{"gene":"PTPN3","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1995,"finding":"Purified PTPH1 exhibits protein tyrosine phosphatase activity toward myelin basic protein (MBP) and RCML substrates; phosphorylation by protein kinase C in vitro decreases Km without affecting Vmax. Removal of the N-terminal band 4.1 homology domain stimulates dephosphorylation of RCML but inhibits activity toward MBP, indicating that the N-terminal domain directly modulates catalytic function and substrate selectivity.","method":"In vitro enzymatic assay with purified baculovirus-expressed protein, limited trypsin cleavage, PKC phosphorylation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct in vitro enzymatic characterization with multiple substrates and domain-deletion experiments, single lab but multiple orthogonal biochemical methods","pmids":["7544351"],"is_preprint":false},{"year":1997,"finding":"PTPH1 associates with 14-3-3β in a serine phosphorylation-dependent manner. Two novel motifs (RSLS359VE and RVDS853EP) in PTPH1 were identified as major 14-3-3β binding sites; mutation of Ser359 and Ser853 to alanine significantly reduced association. The interaction was reconstituted in vitro with recombinant proteins, abolished by phosphatase treatment, and enhanced by Cdc25C-associated kinase treatment.","method":"Yeast two-hybrid screen, in vitro reconstitution with recombinant proteins, site-directed mutagenesis, co-immunoprecipitation from cell lines","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution in vitro, mutagenesis of binding sites, confirmed in cells; multiple orthogonal methods in one rigorous study","pmids":["9341175"],"is_preprint":false},{"year":1999,"finding":"PTPH1 directly dephosphorylates VCP (p97/CDC48) in cells. A substrate-trapping mutant (D811A/Y676F double mutant) specifically trapped VCP in vivo and recognized the C-terminal tyrosines of VCP. Induction of wild-type PTPH1 caused specific dephosphorylation of VCP without altering the overall phosphotyrosine profile of cells. Wild-type PTPH1 expression dramatically inhibited cell growth, while a catalytically impaired mutant did not.","method":"Substrate-trapping mutagenesis (D811A, Y676F), in vitro substrate trapping from cell lysates, tetracycline-inducible expression in NIH3T3 cells, immunoprecipitation, phosphotyrosine western blot","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — substrate-trapping plus in vivo dephosphorylation with catalytic mutant controls, multiple orthogonal methods","pmids":["10364224"],"is_preprint":false},{"year":2000,"finding":"Expression of catalytically active PTPH1 in Jurkat T cells reduces TCR-induced activation of NFAT/AP-1 reporter genes, Erk2 MAP kinase, MEK, and JNK. Catalytically inactive PTPH1-CS had no effect. Deletion of the N-terminal ERM domain reduced the inhibitory effect, indicating the ERM domain contributes to PTPH1's function in T cell signaling.","method":"Transient transfection in Jurkat T cells, luciferase reporter assays, kinase activity assays, catalytically inactive mutant controls","journal":"European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional reporter assays with catalytic mutant and domain-deletion controls, single lab","pmids":["10820377"],"is_preprint":false},{"year":2002,"finding":"PTPH1 interacts with the cytoplasmic domain of TACE (ADAM17) via its PDZ domain binding to the C-terminal group I PDZ-binding motif of TACE (ending in cysteine). Co-expression of catalytically active PTPH1 reduces TACE protein levels and decreases phorbol ester-stimulated shedding of TNF-α compared to catalytically inactive PTPH1, identifying PTPH1 as a negative regulator of TACE.","method":"Yeast two-hybrid screen, in vitro binding assay, co-immunoprecipitation from eukaryotic cells, co-expression functional assay (TACE shedding), ELISA for TNF-α","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vitro binding confirmation, and functional shedding assay with catalytic mutant control; multiple orthogonal methods","pmids":["12207026"],"is_preprint":false},{"year":2003,"finding":"PTPH1 is the predominant phosphatase capable of complexing with phospho-TCR zeta in a substrate-trapping library screen of 47 human PTPs, and transfection assays confirmed PTPH1 directly dephosphorylates TCR zeta ITAMs.","method":"PTP substrate-trapping library (47 PTP catalytic domains), protein purification/chromatography, novel ELISA-based PTPase assay, transfection assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — substrate-trapping library plus transfection functional assay, single lab","pmids":["14672952"],"is_preprint":false},{"year":2006,"finding":"HPV E6 oncoproteins, in complex with E6AP ubiquitin ligase, associate with PTPN3 via binding of E6's C-terminus to the PDZ domain of PTPN3, leading to proteasome-dependent degradation of PTPN3 in vitro and in living cells. Degradation requires E6AP and the proteasome. In transduced keratinocytes, E6-conferred reduced growth factor requirement partially phenocopies PTPN3 knockdown.","method":"In vitro degradation assay, co-immunoprecipitation, proteasome inhibitor experiments, siRNA knockdown in keratinocytes","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vitro and cell-based degradation assays with mechanistic controls (E6AP requirement, proteasome inhibition, PDZ motif requirement), multiple orthogonal methods","pmids":["17166906"],"is_preprint":false},{"year":2006,"finding":"PTPH1 interacts with the cardiac voltage-gated sodium channel Nav1.5 via the PDZ domain of PTPH1 binding to the PDZ-binding motif in the C-terminus of Nav1.5. Co-expression of catalytically active PTPH1 shifts the Nav1.5 availability relationship toward hyperpolarized potentials, while inactive PTPH1 or the tyrosine kinase Fyn does the opposite, indicating that tyrosine phosphorylation destabilizes the inactivated state of Nav1.5.","method":"Yeast two-hybrid screen (cardiac cDNA library), pull-down assay, co-expression in HEK293 cells with electrophysiology","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pull-down plus functional electrophysiology with active vs. inactive mutant, single lab","pmids":["16930557"],"is_preprint":false},{"year":2007,"finding":"Mice lacking catalytically active PTPN3 (gene-trapped and gene-targeted strains) show normal TCR signal transduction, T cell development, cytokine production, and proliferation, demonstrating that PTPN3 phosphatase activity is dispensable for negative regulation of TCR signaling in primary T cells in vivo.","method":"Gene trap and gene targeting in mice, flow cytometry, T cell activation assays, cytokine ELISA, proliferation assays","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent genetic mouse models (gene trap and targeted), comprehensive phenotyping; negative result well-established","pmids":["17339465"],"is_preprint":false},{"year":2008,"finding":"PTPN3 and PTPN4 double-deficient mice, as well as PTPN3/PTPN4/PTPN13 triple-deficient mice, show normal T cell development, TCR-induced cytokine synthesis, proliferation, and Th1/Th2/Th17 differentiation, establishing that PTPN3 and PTPN4 are dispensable for TCR signal transduction even in the absence of