{"gene":"PPM1B","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2015,"finding":"PPM1B (Ppm1b) acts as a direct phosphatase for RIP3 (receptor-interacting protein 3), dephosphorylating its Thr231 and Ser232 auto-phosphorylation sites. This dephosphorylation prevents recruitment of MLKL to the necrosome, thereby suppressing necroptosis both in cultured cells and in vivo (Ppm1b-deficient mice showed enhanced TNF-induced death and elevated RIP3 phosphorylation in a RIP3-dependent manner).","method":"Co-immunoprecipitation, in vitro dephosphorylation assay, Ppm1b-deficient mouse model with TNF challenge, phospho-specific immunoblotting","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro phosphatase assay plus in vivo genetic model with multiple orthogonal readouts; replicated in breast cancer context (PMID:33520691)","pmids":["25751141"],"is_preprint":false},{"year":2008,"finding":"PPM1B (and PPM1A) function as IKKβ phosphatases, dephosphorylating IKKβ at Ser177 and Ser181 to terminate TNFα-induced NF-κB activation. PPM1B associates with the phosphorylated form of IKKβ, and this interaction is transiently induced by TNFα. Knockdown of PPM1B enhances TNFα-induced IKKβ phosphorylation, NF-κB nuclear translocation, and NF-κB-dependent gene expression.","method":"Functional genomic screen, co-immunoprecipitation, overexpression/knockdown, NF-κB reporter assay, immunoblotting for phospho-IKKβ","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, gain- and loss-of-function experiments, multiple orthogonal readouts; consistent with multiple downstream studies","pmids":["18930133"],"is_preprint":false},{"year":2012,"finding":"PPM1B acts as a TBK1 phosphatase, dephosphorylating TBK1 at Ser172 both in vivo and in vitro. PPM1B wild-type but not its phosphatase-deficient R179G mutant inhibits TBK1-mediated antiviral signaling and facilitates VSV replication. Viral infection induces transient association of PPM1B with TBK1. Knockdown of PPM1B enhances virus-induced IRF3 phosphorylation and IFNβ production.","method":"Functional genomics, in vitro dephosphorylation assay, phosphatase-dead mutant (R179G), co-immunoprecipitation, viral infection assay, siRNA knockdown with IRF3/IFNβ readouts","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro phosphatase assay with active-site mutagenesis plus Co-IP and cellular gain/loss-of-function, single lab","pmids":["22750291"],"is_preprint":false},{"year":2013,"finding":"PPM1B is N-myristoylated (at Gly2), and this modification is essential for its ability to dephosphorylate AMPKα in cells. The non-myristoylated G2A mutant prevents membrane association and shows reduced activity toward AMPKα in vitro, though it retains higher specific activity against an artificial substrate (PNPP), suggesting N-myristoylation is required for physiological substrate recognition rather than catalysis per se.","method":"N-myristoylation assay, G2A mutant analysis, membrane fractionation, in vitro phosphatase assay with AMPKα and PNPP","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and multiple substrates, single lab with orthogonal methods","pmids":["23088624"],"is_preprint":false},{"year":2013,"finding":"PPM1B directly interacts with and dephosphorylates PPARγ at Ser112 (and Ser273), increasing PPARγ-mediated transcription. Endogenous PPM1B is localized in the nucleus of mature adipocytes where it binds PPARγ. Knockdown of PPM1B blunts expression of some PPARγ target genes.","method":"Immunoprecipitation coupled to tandem MS, in vitro dephosphorylation assay, nuclear localization by fractionation/immunofluorescence, knockdown in 3T3-L1 adipocytes with transcriptional readout","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro dephosphorylation assay plus Co-IP, nuclear localization, and functional transcriptional readout, single lab with multiple orthogonal methods","pmids":["23320500"],"is_preprint":false},{"year":2011,"finding":"The GAS41–PP2Cβ (PPM1B) complex, but not PPM1B alone, specifically dephosphorylates p53 at Ser366, reducing UV-induced p53 stabilization and increasing cell survival after genotoxic damage. GAS41 acts as a regulatory subunit controlling substrate specificity of PPM1B.","method":"Co-immunoprecipitation, in vitro dephosphorylation assay, ectopic expression, UV irradiation with p53 phosphorylation readout, cell survival assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro dephosphorylation assay plus Co-IP and cellular functional validation, single