ptpC encodes PTP3 (tyrosine-protein phosphatase 3), a 990-residue non-receptor protein tyrosine phosphatase with a single, sequence-divergent classical PTP catalytic domain flanked by long disordered N- and C-terminal regions. PTP3 is the tyrosine phosphatase that deactivates the transcription factor STATc: it binds STATc directly and removes the activating phosphate from STATc Tyr922, opposing STATc dimerisation and nuclear accumulation. Under basal conditions PTP3 is constitutively active and largely cytosolic, counterbalancing a constitutively active STATc tyrosine kinase (the TKL kinase Pyk2). The prestalk inducer DIF-1 and hyperosmotic stress inhibit PTP3, correlating with phosphorylation of S448 and S747 through Ca2+-dependent signalling and the TKL kinase Phg2 and with downregulation by the Cbl homologue CblA, so that STATc becomes tyrosine phosphorylated and nuclear. On stress, PTP3 relocalises from the cytosol to endosome-like vesicles and granules that also contain Pyk2. PTP3 is expressed during growth and early development, enriched in prestalk and anterior-like cells, and its gene appears to be required for viability, as the second of two genomic copies could not be disrupted.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004725 protein tyrosine phosphatase activity | IDA PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | ACCEPT | Summary: Araki et al. 2008 show that PTP3 directly interacts with and dephosphorylates STATc, and that DIF-1 and hyperosmotic stress lower the PTP3 activity that can be assayed biochemically. This is direct experimental support for protein tyrosine phosphatase activity on a physiological substrate. Reason: Direct biochemical evidence of dephosphorylation of a phosphotyrosine protein (STATc). This is the core molecular function of PTP3. Supporting Evidence: PMID:18305004 We show that PTP3 directly interacts with and dephosphorylates STATc PMID:24587195 PTP3 is constitutively active in its non-phosphorylated form and removes the phosphate from Tyr922 of STATc. |
| GO:0004725 protein tyrosine phosphatase activity | IDA PMID:8628311 Multiple roles of the novel protein tyrosine phosphatase PTP... | ACCEPT | Summary: The original characterisation of PTP3 showed that recombinant PTP3 has vanadate-sensitive phosphatase activity. The cached copy is abstract-only, but the abstract supports the activity. Reason: Recombinant enzyme activity that vanadate inhibits supports the annotation, and later substrate-trapping and STATc dephosphorylation data confirm it. Supporting Evidence: PMID:8628311 Recombinant PTP3 exhibited phosphatase activity that was inhibited by vanadate |
| GO:0004725 protein tyrosine phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from the PTP catalytic domain (IPR000242) and EC 3.1.3.48. PTP3 has the PTP active-site signature (PS00383), and experimental data confirm the activity. Reason: The annotation agrees with the domain architecture and with the experimental evidence (PMID:18305004, PMID:8628311). Supporting Evidence: PMID:18305004 We show that PTP3 directly interacts with and dephosphorylates STATc |
| GO:0005515 protein binding | IPI PMID:12220630 OSBPa, a predicted oxysterol binding protein of Dictyosteliu... | MODIFY | Summary: IPI with STATc (Q54BD4, dstC). The cited paper is about the oxysterol-binding protein OSBPa, and the cached copy is abstract-only. The abstract does not mention PTP3 or STATc, so I cannot verify the interaction data in this paper. The PTP3-STATc interaction itself is well established (PMID:18305004), where STATc was trapped as the PTP3 substrate. Protein binding is uninformative; the binding partner is a STAT family protein. Reason: Replace generic protein binding with the more informative STAT family protein binding, which describes the enzyme-substrate interaction with STATc. I do not remove the curator's IPI because the full text of PMID:12220630 is not available to check. Proposed replacements: STAT family protein binding Supporting Evidence: PMID:18305004 We show that the protein tyrosine phosphatase PTP3 interacts directly with STATc |
| GO:0005515 protein binding | IPI PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | MODIFY | Summary: Direct interaction of PTP3 with its substrate STATc (Q54BD4), shown by substrate trapping with the C-to-S mutant. Protein binding is uninformative. Reason: The partner is the STAT family transcription factor STATc. STAT family protein binding states what kind of interaction this is (enzyme-substrate recognition). Proposed replacements: STAT family protein binding Supporting Evidence: PMID:18305004 We show that the protein tyrosine phosphatase PTP3 interacts directly with STATc |