related phosphatases.","method":"Generation of single, double, and triple knockout mice; T cell development, activation, and differentiation assays","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple genetic mouse models with comprehensive T cell phenotyping; negative result independently supported by prior study","pmids":["19107198"],"is_preprint":false},{"year":2010,"finding":"PTPH1 is a specific phosphatase for p38γ MAPK through PDZ-mediated binding; yeast two-hybrid screening and in vitro/in vivo analyses confirmed the interaction. PTPH1 dephosphorylates p38γ, and their complex formation is required for cooperative oncogenic activity in Ras-dependent malignant growth in vitro and in mice.","method":"Yeast two-hybrid screen, in vitro binding assay, co-immunoprecipitation, phosphatase assay, cell transformation assays, mouse xenograft","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Y2H, Co-IP, in vitro dephosphorylation, functional cell and in vivo assays), replicated with subsequent structural study","pmids":["20332238"],"is_preprint":false},{"year":2010,"finding":"PTPH1 stimulates breast cancer growth by binding vitamin D receptor (VDR) and increasing cytoplasmic accumulation of VDR, leading to mutual stabilization of PTPH1 and VDR. This oncogenic activity is independent of PTPH1's phosphatase activity but dependent on its ability to increase VDR protein expression.","method":"Co-immunoprecipitation, siRNA knockdown, overexpression in breast cancer cell lines, subcellular fractionation, cell proliferation assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional assays with phosphatase-dead mutant control, single lab","pmids":["21119599"],"is_preprint":false},{"year":2012,"finding":"p38γ MAPK phosphorylates its phosphatase PTPH1 at Ser-459 in vitro and in vivo through their complex formation, as identified by unbiased proteomics. This phosphorylation is regulated by Ras signaling and is important for Ras, p38γ, and PTPH1 oncogenic activity as well as stress-induced cell growth/death responses.","method":"Unbiased proteomic/mass spectrometric identification of phosphorylation, in vitro kinase assay, in vivo phosphorylation assay, site-directed mutagenesis (S459), genetic and pharmacological pathway analyses","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay plus in vivo phosphorylation plus mutagenesis and unbiased proteomics, multiple methods","pmids":["22730326"],"is_preprint":false},{"year":2014,"finding":"Somatic gain-of-function mutations in PTPN3 (including L232R and L384H) found in intrahepatic cholangiocarcinoma alter phosphatase activity and further increase cell proliferation, colony formation, and migration beyond wild-type PTPN3 when expressed in ICC cell lines.","method":"Whole exome sequencing, transgenic expression of mutant PTPN3 in cholangiocarcinoma cell lines, cell proliferation/colony/migration assays, phosphatase activity assay","journal":"Gastroenterology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional characterization of specific mutations with phosphatase activity measurement, single lab","pmids":["24503127"],"is_preprint":false},{"year":2014,"finding":"PTPN3 dephosphorylates Eps15 (EGFR pathway substrate 15), promoting EGFR lipid raft-mediated endocytosis and lysosomal degradation. Depletion of PTPN3 impairs EGFR degradation and enhances lung cancer cell proliferation and tumorigenicity, while PTPN3 and an Eps15 phosphorylation-deficient mutant suppress cell growth and migration in vitro and tumor xenograft growth in vivo.","method":"Drosophila genetic screen, PTPN3 knockdown/overexpression in lung cancer cells, phosphatase assay with Eps15 substrate, endocytosis assays, xenograft mouse model","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — orthogonal genetic (Drosophila and mammalian KD/OE), biochemical dephosphorylation assay, phosphorylation-deficient mutant rescue, and in vivo xenograft","pmids":["25263444"],"is_preprint":false},{"year":2014,"finding":"The PTPN3–p38γ complex architecture was determined by a hybrid structural method (X-ray crystallography, SAXS, and chemical cross-linking/MS). A unique glutamic acid-containing loop (E-loop) of the PTPN3 phosphatase domain defines substrate specificity toward fully activated p38γ. The PDZ domain of PTPN3 stabilizes the active-state complex through binding the PDZ-binding motif of p38γ, alleviating autoinhibition of PTPN3 and enabling efficient tyrosine dephosphorylation.","method":"X-ray crystallography, small-angle X-ray scattering (SAXS), chemical cross-linking coupled to mass spectrometry, in vitro phosphatase assay","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 1 / Strong — hybrid structural determination plus functional validation of PDZ-mediated allostery, multiple orthogonal methods in one rigorous study","pmids":["25314968"],"is_preprint":false},{"year":2019,"finding":"PTPN3 interacts with Src and DAAM1 (formin-like actin regulator). PTPN3 inhibits Src activity and Src-mediated phosphorylation of DAAM1 Tyr652. Tyrosine phosphorylation of DAAM1 is required for DAAM1 homodimer formation and actin polymerization. Depletion of PTPN3 enhances lung cancer cell migration/invasion and metastasis via promoted actin filament assembly and focal adhesion dynamics; a DAAM1 phosphodeficient mutant rescues these effects.","method":"Co-immunoprecipitation, PTPN3 knockdown in lung cancer cells, Src kinase assay, site-directed mutagenesis of DAAM1 (Y652F), F-actin assembly assay, focal adhesion dynamics, mouse metastasis model","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, kinase/phosphatase assays, phosphorylation-deficient mutant rescue, and in vivo metastasis model; multiple orthogonal methods","pmids":["31406243"],"is_preprint":false},{"year":2019,"finding":"PTPN3 stabilizes TGF-β type I receptor (TβRI) by attenuating the interaction between the E3 ubiquitin ligase Smurf2 and TβRI, thereby facilitating TGF-β-induced R-Smad phosphorylation and transcriptional responses. This function is independent of PTPN3's phosphatase activity. The ICC-associated L232R mutation disables this TGF-β signaling enhancement and abolishes tumor suppression.","method":"Co-immunoprecipitation, PTPN3 knockdown/overexpression, TβRI stability assay, Smad phosphorylation assay, luciferase reporter assay, phosphatase-dead mutant analysis, L232R mutant analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple Co-IP experiments, functional receptor stability assay, Smad signaling readouts, mutant controls, single rigorous study with multiple orthogonal methods","pmids":["31304624"],"is_preprint":false},{"year":2019,"finding":"The X-ray crystal structure of the PTPN3 PDZ domain in complex with the PDZ-binding motif (PBM) of HPV E6 was solved. The viral PBM and endogenous ligand p38γ bind the PDZ domain with similar affinities. PBM binding stabilizes the PDZ domain but does not impact the phosphatase catalytic regulation.","method":"X-ray crystallography, NMR chemical shift mapping, isothermal titration calorimetry/biophysical binding assays","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure solved, NMR and biophysical validation, single