lab with multiple orthogonal methods","pmids":["21317290"],"is_preprint":false},{"year":2015,"finding":"PPM1B is an essential component of the Groucho4 repressor complex recruited by Pax2 to chromatin. PPM1B dephosphorylates the Pax2 activation domain, displacing the adaptor PTIP, thereby inhibiting H3K4 methylation and switching Pax2 from a transcriptional activator to a repressor. Loss of PPM1B prevents Groucho-mediated gene repression.","method":"Co-immunoprecipitation, chromatin immunoprecipitation, loss-of-function (PPM1B knockout/depletion) with gene expression and histone methylation readouts","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ChIP, and loss-of-function with histone modification readout, multiple orthogonal methods in single lab","pmids":["25631048"],"is_preprint":false},{"year":2012,"finding":"PPM1B interacts with EKLF (KLF1) via the EKLF PEST1 sequence. PPM1B superactivates EKLF at the β-globin and BKLF promoters in an erythroid cell line, dependent on intact PPM1B phosphatase activity. Conversely, depletion of PPM1B in CD34+ cells leads to higher endogenous β-globin gene activation after differentiation, indicating a complex, context-dependent regulatory role.","method":"Co-immunoprecipitation, promoter-reporter assay, PPM1B phosphatase-dead mutant, shRNA knockdown in CD34+ cells with gene expression readout","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP with mutant validation and functional reporter, but complex/contradictory phenotypic outcome across assay systems, single lab","pmids":["22393050"],"is_preprint":false},{"year":2013,"finding":"PKA phosphorylates PPM1B (PP2Cβ) at Ser195, promoting its ubiquitin-dependent proteasomal degradation and thereby activating NF-κB-mediated inflammatory signaling. PKA inhibition (by H89) stabilizes PPM1B and restores its anti-inflammatory function.","method":"Mutagenesis of serine residues, PKA kinase assay, proteasome inhibitor experiments, H89 PKA inhibitor, immunoblotting for PPM1B stability and NF-κB pathway","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — site-directed mutagenesis with kinase and degradation assays, single lab, single study","pmids":["23756813"],"is_preprint":false},{"year":2021,"finding":"PPM1B directly dephosphorylates DYRK1A at Ser258 (a DYRK1A autophosphorylation site), thereby inhibiting DYRK1A kinase activity. PPM1B-mediated dephosphorylation of DYRK1A subsequently reduces tau phosphorylation at Thr212 and inhibits toxic tau oligomerization and aggregation.","method":"LC-MS/MS identification of DYRK1A-PPM1B interaction, Co-immunoprecipitation, in vitro dephosphorylation assay, tau phosphorylation and aggregation readouts in HEK293 cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro dephosphorylation assay with MS identification of interaction, downstream tau phosphorylation and aggregation validated, single lab with multiple orthogonal methods","pmids":["33380426"],"is_preprint":false},{"year":2022,"finding":"PPM1B is sequestered by 14-3-3ε under basal conditions; leucine deprivation induces crotonylation of 14-3-3ε (regulated by HDAC7), disrupting the 14-3-3ε amphipathic pocket and releasing PPM1B. Free PPM1B then dephosphorylates ULK1, initiating autophagy.","method":"Crotonylome profiling, molecular dynamics simulation, co-immunoprecipitation, 14-3-3ε crotonylation-deficient mutant, autophagy assays, ULK1 phosphorylation immunoblotting","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP showing 14-3-3ε–PPM1B interaction and release, crotonylation mutant with functional autophagy readout, single lab","pmids":["36543144"],"is_preprint":false},{"year":2016,"finding":"PPM1B is a substrate of the Cul4A-DDB1-DCAF4L2 E3 ubiquitin ligase complex; DCAF4L2 overexpression promotes PPM1B degradation, leading to NF-κB pathway activation and increased colorectal cancer invasion and metastasis. Knockdown of PPM1B abrogates the shDCAF4L2-mediated inhibition of cell invasion.","method":"Mass spectrometry identification of E3 complex components, co-immunoprecipitation, knockdown/overexpression with invasion assay, immunoblotting for NF-κB","journal":"American journal of translational research","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — MS identification of complex plus functional rescue experiments, single lab","pmids":["27158335"],"is_preprint":false},{"year":2024,"finding":"PPM1B directly interacts with YBX1 and dephosphorylates YBX1 at Ser314. This dephosphorylation affects