mechanism in the budding yeast (Saccharomyces cerevisiae) involves both a two-component signal transducer (Sln1p, Ypd1p and Ssk1p) and a MAP kinase cascade (Ssk2p/Ssk22p, Pbs2p, and Hog1p). |
| GO:0007234 osmosensory signaling via phosphorelay pathway | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA-based osmosensory signaling via phosphorelay pathway. Reason: Correct; consistent with the experimental annotations from PMID:8808622. Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. |
| GO:0007234 osmosensory signaling via phosphorelay pathway | IMP PMID:8808622 Yeast HOG1 MAP kinase cascade is regulated by a multistep ph... | ACCEPT | Summary: Genetic evidence (H64 mutation, ypd1 mutants) from Posas et al. 1996 that Ypd1 is required in the SLN1-YPD1-SSK1 osmosensor. Reason: Core process; mutational analysis of His64 (H64Q loss of function, UniProt) supports Ypd1 acting within the pathway, and Ypd1 carries out a step of it. Supporting Evidence: PMID:8808622 Ypd1p binds to both Sln1p and Ssk1p and mediates the multistep phosphotransfer reaction (phosphorelay). file:yeast/YPD1/YPD1-uniprot.txt /note="H->Q: Loss of function." |
| GO:0009927 histidine phosphotransfer kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for histidine phosphotransfer kinase activity across the AHP1-5/YPD1 HPt family. Reason: Core molecular function. The GO definition (phospho-His intermediate transferring phosphate between a hybrid kinase and a response regulator) describes exactly what Ypd1 does between Sln1 and Ssk1/Skn7, supported by in vitro phosphotransfer and kinetic data. Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. PMID:15628880 In Saccharomyces cerevisiae, the histidine-containing phosphotransfer (HPt) protein YPD1 transfers phosphoryl groups between the three different response regulator domains of SLN1, SSK1, and SKN7 (designated R1, R2, and R3, respectively). file:yeast/YPD1/YPD1-uniprot.txt Catalyzes the phosphoryl group transfer from the membrane-bound osmosensing histidine kinase SLN1 to two distinct response regulator proteins, SSK1 in the cytoplasm, and transcription factor SKN7 in the nucleus. |
| GO:0009927 histidine phosphotransfer kinase activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro IPR045871 (AHP1-5/YPD1) mapping to histidine phosphotransfer kinase activity. Reason: Core MF, experimentally established for Ypd1 (PMID:8808622, PMID:15628880). Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. PMID:15628880 In Saccharomyces cerevisiae, the histidine-containing phosphotransfer (HPt) protein YPD1 transfers phosphoryl groups between the three different response regulator domains of SLN1, SSK1, and SKN7 (designated R1, R2, and R3, respectively). |
| GO:0016772 transferase activity, transferring phosphorus-containing groups | IDA PMID:8808622 Yeast HOG1 MAP kinase cascade is regulated by a multistep ph... | MODIFY | Summary: Phosphotransfer from Sln1 to Ypd1-His64 and on to Ssk1-Asp554 shown in vitro (Posas et al. 1996), annotated to the broad transferase term. Reason: The activity is real, but the parent term is uninformative; the specific child GO:0009927 histidine phosphotransfer kinase activity (is_a descendant of GO:0016772) precisely describes the His-Asp relay activity demonstrated in this paper. Proposed replacements: histidine phosphotransfer kinase activity Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. |
| GO:0016772 transferase activity, transferring phosphorus-containing groups | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-based broad transferase (phosphorus-containing groups) activity. Reason: Correct but overly general; GO:0009927 histidine phosphotransfer kinase activity is the appropriate specific term for an HPt protein and is already supported by IBA and experimental data. Proposed replacements: histidine phosphotransfer kinase activity Supporting Evidence: PMID:8808622 This phosphate is then sequentially transferred to Sln1p-Asp-1144, then to Ypd1p-His64, and finally to Ssk1p-Asp554. file:yeast/YPD1/YPD1-deep-research-falcon.md Its primary function is to act as a mobile phosphate-transfer intermediate and branch point in the Sln1 multistep phosphorelay. |
| GO:0043424 protein histidine kinase binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for binding to hybrid histidine kinases in the AHP/YPD1 family. Reason: HPt proteins dock on the receiver domain of their upstream hybrid histidine kinase; Ypd1 binds Sln1 (co-crystal structure and genetic/biochemical data). Kept as supporting the core phosphotransfer function. Supporting Evidence: PMID:14656441 Here we report the first crystal structure of a prototypical monomeric histidine-containing phosphotransfer (HPt) protein YPD1 in complex with its upstream phosphodonor, the response regulator domain associated with SLN1. PMID:8808622 Ypd1p binds to both Sln1p and Ssk1p and mediates the multistep phosphotransfer reaction (phosphorelay). |
| GO:0043424 protein histidine kinase binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro IPR045871 mapping to protein histidine kinase binding. Reason: Consistent with direct evidence for Ypd1 binding the Sln1 hybrid histidine kinase. Supporting Evidence: PMID:14656441 Here we report the first crystal structure of a prototypical monomeric histidine-containing phosphotransfer (HPt) protein YPD1 in complex with its upstream phosphodonor, the response regulator domain associated with SLN1. |
| GO:0043424 protein histidine kinase binding | IPI PMID:8808622 Yeast HOG1 MAP kinase cascade is regulated by a multistep ph... | ACCEPT | Summary: Ypd1 binds the Sln1 hybrid histidine kinase (Posas et al. 1996; WITH SGD:S000001409). Reason: Direct, informative binding annotation to the upstream phosphodonor kinase; a necessary part of the phosphorelay mechanism, confirmed structurally (PMID:14656441). Supporting Evidence: PMID:8808622 Ypd1p binds to both Sln1p and Ssk1p and mediates the multistep phosphotransfer reaction (phosphorelay). PMID:14656441 Here we report the first crystal structure of a prototypical monomeric histidine-containing phosphotransfer (HPt) protein YPD1 in complex with its upstream phosphodonor, the response regulator domain associated with SLN1. |
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Download this section (compressed HTML)Q: Should the Ypd1 docking interactions with receiver domains of response regulators (Ssk1, Skn7) be representable in GO (e.g. via has_input on GO:0009927 in a GO-CAM), given that no informative "response regulator binding" MF term exists?
Q: Is Ypd1 nucleocytoplasmic shuttling an active, regulated transport step or passive diffusion of a 19-kDa protein, and does the nuclear pool change under stresses that act through Skn7 (e.g. cell-wall or oxidative stress)?
Experiment: In vivo Phos-tag or 31P-NMR/antibody-based detection of phospho-His64 Ypd1 in cytoplasmic versus nuclear fractions before and after hyperosmotic shock, to test whether the two pools differ in phosphorylation and relay flux.
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Download this section (compressed HTML)Osmotic stress-responsive phosphorelay intermediate sensor protein; phosphorylated by the plasma membrane sensor Sln1p in response to osmotic stress and then in turn phosphorylates the response regulators Ssk1p in the cytosol and Skn7p in the nucleus
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