lab","pmids":["31092861"],"is_preprint":false},{"year":2019,"finding":"HPV8 E6 protein binds PTPH1 and increases PTPH1 protein expression and phosphatase activity. PTPH1 suppression in immortalized keratinocytes reduces cell proliferation and reduces EGFR protein levels, suggesting PTPH1 supports EGFR-dependent keratinocyte proliferation.","method":"Co-immunoprecipitation, siRNA knockdown in keratinocytes, cell proliferation assay, western blot for EGFR","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and siRNA knockdown with EGFR readout, single lab","pmids":["30875834"],"is_preprint":false},{"year":2021,"finding":"PTPN3 PDZ domain binds the C-terminal PBM of hepatitis B virus core protein (HBc) within capsids or as homodimers; crystal structure of PTPN3-PDZ/HBc-PBM complex was solved, revealing a class I PDZ interaction despite atypical C-terminal cysteine in the PBM. Overexpression of PTPN3 significantly affects HBV infection in HepG2-NTCP cells.","method":"X-ray crystallography, pull-down assays, PDZ domain library screening, HBV infection assay in HepG2-NTCP cells, proteomics","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional HBV infection validation and proteomics, single lab with multiple orthogonal methods","pmids":["33441627"],"is_preprint":false},{"year":2023,"finding":"The linker connecting the PDZ and phosphatase domains of PTPN3 is involved in autoinhibition of the phosphatase catalytic activity. Binding of PBMs to the PDZ domain does not impact this catalytic regulation. X-ray structures of complexes between PTPN3-PDZ and PBMs of HPV18 E6 and TACE were solved, revealing structural determinants of PBM recognition.","method":"X-ray crystallography, PDZome binding profile screening, phosphatase activity assay with linker mutants","journal":"Frontiers in molecular biosciences","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — crystal structure plus functional phosphatase assay with linker variants, single lab","pmids":["37200868"],"is_preprint":false},{"year":2024,"finding":"PTPH1 acts as a PDZ-domain scaffold for HER2 receptor tyrosine kinase, binding HER2, p38γ, PBK, and YAP1 via its PDZ domain. PTPH1 dephosphorylates HER2 and reciprocally increases HER2 protein expression. PTPH1 is phosphorylated at S459 by p38γ and/or PBK, regulating scaffold protein turnover. PTPH1 and HER2 cooperate to increase PBK and YAP1 transcription, and combinational inhibition of scaffold-kinases suppresses xenograft growth.","method":"Co-immunoprecipitation, PDZ domain binding assays, HER2 dephosphorylation assay, phosphorylation at S459, transcription assays, mouse xenograft model","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple Co-IP and functional assays with in vivo validation, single lab","pmids":["39803648"],"is_preprint":false}],"current_model":"PTPN3 (PTPH1) is a multidomain non-receptor protein tyrosine phosphatase containing FERM/band 4.1, PDZ, and catalytic PTP domains; it dephosphorylates substrates including VCP/p97, p38γ MAPK, TCR-zeta, Eps15, and DAAM1, while its PDZ domain mediates interactions with TACE, Nav1.5, HER2, p38γ, VDR, HPV E6, and HBc, and its N-terminal domain modulates both substrate selectivity and membrane targeting; additionally, PTPN3 stabilizes TβRI by blocking Smurf2 binding independent of phosphatase activity, and its activity and complex formation are regulated by 14-3-3β binding (serine phosphorylation-dependent) and by p38γ-mediated phosphorylation at Ser-459, with the PDZ domain autoinhibiting the catalytic domain via a connecting linker."},"narrative":{"mechanistic_narrative":"PTPN3 (PTPH1) is a multidomain non-receptor protein tyrosine phosphatase that couples a PDZ-based substrate-recruitment module to a catalytic PTP domain, acting as both an enzyme and a scaffold across signaling, oncogenic, and viral contexts [PMID:7544351, PMID:25314968]. Its N-terminal band 4.1/ERM domain directly modulates catalytic output and substrate selectivity, and the PDZ domain autoinhibits the catalytic domain through a connecting linker, an autoinhibition relieved when a PDZ-binding motif (PBM) ligand engages the PDZ domain [PMID:7544351, PMID:25314968, PMID:37200868]. Through this PDZ-mediated recruitment PTPN3 dephosphorylates defined substrates: it traps and dephosphorylates VCP/p97 at its C-terminal tyrosines [PMID:10364224], dephosphorylates the stress kinase p38γ MAPK in a complex whose architecture and substrate specificity are defined by a glutamate-containing E-loop [PMID:20332238, PMID:25314968], dephosphorylates Eps15 to promote EGFR endocytosis and lysosomal degradation [PMID:25263444], and inhibits Src to limit DAAM1 Tyr652 phosphorylation, dimerization, and actin assembly [PMID:31406243]. PTPN3 activity is reciprocally regulated by its partners: p38γ phosphorylates PTPN3 at Ser-459 in a Ras-controlled feedback loop, and 14-3-3β binds PTPN3 in a serine-phosphorylation-dependent manner [PMID:9341175, PMID:22730326]. In cancer, PTPN3 exhibits context-dependent roles—it cooperates with p38γ and scaffolds HER2 to drive oncogenic growth and acts as a Ras effector [PMID:20332238, PMID:39803648], yet suppresses lung cancer proliferation and metastasis via Eps15/EGFR and Src/DAAM1 control [PMID:25263444, PMID:31406243]. Independent of its phosphatase activity, PTPN3 stabilizes the TGF-β type I receptor by blocking Smurf2 binding, and the cholangiocarcinoma-associated L232R mutation disables this tumor-suppressive function [PMID:31304624]. The PDZ domain also binds viral PBMs from HPV E6 (targeting PTPN3 for E6AP/proteasome-dependent degradation) and hepatitis B core protein, linking PTPN3 to viral pathogenesis [PMID:17166906, PMID:31092861, PMID:33441627]. Genetic ablation of PTPN3 catalytic activity in mice leaves TCR signaling and T cell development intact, indicating its proposed role in negative TCR regulation is dispensable in vivo [PMID:17339465, PMID:19107198].","teleology":[{"year":1995,"claim":"Established PTPN3 as a bona fide tyrosine phosphatase and showed that its N-terminal band 4.1 domain is not merely structural but tunes catalytic rate and substrate choice.","evidence":"In vitro enzymatic assays with purified protein, trypsin cleavage, and PKC phosphorylation","pmids":["7544351"],"confidence":"High","gaps":["Physiological substrates not yet identified","Mechanism by which the N-terminal domain alters substrate selectivity unresolved"]},{"year":1997,"claim":"Identified phospho-serine-dependent 14-3-3β binding at two motifs as a regulatory input controlling PTPN3, framing the phosphatase as itself a regulated node.","evidence":"Yeast two-hybrid, in vitro reconstitution, site-directed mutagenesis of Ser359/Ser853, co-IP","pmids":["9341175"],"confidence":"High","gaps":["Functional consequence of 14-3-3 binding for catalytic activity or localization not defined","Kinase generating the phospho-motifs in cells unclear"]},{"year":1999,"claim":"Defined VCP/p97 as a direct cellular substrate via substrate-trapping, linking PTPN3 catalytic activity to growth inhibition.","evidence":"Substrate-trapping double mutant, inducible expression in NIH3T3, phosphotyrosine blots","pmids":["10364224"],"confidence":"High","gaps":["Downstream consequences