USP10-mediated deubiquitination of YBX1, reducing YBX1 protein stability, which suppresses PANoptosis inhibition and decreases oxaliplatin resistance in gastric cancer cells.","method":"Co-immunoprecipitation, overexpression/silencing experiments, phosphorylation site mutagenesis (S314), ubiquitination assays, cell death and drug resistance assays","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP with mutagenesis and functional readout, single lab","pmids":["38364962"],"is_preprint":false},{"year":2023,"finding":"TXLNA interacts with TBK1 and impairs PPM1B binding to TBK1, thereby inhibiting PPM1B-mediated dephosphorylation of TBK1 at Ser172 and contributing to aberrant TBK1 activation in cancer cells.","method":"BioID biotinylation with TMT quantitative proteomics, APEX2 proximity labeling with TMT proteomics, co-immunoprecipitation, phospho-TBK1 immunoblotting","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — proximity labeling proteomics plus Co-IP, single lab, single study","pmids":["37506885"],"is_preprint":false},{"year":2025,"finding":"TRIM25 physically interacts with PPM1B and promotes its ubiquitin-dependent degradation, leading to increased CDK2 phosphorylation and gastric cancer cell proliferation. PPM1B overexpression induces G1 phase cell cycle arrest and suppresses tumor growth, placing PPM1B upstream of CDK2 in the TRIM25/PPM1B/CDK2 signaling axis.","method":"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown/knockout with cell cycle and proliferation readouts, in vivo tumor growth assay","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP with ubiquitination assay and functional cell cycle readout, single lab","pmids":["39979355"],"is_preprint":false},{"year":2025,"finding":"BRISC complex component ABRO1 directly binds YAP and undergoes liquid-liquid phase separation with YAP and PPM1B in a YAP-dependent manner, promoting K63-linked deubiquitination of PPM1B at K326. Smooth muscle cell-specific PPM1B overexpression attenuates high-fat/high-sucrose diet-induced arterial stiffness in a K326 K63-polyubiquitination-dependent manner. ABRO1 or BRCC3 knockout attenuates arterial stiffness and TGF-β–Smad signaling activation.","method":"siRNA screening, mass spectrometry, GST pull-down, co-immunoprecipitation, protein purification, immunofluorescence, Doppler ultrasound, telemetry, smooth muscle cell-specific knockout mice","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — GST pull-down, Co-IP, in vivo genetic models with multiple orthogonal methods, multiple mechanistic layers validated","pmids":["39742393"],"is_preprint":false},{"year":2023,"finding":"PPM1B forms a triple complex with RBM10 and YBX1, in which PPM1B serves as the phosphatase for YBX1. RBM10 knockdown attenuates the YBX1–PPM1B association, elevating YBX1 phosphorylation and nuclear translocation; these tumorigenic phenotypes are reversed by PPM1B overexpression.","method":"Co-immunoprecipitation (triple complex), phosphorylation immunoblotting, overexpression/knockdown, nuclear-cytoplasmic fractionation, xenograft rescue experiment","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP of triple complex with functional rescue in vivo, single lab","pmids":["38246397"],"is_preprint":false},{"year":2021,"finding":"Ppm1b negatively regulates 3-bromopyruvate (3-BP)-induced necroptosis in breast cancer cells through dephosphorylation of RIP3, consistent with the established Ppm1b–RIP3 phosphatase relationship.","method":"Immunoblotting for phospho-RIP3, cell viability assay, overexpression/knockdown, mouse xenograft model","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single study replicating established RIP3 dephosphorylation mechanism in a new cellular context without in vitro reconstitution","pmids":["33520691"],"is_preprint":false},{"year":1998,"finding":"Recombinant human PP2Cβ (PPM1B) expressed in E. coli exhibits metal ion-dependent (Mg2+/Mn2+) serine/threonine phosphatase activity that is insensitive to okadaic acid, similar to PP2Cα.","method":"Cloning from human liver cDNA library, recombinant protein expression in E. coli, phosphatase activity assay with cation dependence and okadaic acid inhibition tests","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro enzymatic characterization, single study, foundational biochemistry","pmids":["9684878"],"is_preprint":false},{"year":2020,"finding":"In Clostridium difficile toxin B (TcdB)-induced colonic inflammation, PPM1B expression is transcriptionally