| GO:0005515 protein binding | IPI PMID:24587195 Identification of the protein kinases Pyk3 and Phg2 as regul... | MODIFY | Summary: Phg2 (Q54QQ1), a TKL-group serine/threonine kinase, binds PTP3 in reciprocal in vitro pull-downs. Phg2 is needed for full stress-induced phosphorylation of PTP3 on S747 and acts upstream of PTP3 as an inhibitor. PTP3 is the regulated substrate or target in this interaction. Reason: Protein binding is uninformative. The partner is a protein kinase that regulates PTP3, so protein kinase binding is the more informative term. It is a regulatory interaction, not part of the core catalytic function. Proposed replacements: protein kinase binding Supporting Evidence: PMID:24587195 The pull-down experiments showed for both approaches in vitro binding of Phg2 to PTP3. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping. Consistent with experimental data showing that PTP3 is cytosolic in unstimulated cells (cytosol is the more specific, experimentally supported location). Reason: Correct, if general. Experimental data support the more specific cytosol. Supporting Evidence: PMID:10207040 translocation from the cytosol to subcellular structures that co-localize to endosomal vesicles |
| GO:0005768 endosome | IDA PMID:10207040 Regulation of Dictyostelium protein-tyrosine phosphatase-3 (... | KEEP AS NON CORE | Summary: Under osmotic shock and other stresses, Ser/Thr-phosphorylated PTP3 moves from the cytosol to structures that co-localize with endosomal vesicles. This relocalisation is stress-induced, not the basal location. Reason: Supported by immunolocalisation, but conditional (stress-induced). The basal, functionally active pool is cytosolic. Supporting Evidence: PMID:10207040 correlates with its translocation from the cytosol to subcellular structures that co-localize to endosomal vesicles PMID:24587195 PTP3 is localised in the cytosol of unstimulated cells and accumulated at endosomes, when cells were subjected to hyperosmotic stress |
| GO:0005829 cytosol | IDA PMID:10207040 Regulation of Dictyostelium protein-tyrosine phosphatase-3 (... | ACCEPT | Summary: PTP3 is cytosolic in unstimulated cells, where it keeps STATc dephosphorylated. The is_active_in qualifier is appropriate. Reason: The cytosol is the main site of PTP3 activity under basal conditions. Supporting Evidence: PMID:10207040 translocation from the cytosol to subcellular structures that co-localize to endosomal vesicles |
| GO:0006970 response to osmotic stress | IMP PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | KEEP AS NON CORE | Summary: Hyperosmotic stress inhibits PTP3 and induces its Ser/Thr phosphorylation, which lets STATc be activated. PTP3 overexpression blocks stress-induced STATc activation. PTP3 is therefore a regulated node in the osmotic stress response pathway, not an effector of osmoprotection. Reason: PTP3 takes part in transducing the osmotic stress signal to STATc. This is real but contextual; the core role is STATc deactivation. Supporting Evidence: PMID:18305004 Treatment of cells with DIF-1 or exposure to hyper-osmotic stress induces a decrease in biochemically assayable PTP3 activity |
| GO:0019722 calcium-mediated signaling | IMP PMID:20159963 Dual regulation of a Dictyostelium STAT by cGMP and Ca2+ sig... | KEEP AS NON CORE | Summary: Agents that raise intracellular Ca2+ stimulate phosphorylation of PTP3 on S448 and S747 and activate STATc. Ca2+ signalling represses STATc dephosphorylation by inhibiting PTP3. PTP3 is a downstream target of Ca2+ signalling, and the broad acts_upstream_of_or_within qualifier covers this. The cached copy is abstract-only. Reason: PTP3 is the target that Ca2+ signalling acts on in the STATc pathway. The annotation is acceptable with its broad qualifier but is not a core function. Supporting Evidence: PMID:20159963 parallel, stress-induced Ca(2+) signalling represses STATc dephosphorylation through its inhibitory effect on PTP3 |
| GO:0034504 protein localization to nucleus | IMP PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | MODIFY | Summary: PTP3 opposes nuclear accumulation of STATc: overexpression of PTP3 prevents STATc nuclear accumulation, and a dominant inhibitor of PTP3 causes ectopic STATc nuclear localisation. The effect works through STATc dephosphorylation, which blocks phosphotyrosine-SH2 dimerisation. The direction of PTP3's effect is therefore negative. Reason: The mutant phenotypes show that PTP3 negatively regulates STATc nuclear localisation; it does not carry out nuclear import. Negative regulation of protein localization to nucleus describes the IMP data correctly. Proposed replacements: negative regulation of protein localization to nucleus Supporting Evidence: PMID:18305004 Conversely, overexpression of a dominant inhibitor of PTP3 leads to constitutive tyrosine phosphorylation and ectopic nuclear localisation of STATc |