of VCP dephosphorylation not mapped","Recruitment mechanism to VCP unknown"]},{"year":2003,"claim":"Cell-based assays nominated PTPN3 as a negative regulator of TCR-zeta and proximal T cell signaling.","evidence":"Reporter assays in Jurkat cells, substrate-trapping PTP library screen, transfection dephosphorylation assays","pmids":["10820377","14672952"],"confidence":"Medium","gaps":["Overexpression-based; physiological relevance untested","ERM-domain contribution not mechanistically resolved"]},{"year":2009,"claim":"Genetic mouse models overturned the proposed T cell role, showing PTPN3 catalytic activity is dispensable for TCR signaling even with related phosphatases removed.","evidence":"Single, double (PTPN3/PTPN4) and triple (with PTPN13) knockout mice with comprehensive T cell phenotyping","pmids":["17339465","19107198"],"confidence":"High","gaps":["Redundancy with non-tested phosphatases not excluded","Does not address non-immune functions"]},{"year":2002,"claim":"Defined the PDZ domain as a substrate/partner recruitment module by mapping PTPN3 to the TACE/ADAM17 C-terminal PBM and showing negative regulation of TNF-α shedding.","evidence":"Y2H, in vitro binding, reciprocal co-IP, shedding/ELISA functional assay","pmids":["12207026"],"confidence":"High","gaps":["Whether TACE is dephosphorylated or only down-regulated in level unresolved"]},{"year":2007,"claim":"Extended PDZ-mediated partnering to the cardiac channel Nav1.5, with catalytic activity altering channel availability.","evidence":"Y2H, pull-down, co-expression electrophysiology with active vs inactive PTPN3","pmids":["16930557"],"confidence":"Medium","gaps":["Direct dephosphorylation of Nav1.5 not demonstrated","In vivo cardiac relevance untested"]},{"year":2012,"claim":"Established a reciprocal PTPN3–p38γ oncogenic module: PTPN3 dephosphorylates p38γ while p38γ phosphorylates PTPN3 at Ser-459 under Ras control, defining a feedback circuit driving transformation.","evidence":"Y2H, co-IP, in vitro/in vivo phosphatase and kinase assays, proteomics, S459 mutagenesis, mouse xenograft","pmids":["20332238","22730326"],"confidence":"High","gaps":["How S459 phosphorylation alters catalytic or scaffold function not fully defined"]},{"year":2014,"claim":"Resolved the structural basis of substrate specificity and PDZ-relieved autoinhibition, explaining how PDZ binding licenses catalysis toward activated p38γ.","evidence":"Hybrid X-ray/SAXS/cross-linking-MS of the PTPN3–p38γ complex with phosphatase assays","pmids":["25314968"],"confidence":"High","gaps":["Generality of E-loop specificity to other substrates untested in this study"]},{"year":2014,"claim":"Revealed opposing cancer roles: phosphatase-independent VDR stabilization promotes breast cancer growth, ICC gain-of-function mutations enhance proliferation, while Eps15 dephosphorylation drives EGFR degradation to suppress lung cancer.","evidence":"Co-IP, knockdown/overexpression, phosphatase assays, ICC mutant (L232R/L384H) functional assays, Drosophila screen, xenograft","pmids":["21119599","24503127","25263444"],"confidence":"High","gaps":["Tissue determinants of oncogenic vs tumor-suppressive behavior unresolved","VDR-stabilization mechanism not structurally defined"]},{"year":2019,"claim":"Expanded the phosphatase-independent scaffold function: PTPN3 stabilizes TβRI by blocking Smurf2, and separately controls Src–DAAM1 to restrain actin-driven metastasis, with ICC L232R abolishing TGF-β tumor suppression.","evidence":"Co-IP, receptor stability and Smad reporter assays, Src/phosphatase assays, DAAM1 Y652F rescue, metastasis model, L232R/phosphatase-dead mutants","pmids":["31304624","31406243"],"confidence":"High","gaps":["How a single L232R mutation toggles between gain- and loss-of-function across pathways unresolved"]},{"year":2021,"claim":"Defined PTPN3 as a target of viral PBMs, structurally characterizing PDZ recognition of HPV E6, HBc, and TACE motifs and the linker-mediated autoinhibition independent of PBM binding.","evidence":"X-ray crystallography of PDZ–PBM complexes, PDZome screening, ITC/NMR, HPV E6/E6AP degradation assays, HBV infection assays, phosphatase assays with linker mutants","pmids":["17166906","30875834","31092861","33441627","37200868"],"confidence":"High","gaps":["Functional impact of PTPN3 on HBV/HPV life cycle only partially defined","Why PBM binding does not relieve linker autoinhibition for non-p38γ ligands unclear"]},{"year":2024,"claim":"Positioned PTPN3 as a multi-kinase PDZ scaffold organizing HER2, p38γ, PBK and YAP1 to drive a transcriptional oncogenic program.","evidence":"Co-IP, PDZ binding assays, HER2 dephosphorylation, S459 phosphorylation, transcription assays, xenograft","pmids":["39803648"],"confidence":"Medium","gaps":["Single lab; direct vs indirect assembly of the four-protein scaffold not fully dissected"]},{"year":null,"claim":"How PTPN3 selects between phosphatase-dependent and scaffold (phosphatase-independent) modes in a given tissue, and what unifies its opposing tumor-promoting and tumor-suppressing outputs, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated model reconciling oncogenic vs tumor-suppressor activities","In vivo substrate repertoire beyond cancer cell models undefined","Endogenous regulatory inputs (14-3-3, S459) not connected to physiological outcomes"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,10,14,16]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,2,10]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[17,22]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7,17]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[11]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[4,7]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10,17,22]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[13,14,16]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[14]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5,8,9]}],"complexes":[],"partners":["P38Γ (MAPK12)","VCP","TACE (ADAM17)","SCN5A (NAV1.5)","VDR","HER2 (ERBB2)","DAAM1","TGFBR1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P26045","full_name":"Tyrosine-protein phosphatase non-receptor type 3","aliases":["Protein-tyrosine phosphatase H1","PTP-H1"],"length_aa":913,"mass_kda":104.0,"function":"May act at junctions between the membrane and the cytoskeleton. Possesses tyrosine phosphatase activity","subcellular_location":"Cell membrane; Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/P26045/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PTPN3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PTPN3","total_profiled":1310},"omim":[{"mim_id":"608712","title":"PROTEIN-TYROSINE PHOSPHATASE, RECEPTOR-TYPE, T; PTPRT","url":"https://www.omim.org/entry/608712"},{"mim_id":"603155","title":"PROTEIN-TYROSINE PHOSPHATASE, NONRECEPTOR-TYPE, 14; PTPN14","url":"https://www.omim.org/entry/603155"},{"mim_id":"600267","title":"PROTEIN-TYROSINE PHOSPHATASE, NONRECEPTOR-TYPE, 13; PTPN13","url":"https://www.omim.org/entry/600267"},{"mim_id":"179590","title":"PROTEIN-TYROSINE PHOSPHATASE, RECEPTOR-TYPE, F; PTPRF","url":"https://www.omim.org/entry/179590"},{"mim_id":"176886","title":"PROTEIN-TYROSINE PHOSPHATASE, RECEPTOR-TYPE, GAMMA; PTPRG","url":"https://www.omim.org/entry/176886"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"skeletal 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Removal of the N-terminal band 4.1 homology domain stimulates dephosphorylation of RCML but inhibits activity toward MBP, indicating that the N-terminal domain directly modulates catalytic function and substrate selectivity.