regulated by the AKT/FOXO3 signaling pathway; PPM1B acts as a key mediator promoting phosphorylation of NF-κB p65 and pro-inflammatory cytokine production.","method":"Dual-luciferase reporter assay, chromatin immunoprecipitation, lentiviral overexpression/knockdown, ELISA for cytokines, mouse model with PI3K/AKT inhibitor","journal":"American journal of translational research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic direction is somewhat unclear (PPM1B reported to promote p65 phosphorylation here, contrasting with established NF-κB inhibitory role), single study","pmids":["33194024"],"is_preprint":false},{"year":2018,"finding":"PPM1B depletion in U2OS cells suppresses cell growth accompanied by hyper-phosphorylation of RB1 and up-regulation of E2F1 target genes (p27 and caspase 7), placing PPM1B as a negative regulator of the p38-RB1-E2F1 pathway. PPM1B depletion also sensitizes cells to bleomycin-induced cell death.","method":"Lentiviral shRNA knockdown, immunoblotting for phospho-RB1, qRT-PCR for E2F1 targets, colony/proliferation assay, bleomycin cell death assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — clean knockdown with defined molecular readouts, single lab, single study","pmids":["29654756"],"is_preprint":false},{"year":2020,"finding":"HN252, a p-terphenyl derivative, was identified as a potent PPM1B inhibitor (Ki = 0.52 µM). Using this inhibitor, five proteins were validated as PPM1B substrates by immunoprecipitation: CDK2 (known) and AKT1, HSP90B, β-catenin, and BRCA1 (novel).","method":"In vitro phosphatase inhibition assay (Ki determination), cellular target engagement, immunoprecipitation validation of phosphorylated substrates","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — in vitro Ki measurement plus Co-IP substrate validation, single lab, single study; substrate validation limited to Co-IP without in vitro reconstitution","pmids":["33048454"],"is_preprint":false},{"year":2025,"finding":"PPM1B utilizes a trinuclear metal (Mg2+/Mn2+) architecture for phosphatase activity. The third metal ion (M3) directly coordinates the substrate phosphate, positioning it for in-line SN2 hydrolysis, and also positions a water molecule to protonate the departing alkoxide. This M3 function is mechanistically convergent with the arginine clamp in phosphoprotein phosphatases (PPP), but achieved through a fundamentally different catalytic architecture.","method":"Structural/biochemical studies of PPM1B in the context of Pseudomonas aeruginosa infection; trinuclear metal center characterized; functional studies of M3 role in catalysis (preprint)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structural and mechanistic catalytic study, but preprint without peer review; single study","pmids":["42094482"],"is_preprint":true},{"year":2025,"finding":"In lung cancer cells, decreased PPM1B expression leads to increased inhibitory phosphorylation of MYPT1 (regulatory subunit of myosin phosphatase) at Thr853, which activates PRMT5 (via phospho-Thr80), resulting in symmetric dimethylation of histone H2A and decreased retinoblastoma protein expression, driving tumor progression.","method":"Western blotting, PCR, immunohistochemistry in patient tissues; correlation of PPM1B loss with MYPT1 phospho-Thr853, PRMT5 phospho-Thr80, and H2A symmetric dimethylation levels","journal":"Biomolecules","confidence":"Low","confidence_rationale":"Tier 3-4 / Weak — correlative immunoblotting/IHC in tissues without direct in vitro reconstitution of the PPM1B–MYPT1 dephosphorylation step, single lab","pmids":["41301499"],"is_preprint":false},{"year":2024,"finding":"YAP regulates PPM1B ubiquitination and nuclear translocation in astrocytes; knockdown of PPM1B in astrocytes inhibits TGF-β signaling. Icariin treatment inhibits YAP, thereby affecting PPM1B ubiquitination and nuclear translocation to suppress reactive astrocyte activation.","method":"Immunoprecipitation-Western blot for ubiquitination, cytoplasm-nuclear separation fractionation, PPM1B knockdown with TGF-β signaling readout","journal":"Frontiers in pharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/fractionation study, mechanism linking YAP to PPM1B ubiquitination not fully characterized, single lab","pmids":["39439899"],"is_preprint":false},{"year":2014,"finding":"PPM1B depletion induces premature senescence in IMR-90 fibroblasts, with senescence partially rescued by p38 MAPK inactivation, identifying PPM1B as a regulator of both p38 