| GO:0035556 intracellular signal transduction | IMP PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | KEEP AS NON CORE | Summary: PTP3 is a component of the intracellular STATc signalling pathway that links DIF-1 and stress to STATc activation. The term is correct but general; the more specific negative regulation of receptor signaling pathway via STAT is also annotated. Reason: Correct but uninformative. The negative regulation of STAT signalling annotation captures the specific role better. Supporting Evidence: PMID:18305004 it forms part of the signalling mechanism that determines the tyrosine phosphorylation and nuclear localisation status of STATc |
| GO:1903013 response to differentiation-inducing factor 1 | IDA PMID:22365144 Perturbations of the actin cytoskeleton activate a Dictyoste... | ACCEPT | Summary: DIF-1 increases phosphorylation of PTP3 at S747 and transiently reduces its activity, which is how DIF-1 activates STATc in prestalk (pstO) cell differentiation. PTP3 is a key regulated node in the DIF-1 response. Reason: Direct experimental evidence that PTP3 is modified in response to DIF-1, and that its inhibition mediates the DIF-1 response through STATc. Supporting Evidence: PMID:22365144 The demonstration that DIF-1 treatment leads to increased phosphorylation at S747 of PTP3 reveals an additional convergence point for the developmental, DIF-1 signalling pathway |
| GO:1904893 negative regulation of receptor signaling pathway via STAT | IMP PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | ACCEPT | Summary: PTP3 dephosphorylates STATc on Tyr922, which turns STATc signalling off. Overexpression makes STATc refractory to activation, and dominant-negative PTP3 makes STATc constitutively active. This is the core biological role of PTP3. Reason: Strong gain- and loss-of-function evidence that PTP3 is the negative regulator (deactivating phosphatase) of STATc signalling. Supporting Evidence: PMID:18305004 STATc is refractory to activation in PTP3 overexpressing cells PMID:18840649 PTP3, the protein tyrosine phosphatase responsible for dephosphorylating STATc |
| GO:0035335 peptidyl-tyrosine dephosphorylation | IDA PMID:18305004 Evidence that DIF-1 and hyper-osmotic stress activate a Dict... | NEW | Summary: PTP3 itself catalyses removal of the phosphate from STATc Tyr922, the step that the peptidyl-tyrosine dephosphorylation process describes. PTP3 is the entity that performs the step, so this is participation, not mere necessity. Reason: Direct evidence that PTP3 dephosphorylates a specific phosphotyrosine residue (STATc Tyr922). The process term complements the existing MF annotation and is neither an ancestor nor a descendant of any annotated term. Supporting Evidence: PMID:18305004 We show that PTP3 directly interacts with and dephosphorylates STATc PMID:24587195 PTP3 is constitutively active in its non-phosphorylated form and removes the phosphate from Tyr922 of STATc. |
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Download this section (compressed HTML)Q: How does Ser/Thr phosphorylation at S448 and S747 inhibit PTP3: through a conformational change, or through selective oxidation of the catalytic cysteine in endosome-like compartments, as Araki et al. (2008) suggested?
Q: Which kinase phosphorylates PTP3 on S448, and does Phg2 phosphorylate S747 directly or act through another kinase?
Q: Is ptpC essential for viability, given that the second genomic copy could not be disrupted? Does it have essential substrates besides STATc?
Experiment: Express phosphomimetic (S448D/S747D) and non-phosphorylatable (S448A/S747A) PTP3 in Dictyostelium. Measure activity of the purified protein on a STATc pTyr922 phosphopeptide under reducing and non-reducing conditions, and measure STATc activation after DIF-1 or sorbitol in cells expressing the mutants.
Hypothesis: Phosphorylation of S448/S747 is enough to inhibit PTP3 catalytic activity toward STATc pTyr922.
Experiment: Use conditional (inducible degron or CRISPR-based) depletion of both ptpC copies, then run substrate-trapping proteomics with the C-to-S mutant to identify all PTP3-bound phosphotyrosine proteins.
Hypothesis: PTP3 is required for viability because of substrates other than STATc.
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