\",\n      \"method\": \"In vitro enzymatic assay with purified baculovirus-expressed protein, limited trypsin cleavage, PKC phosphorylation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct in vitro enzymatic characterization with multiple substrates and domain-deletion experiments, single lab but multiple orthogonal biochemical methods\",\n      \"pmids\": [\"7544351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"PTPH1 associates with 14-3-3β in a serine phosphorylation-dependent manner. Two novel motifs (RSLS359VE and RVDS853EP) in PTPH1 were identified as major 14-3-3β binding sites; mutation of Ser359 and Ser853 to alanine significantly reduced association. The interaction was reconstituted in vitro with recombinant proteins, abolished by phosphatase treatment, and enhanced by Cdc25C-associated kinase treatment.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro reconstitution with recombinant proteins, site-directed mutagenesis, co-immunoprecipitation from cell lines\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution in vitro, mutagenesis of binding sites, confirmed in cells; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"9341175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"PTPH1 directly dephosphorylates VCP (p97/CDC48) in cells. A substrate-trapping mutant (D811A/Y676F double mutant) specifically trapped VCP in vivo and recognized the C-terminal tyrosines of VCP. Induction of wild-type PTPH1 caused specific dephosphorylation of VCP without altering the overall phosphotyrosine profile of cells. Wild-type PTPH1 expression dramatically inhibited cell growth, while a catalytically impaired mutant did not.\",\n      \"method\": \"Substrate-trapping mutagenesis (D811A, Y676F), in vitro substrate trapping from cell lysates, tetracycline-inducible expression in NIH3T3 cells, immunoprecipitation, phosphotyrosine western blot\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — substrate-trapping plus in vivo dephosphorylation with catalytic mutant controls, multiple orthogonal methods\",\n      \"pmids\": [\"10364224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Expression of catalytically active PTPH1 in Jurkat T cells reduces TCR-induced activation of NFAT/AP-1 reporter genes, Erk2 MAP kinase, MEK, and JNK. Catalytically inactive PTPH1-CS had no effect. Deletion of the N-terminal ERM domain reduced the inhibitory effect, indicating the ERM domain contributes to PTPH1's function in T cell signaling.\",\n      \"method\": \"Transient transfection in Jurkat T cells, luciferase reporter assays, kinase activity assays, catalytically inactive mutant controls\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional reporter assays with catalytic mutant and domain-deletion controls, single lab\",\n      \"pmids\": [\"10820377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"PTPH1 interacts with the cytoplasmic domain of TACE (ADAM17) via its PDZ domain binding to the C-terminal group I PDZ-binding motif of TACE (ending in cysteine). Co-expression of catalytically active PTPH1 reduces TACE protein levels and decreases phorbol ester-stimulated shedding of TNF-α compared to catalytically inactive PTPH1, identifying PTPH1 as a negative regulator of TACE.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro binding assay, co-immunoprecipitation from eukaryotic cells, co-expression functional assay (TACE shedding), ELISA for TNF-α\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vitro binding confirmation, and functional shedding assay with catalytic mutant control; multiple orthogonal methods\",\n      \"pmids\": [\"12207026\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"PTPH1 is the predominant phosphatase capable of complexing with phospho-TCR zeta in a substrate-trapping library screen of 47 human PTPs, and transfection assays confirmed PTPH1 directly dephosphorylates TCR zeta ITAMs.\",\n      \"method\": \"PTP substrate-trapping library (47 PTP catalytic domains), protein purification/chromatography, novel ELISA-based PTPase assay, transfection assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — substrate-trapping library plus transfection functional assay, single lab\",\n      \"pmids\": [\"14672952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"HPV E6 oncoproteins, in complex with E6AP ubiquitin ligase, associate with PTPN3 via binding of E6's C-terminus to the PDZ domain of PTPN3, leading to proteasome-dependent degradation of PTPN3 in vitro and in living cells. Degradation requires E6AP and the proteasome. In transduced keratinocytes, E6-conferred reduced growth factor requirement partially phenocopies PTPN3 knockdown.\",\n      \"method\": \"In vitro degradation assay, co-immunoprecipitation, proteasome inhibitor experiments, siRNA knockdown in keratinocytes\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vitro and cell-based degradation assays with mechanistic controls (E6AP requirement, proteasome inhibition, PDZ motif requirement), multiple orthogonal methods\",\n      \"pmids\": [\"17166906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"PTPH1 interacts with the cardiac voltage-gated sodium channel Nav1.5 via the PDZ domain of PTPH1 binding to the PDZ-binding motif in the C-terminus of Nav1.5. Co-expression of catalytically active PTPH1 shifts the Nav1.5 availability relationship toward hyperpolarized potentials, while inactive PTPH1 or the tyrosine kinase Fyn does the opposite, indicating that tyrosine phosphorylation destabilizes the inactivated state of Nav1.5.\",\n      \"method\": \"Yeast two-hybrid screen (cardiac cDNA library), pull-down assay, co-expression in HEK293 cells with electrophysiology\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pull-down plus functional electrophysiology with active vs. inactive mutant, single lab\",\n      \"pmids\": [\"16930557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mice lacking catalytically active PTPN3 (gene-trapped and gene-targeted strains) show normal TCR signal transduction, T cell development, cytokine production, and proliferation, demonstrating that PTPN3 phosphatase activity is dispensable for negative regulation of TCR signaling in primary T cells in vivo.\",\n      \"method\": \"Gene trap and gene targeting in mice, flow cytometry, T cell activation assays, cytokine ELISA, proliferation assays\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent genetic mouse models (gene trap and targeted), comprehensive phenotyping; negative result well-established\",\n      \"pmids\": [\"17339465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PTPN3 and PTPN4 double-deficient mice, as well as PTPN3/PTPN4/PTPN13 triple-deficient mice, show normal T cell development, TCR-induced cytokine synthesis, proliferation, and Th1/Th2/Th17 differentiation, establishing that PTPN3 and PTPN4 are dispensable for TCR signal transduction even in the absence of related phosphatases.