MAPK-dependent and p38 MAPK-independent senescence pathways.","method":"Lentiviral shRNA knockdown, senescence markers (β-galactosidase, growth arrest), p38 MAPK inhibitor rescue","journal":"Mechanisms of ageing and development","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — clean knockdown with senescence phenotype and pharmacological pathway rescue, single lab","pmids":["24674756"],"is_preprint":false}],"current_model":"PPM1B is a metal ion (Mg2+/Mn2+)-dependent, N-myristoylated serine/threonine phosphatase that operates through a trinuclear metal catalytic mechanism and negatively regulates multiple signaling pathways by dephosphorylating key substrates including RIP3 (suppressing necroptosis), IKKβ (terminating NF-κB activation), TBK1 (limiting antiviral/interferon responses), AMPKα, ULK1 (initiating autophagy upon release from 14-3-3ε), DYRK1A (reducing tau hyperphosphorylation), PPARγ, p53-Ser366 (in complex with GAS41), YBX1-Ser314, and Pax2; its activity and stability are regulated by PKA-mediated phosphorylation at Ser195 (promoting proteasomal degradation), K63-linked ubiquitination (regulated by the BRISC/ABRO1 complex), and ubiquitin-dependent degradation mediated by E3 ligases DCAF4L2-Cul4A-DDB1, TRIM25, and PLEK2, while substrate specificity can be conferred by associated regulatory subunits such as GAS41."},"narrative":{"mechanistic_narrative":"PPM1B is a metal ion-dependent (Mg2+/Mn2+), okadaic acid-insensitive serine/threonine protein phosphatase that broadly terminates phosphorylation-driven signaling by dephosphorylating activated kinases and transcriptional regulators [PMID:9684878, PMID:42094482]. Catalysis proceeds through a trinuclear metal center in which a third metal ion coordinates the substrate phosphate for in-line hydrolysis [PMID:42094482]. A dominant theme is the restraint of inflammatory and innate-immune signaling: PPM1B dephosphorylates IKKβ at Ser177/Ser181 to extinguish TNFα-induced NF-κB activation [PMID:18930133] and dephosphorylates TBK1 at Ser172 to limit IRF3-driven antiviral interferon responses [PMID:22750291]. It also dephosphorylates RIP3 at Thr231/Ser232 to block MLKL recruitment and suppress necroptosis [PMID:25751141, PMID:33520691]. Beyond immune control, PPM1B targets metabolic and growth regulators including AMPKα (an interaction requiring N-myristoylation at Gly2 for membrane association and physiological substrate recognition) [PMID:23088624], ULK1 to trigger autophagy upon release from a sequestering 14-3-3ε pool [PMID:36543144], DYRK1A at Ser258 to reduce downstream tau phosphorylation and aggregation [PMID:33380426], and several transcriptional regulators (PPARγ at Ser112/Ser273, p53-Ser366 as part of a GAS41 complex that confers substrate specificity, and Pax2 within the Groucho corepressor module) [PMID:23320500, PMID:21317290, PMID:25631048]. PPM1B abundance and activity are themselves tightly controlled: PKA phosphorylation at Ser195 and the E3 ligases DCAF4L2-Cul4A-DDB1 and TRIM25 drive its proteasomal degradation, whereas the BRISC/ABRO1 complex stabilizes it via K63-linked deubiquitination at K326 in a YAP-coupled phase-separated assembly [PMID:23756813, PMID:27158335, PMID:39979355, PMID:39742393]. Through these activities PPM1B functions as a tumor- and disease-relevant brake on NF-κB-driven cancer invasion, cell-cycle progression via CDK2, and diet-induced arterial stiffness through TGF-β–Smad signaling [PMID:27158335, PMID:39979355, PMID:39742393].","teleology":[{"year":1998,"claim":"Established the basic biochemical identity of PPM1B as a phosphatase, answering whether the cloned gene product had catalytic activity and what cofactors it required.","evidence":"Recombinant human PP2Cβ expressed in E. coli assayed for cation dependence and okadaic acid sensitivity","pmids":["9684878"],"confidence":"Medium","gaps":["No physiological substrate identified","No structural basis for catalysis defined"]},{"year":2008,"claim":"Identified IKKβ as a physiological substrate, defining PPM1B's role in terminating TNFα-induced NF-κB signaling rather than acting only on artificial substrates.","evidence":"Functional genomic screen, reciprocal Co-IP, gain/loss-of-function with NF-κB reporter and phospho-IKKβ readouts","pmids":["18930133"],"confidence":"High","gaps":["No in vivo genetic confirmation in this study","Dynamics of TNFα-induced association not structurally defined"]},{"year":2011,"claim":"Demonstrated that a regulatory subunit (GAS41) confers