\",\n      \"method\": \"Generation of single, double, and triple knockout mice; T cell development, activation, and differentiation assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple genetic mouse models with comprehensive T cell phenotyping; negative result independently supported by prior study\",\n      \"pmids\": [\"19107198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PTPH1 is a specific phosphatase for p38γ MAPK through PDZ-mediated binding; yeast two-hybrid screening and in vitro/in vivo analyses confirmed the interaction. PTPH1 dephosphorylates p38γ, and their complex formation is required for cooperative oncogenic activity in Ras-dependent malignant growth in vitro and in mice.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro binding assay, co-immunoprecipitation, phosphatase assay, cell transformation assays, mouse xenograft\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Y2H, Co-IP, in vitro dephosphorylation, functional cell and in vivo assays), replicated with subsequent structural study\",\n      \"pmids\": [\"20332238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PTPH1 stimulates breast cancer growth by binding vitamin D receptor (VDR) and increasing cytoplasmic accumulation of VDR, leading to mutual stabilization of PTPH1 and VDR. This oncogenic activity is independent of PTPH1's phosphatase activity but dependent on its ability to increase VDR protein expression.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, overexpression in breast cancer cell lines, subcellular fractionation, cell proliferation assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional assays with phosphatase-dead mutant control, single lab\",\n      \"pmids\": [\"21119599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"p38γ MAPK phosphorylates its phosphatase PTPH1 at Ser-459 in vitro and in vivo through their complex formation, as identified by unbiased proteomics. This phosphorylation is regulated by Ras signaling and is important for Ras, p38γ, and PTPH1 oncogenic activity as well as stress-induced cell growth/death responses.\",\n      \"method\": \"Unbiased proteomic/mass spectrometric identification of phosphorylation, in vitro kinase assay, in vivo phosphorylation assay, site-directed mutagenesis (S459), genetic and pharmacological pathway analyses\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay plus in vivo phosphorylation plus mutagenesis and unbiased proteomics, multiple methods\",\n      \"pmids\": [\"22730326\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Somatic gain-of-function mutations in PTPN3 (including L232R and L384H) found in intrahepatic cholangiocarcinoma alter phosphatase activity and further increase cell proliferation, colony formation, and migration beyond wild-type PTPN3 when expressed in ICC cell lines.\",\n      \"method\": \"Whole exome sequencing, transgenic expression of mutant PTPN3 in cholangiocarcinoma cell lines, cell proliferation/colony/migration assays, phosphatase activity assay\",\n      \"journal\": \"Gastroenterology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional characterization of specific mutations with phosphatase activity measurement, single lab\",\n      \"pmids\": [\"24503127\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PTPN3 dephosphorylates Eps15 (EGFR pathway substrate 15), promoting EGFR lipid raft-mediated endocytosis and lysosomal degradation. Depletion of PTPN3 impairs EGFR degradation and enhances lung cancer cell proliferation and tumorigenicity, while PTPN3 and an Eps15 phosphorylation-deficient mutant suppress cell growth and migration in vitro and tumor xenograft growth in vivo.\",\n      \"method\": \"Drosophila genetic screen, PTPN3 knockdown/overexpression in lung cancer cells, phosphatase assay with Eps15 substrate, endocytosis assays, xenograft mouse model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — orthogonal genetic (Drosophila and mammalian KD/OE), biochemical dephosphorylation assay, phosphorylation-deficient mutant rescue, and in vivo xenograft\",\n      \"pmids\": [\"25263444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The PTPN3–p38γ complex architecture was determined by a hybrid structural method (X-ray crystallography, SAXS, and chemical cross-linking/MS). A unique glutamic acid-containing loop (E-loop) of the PTPN3 phosphatase domain defines substrate specificity toward fully activated p38γ. The PDZ domain of PTPN3 stabilizes the active-state complex through binding the PDZ-binding motif of p38γ, alleviating autoinhibition of PTPN3 and enabling efficient tyrosine dephosphorylation.\",\n      \"method\": \"X-ray crystallography, small-angle X-ray scattering (SAXS), chemical cross-linking coupled to mass spectrometry, in vitro phosphatase assay\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — hybrid structural determination plus functional validation of PDZ-mediated allostery, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"25314968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PTPN3 interacts with Src and DAAM1 (formin-like actin regulator). PTPN3 inhibits Src activity and Src-mediated phosphorylation of DAAM1 Tyr652. Tyrosine phosphorylation of DAAM1 is required for DAAM1 homodimer formation and actin polymerization. Depletion of PTPN3 enhances lung cancer cell migration/invasion and metastasis via promoted actin filament assembly and focal adhesion dynamics; a DAAM1 phosphodeficient mutant rescues these effects.\",\n      \"method\": \"Co-immunoprecipitation, PTPN3 knockdown in lung cancer cells, Src kinase assay, site-directed mutagenesis of DAAM1 (Y652F), F-actin assembly assay, focal adhesion dynamics, mouse metastasis model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, kinase/phosphatase assays, phosphorylation-deficient mutant rescue, and in vivo metastasis model; multiple orthogonal methods\",\n      \"pmids\": [\"31406243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PTPN3 stabilizes TGF-β type I receptor (TβRI) by attenuating the interaction between the E3 ubiquitin ligase Smurf2 and TβRI, thereby facilitating TGF-β-induced R-Smad phosphorylation and transcriptional responses. This function is independent of PTPN3's phosphatase activity. The ICC-associated L232R mutation disables this TGF-β signaling enhancement and abolishes tumor suppression.\",\n      \"method\": \"Co-immunoprecipitation, PTPN3 knockdown/overexpression, TβRI stability assay, Smad phosphorylation assay, luciferase reporter assay, phosphatase-dead mutant analysis, L232R mutant analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple Co-IP experiments, functional receptor stability assay, Smad signaling readouts, mutant controls, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"31304624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The X-ray crystal structure of the PTPN3 PDZ domain in complex with the PDZ-binding motif (PBM) of HPV E6 was solved. The viral PBM and endogenous ligand p38γ bind the PDZ domain with similar affinities. PBM binding stabilizes the PDZ domain but does not impact the phosphatase catalytic regulation.\",\n      \"method\": \"X-ray crystallography, NMR chemical shift mapping, isothermal titration calorimetry/biophysical binding assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure solved, NMR and biophysical validation, single lab\",\n      \"pmids\": [\"31092861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"HPV8 E6 protein binds PTPH1 and increases PTPH1 protein expression and phosphatase activity. PTPH1 suppression in immortalized keratinocytes reduces cell proliferation and reduces EGFR protein levels, suggesting PTPH1 supports EGFR-dependent keratinocyte proliferation.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown in keratinocytes, cell proliferation assay, western blot for EGFR\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and siRNA knockdown with EGFR readout, single lab\",\n      \"pmids\": [\"30875834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PTPN3 PDZ domain binds the C-terminal PBM of hepatitis B virus core protein (HBc) within capsids or as homodimers; crystal structure of PTPN3-PDZ/HBc-PBM complex was solved, revealing a class I PDZ interaction despite atypical C-terminal cysteine in the PBM. Overexpression of PTPN3 significantly affects HBV infection in HepG2-NTCP cells.\",\n      \"method\": \"X-ray crystallography, pull-down assays, PDZ domain library screening, HBV infection assay in HepG2-NTCP cells, proteomics\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional HBV infection validation and proteomics, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"33441627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The linker connecting the PDZ and phosphatase domains of PTPN3 is involved in autoinhibition of the phosphatase catalytic activity. Binding of PBMs to the PDZ domain does not impact this catalytic regulation. X-ray structures of complexes between PTPN3-PDZ and PBMs of HPV18 E6 and TACE were solved, revealing structural determinants of PBM recognition.\",\n      \"method\": \"X-ray crystallography, PDZome binding profile screening, phosphatase activity assay with linker mutants\",\n      \"journal\": \"Frontiers in molecular biosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus functional phosphatase assay with linker variants, single lab\",\n      \"pmids\": [\"37200868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PTPH1 acts as a PDZ-domain scaffold for HER2 receptor tyrosine kinase, binding HER2, p38γ, PBK, and YAP1 via its PDZ domain. PTPH1 dephosphorylates HER2 and reciprocally increases HER2 protein expression. PTPH1 is phosphorylated at S459 by p38γ and/or PBK, regulating scaffold protein turnover. PTPH1 and HER2 cooperate to increase PBK and YAP1 transcription, and combinational inhibition of scaffold-kinases suppresses xenograft growth.\",\n      \"method\": \"Co-immunoprecipitation, PDZ domain binding assays, HER2 dephosphorylation assay, phosphorylation at S459, transcription assays, mouse xenograft model\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple Co-IP and functional assays with in vivo validation, single lab\",\n      \"pmids\": [\"39803648\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PTPN3 (PTPH1) is a multidomain non-receptor protein tyrosine phosphatase containing FERM/band 4.1, PDZ, and catalytic PTP domains; it dephosphorylates substrates including VCP/p97, p38γ MAPK, TCR-zeta, Eps15, and DAAM1, while its PDZ domain mediates interactions with TACE, Nav1.5, HER2, p38γ, VDR, HPV E6, and HBc, and its N-terminal domain modulates both substrate selectivity and membrane targeting; additionally, PTPN3 stabilizes TβRI by blocking Smurf2 binding independent of phosphatase activity, and its activity and complex formation are regulated by 14-3-3β binding (serine phosphorylation-dependent) and by p38γ-mediated phosphorylation at Ser-459, with the PDZ domain autoinhibiting the catalytic domain via a connecting linker.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PTPN3 (PTPH1) is a multidomain non-receptor protein tyrosine phosphatase that couples a PDZ-based substrate-recruitment module to a catalytic PTP domain, acting as both an enzyme and a scaffold across signaling, oncogenic, and viral contexts [#0, #15]. Its N-terminal band 4.1/ERM domain directly modulates catalytic output and substrate selectivity, and the PDZ domain autoinhibits the catalytic domain through a connecting linker, an autoinhibition relieved when a PDZ-binding motif (PBM) ligand engages the PDZ domain [#0, #15, #21]. Through this PDZ-mediated recruitment PTPN3 dephosphorylates defined substrates: it traps and dephosphorylates VCP/p97 at its C-terminal tyrosines [#2], dephosphorylates the stress kinase p38\\u03b3 MAPK in a complex whose architecture and substrate specificity are defined by a glutamate-containing E-loop [#10, #15], dephosphorylates Eps15 to promote EGFR endocytosis and lysosomal degradation [#14], and inhibits Src to limit DAAM1 Tyr652 phosphorylation, dimerization, and actin assembly [#16]. PTPN3 activity is reciprocally regulated by its partners: p38\\u03b3 phosphorylates PTPN3 at Ser-459 in a Ras-controlled feedback loop, and 14-3-3\\u03b2 binds PTPN3 in a serine-phosphorylation-dependent manner [#1, #12]. In cancer, PTPN3 exhibits context-dependent roles\\u2014it cooperates with p38\\u03b3 and scaffolds HER2 to drive oncogenic growth and acts as a Ras effector [#10, #22], yet suppresses lung cancer proliferation and metastasis via Eps15/EGFR and Src/DAAM1 control [#14, #16]. Independent of its phosphatase activity, PTPN3 stabilizes the TGF-\\u03b2 type I receptor by blocking Smurf2 binding, and the cholangiocarcinoma-associated L232R mutation disables this tumor-suppressive function [#17]. The PDZ domain also binds viral PBMs from HPV E6 (targeting PTPN3 for E6AP/proteasome-dependent degradation) and hepatitis B core protein, linking PTPN3 to viral pathogenesis [#6, #18, #20]. Genetic ablation of PTPN3 catalytic activity in mice leaves TCR signaling and T cell development intact, indicating its proposed role in negative TCR regulation is dispensable in vivo [#8, #9].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Established PTPN3 as a bona fide tyrosine phosphatase and showed that its N-terminal band 4.1 domain is not merely structural but tunes catalytic rate and substrate choice.\",\n      \"evidence\": \"In vitro enzymatic assays with purified protein, trypsin cleavage, and PKC phosphorylation\",\n      \"pmids\": [\"7544351\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological substrates not yet identified\", \"Mechanism by which the N-terminal domain alters substrate selectivity unresolved\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Identified phospho-serine-dependent 14-3-3\\u03b2 binding at two motifs as a regulatory input controlling PTPN3, framing the phosphatase as itself a regulated node.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro reconstitution, site-directed mutagenesis of Ser359/Ser853, co-IP\",\n      \"pmids\": [\"9341175\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of 14-3-3 binding for catalytic activity or localization not defined\", \"Kinase generating the phospho-motifs in cells unclear\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Defined VCP/p97 as a direct cellular substrate via substrate-trapping, linking PTPN3 catalytic activity to growth inhibition.\",\n      \"evidence\": \"Substrate-trapping double mutant, inducible expression in NIH3T3, phosphotyrosine blots\",\n      \"pmids\": [\"10364224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream consequences of VCP dephosphorylation not mapped\", \"Recruitment mechanism to VCP unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Cell-based assays nominated PTPN3 as a negative regulator of TCR-zeta and proximal T cell signaling.\",\n      \"evidence\": \"Reporter assays in Jurkat cells, substrate-trapping PTP library screen, transfection dephosphorylation assays\",\n      \"pmids\": [\"10820377\", \"14672952\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Overexpression-based; physiological relevance untested\", \"ERM-domain contribution not mechanistically resolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Genetic mouse models overturned the proposed T cell role, showing PTPN3 catalytic activity is dispensable for TCR signaling even with related phosphatases removed.\",\n      \"evidence\": \"Single, double (PTPN3/PTPN4) and triple (with PTPN13) knockout mice with comprehensive T cell phenotyping\",\n      \"pmids\": [\"17339465\", \"19107198\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Redundancy with non-tested phosphatases not excluded\", \"Does not address non-immune functions\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defined the PDZ domain as a substrate/partner recruitment module by mapping PTPN3 to the TACE/ADAM17 C-terminal PBM and showing negative regulation of TNF-\\u03b1 shedding.\",\n      \"evidence\": \"Y2H, in vitro binding, reciprocal co-IP, shedding/ELISA functional assay\",\n      \"pmids\": [\"12207026\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TACE is dephosphorylated or only down-regulated in level unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Extended PDZ-mediated partnering to the cardiac channel Nav1.5, with catalytic activity altering channel availability.\",\n      \"evidence\": \"Y2H, pull-down, co-expression electrophysiology with active vs inactive PTPN3\",\n      \"pmids\": [\"16930557\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct dephosphorylation of Nav1.5 not demonstrated\", \"In vivo cardiac relevance untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Established a reciprocal PTPN3\\u2013p38\\u03b3 oncogenic module: PTPN3 dephosphorylates p38\\u03b3 while p38\\u03b3 phosphorylates PTPN3 at Ser-459 under Ras control, defining a feedback circuit driving transformation.\",\n      \"evidence\": \"Y2H, co-IP, in vitro/in vivo phosphatase and kinase assays, proteomics, S459 mutagenesis, mouse xenograft\",\n      \"pmids\": [\"20332238\", \"22730326\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How S459 phosphorylation alters catalytic or scaffold function not fully defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the structural basis of substrate specificity and PDZ-relieved autoinhibition, explaining how PDZ binding licenses catalysis toward activated p38\\u03b3.\",\n      \"evidence\": \"Hybrid X-ray/SAXS/cross-linking-MS of the PTPN3\\u2013p38\\u03b3 complex with phosphatase assays\",\n      \"pmids\": [\"25314968\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality of E-loop specificity to other substrates untested in this study\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed opposing cancer roles: phosphatase-independent VDR stabilization promotes breast cancer growth, ICC gain-of-function mutations enhance proliferation, while Eps15 dephosphorylation drives EGFR degradation to suppress lung cancer.\",\n      \"evidence\": \"Co-IP, knockdown/overexpression, phosphatase assays, ICC mutant (L232R/L384H) functional assays, Drosophila screen, xenograft\",\n      \"pmids\": [\"21119599\", \"24503127\", \"25263444\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tissue determinants of oncogenic vs tumor-suppressive behavior unresolved\", \"VDR-stabilization mechanism not structurally defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Expanded the phosphatase-independent scaffold function: PTPN3 stabilizes T\\u03b2RI by blocking Smurf2, and separately controls Src\\u2013DAAM1 to restrain actin-driven metastasis, with ICC L232R abolishing TGF-\\u03b2 tumor suppression.\",\n      \"evidence\": \"Co-IP, receptor stability and Smad reporter assays, Src/phosphatase assays, DAAM1 Y652F rescue, metastasis model, L232R/phosphatase-dead mutants\",\n      \"pmids\": [\"31304624\", \"31406243\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single L232R mutation toggles between gain- and loss-of-function across pathways unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined PTPN3 as a target of viral PBMs, structurally characterizing PDZ recognition of HPV E6, HBc, and TACE motifs and the linker-mediated autoinhibition independent of PBM binding.\",\n      \"evidence\": \"X-ray crystallography of PDZ\\u2013PBM complexes, PDZome screening, ITC/NMR, HPV E6/E6AP degradation assays, HBV infection assays, phosphatase assays with linker mutants\",\n      \"pmids\": [\"17166906\", \"30875834\", \"31092861\", \"33441627\", \"37200868\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional impact of PTPN3 on HBV/HPV life cycle only partially defined\", \"Why PBM binding does not relieve linker autoinhibition for non-p38\\u03b3 ligands unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Positioned PTPN3 as a multi-kinase PDZ scaffold organizing HER2, p38\\u03b3, PBK and YAP1 to drive a transcriptional oncogenic program.\",\n      \"evidence\": \"Co-IP, PDZ binding assays, HER2 dephosphorylation, S459 phosphorylation, transcription assays, xenograft\",\n      \"pmids\": [\"39803648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; direct vs indirect assembly of the four-protein scaffold not fully dissected\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PTPN3 selects between phosphatase-dependent and scaffold (phosphatase-independent) modes in a given tissue, and what unifies its opposing tumor-promoting and tumor-suppressing outputs, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated model reconciling oncogenic vs tumor-suppressor activities\", \"In vivo substrate repertoire beyond cancer cell models undefined\", \"Endogenous regulatory inputs (14-3-3, S459) not connected to physiological outcomes\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 10, 14, 16]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 2, 10]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [17, 22]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10, 17, 22]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [13, 14, 16]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5, 8, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"p38\\u03b3 (MAPK12)\", \"VCP\", \"TACE (ADAM17)\", \"SCN5A (Nav1.5)\", \"VDR\", \"HER2 (ERBB2)\", \"DAAM1\", \"TGFBR1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}