substrate specificity, answering how PPM1B selects targets such as p53-Ser366 that it cannot dephosphorylate alone.","evidence":"Co-IP, in vitro dephosphorylation assay, UV-induced p53 phosphorylation and cell survival readouts","pmids":["21317290"],"confidence":"High","gaps":["Structural basis for GAS41-conferred specificity unknown","Generality of subunit-directed targeting to other substrates not established"]},{"year":2012,"claim":"Extended PPM1B's immune-regulatory role to antiviral signaling by identifying TBK1-Ser172 as a substrate, using a phosphatase-dead mutant to prove catalytic dependence.","evidence":"In vitro dephosphorylation, R179G active-site mutant, viral infection assays, siRNA with IRF3/IFNβ readouts","pmids":["22750291"],"confidence":"High","gaps":["In vivo relevance to antiviral defense not tested","Recruitment mechanism to TBK1 undefined"]},{"year":2012,"claim":"Revealed context-dependent transcriptional regulation through EKLF/KLF1, complicating a purely repressive model.","evidence":"Co-IP via PEST1 sequence, promoter-reporter with phosphatase-dead mutant, shRNA in CD34+ cells","pmids":["22393050"],"confidence":"Medium","gaps":["Opposite outcomes across assay systems unresolved","Direct EKLF dephosphorylation site not mapped"]},{"year":2013,"claim":"Showed N-myristoylation is required for physiological substrate recognition (AMPKα) rather than catalysis itself, explaining membrane targeting of an otherwise soluble phosphatase.","evidence":"N-myristoylation assay, G2A mutant, membrane fractionation, in vitro assays with AMPKα and PNPP","pmids":["23088624"],"confidence":"High","gaps":["Which membranes PPM1B associates with not defined","Whether myristoylation gates other substrates untested"]},{"year":2013,"claim":"Expanded PPM1B into transcriptional/metabolic control by identifying nuclear PPARγ dephosphorylation in adipocytes.","evidence":"IP-MS, in vitro dephosphorylation, nuclear localization, knockdown in 3T3-L1 with transcriptional readout","pmids":["23320500"],"confidence":"High","gaps":["In vivo metabolic consequence not tested","Relative contribution of Ser112 vs Ser273 unclear"]},{"year":2013,"claim":"Identified PKA-Ser195 phosphorylation as a degradation switch, answering how upstream signaling can inactivate PPM1B to license inflammation.","evidence":"Serine mutagenesis, PKA kinase assay, proteasome inhibitor and H89 experiments, stability immunoblotting","pmids":["23756813"],"confidence":"Medium","gaps":["Responsible E3 ligase not identified in this study","Single lab, no in vivo validation"]},{"year":2015,"claim":"Defined PPM1B as the RIP3 phosphatase that suppresses necroptosis, establishing a direct cell-death control function validated in vivo.","evidence":"Co-IP, in vitro dephosphorylation of Thr231/Ser232, Ppm1b-deficient mice with TNF challenge","pmids":["25751141","33520691"],"confidence":"High","gaps":["Regulation of PPM1B–RIP3 association dynamics incomplete","Tissue-specific necroptosis contributions not mapped"]},{"year":2015,"claim":"Showed PPM1B acts within the Groucho/Pax2 corepressor complex to switch a transcriptional activator to a repressor, linking phosphatase activity to chromatin state.","evidence":"Co-IP, ChIP, loss-of-function with gene expression and H3K4 methylation readouts","pmids":["25631048"],"confidence":"High","gaps":["Pax2 dephosphorylation site not precisely mapped","Generality to other Groucho-recruited factors unknown"]},{"year":2016,"claim":"Identified DCAF4L2-Cul4A-DDB1 as an E3 ligase degrading PPM1B, mechanistically connecting PPM1B loss to NF-κB-driven cancer invasion.","evidence":"MS of E3 complex, Co-IP, knockdown/overexpression with invasion assay and NF-κB readout","pmids":["27158335"],"confidence":"Medium","gaps":["Ubiquitination site on PPM1B not mapped","In vivo metastasis dependence on PPM1B not fully isolated"]},{"year":2018,"claim":"Placed PPM1B as a negative regulator of the p38-RB1-E2F1 growth axis, linking it to proliferation control.","evidence":"shRNA knockdown in U2OS, phospho-RB1 immunoblotting, E2F1 target qRT-PCR, bleomycin sensitivity","pmids":["29654756"],"confidence":"Medium","gaps":["Direct substrate in the pathway not identified","Single lab, single cell line"]},{"year":2021,"claim":"Linked PPM1B to neurodegeneration-relevant signaling by showing it dephosphorylates DYRK1A-Ser258 to reduce tau hyperphosphorylation and aggregation.","evidence":"LC-MS/MS interaction mapping, Co-IP, in vitro dephosphorylation, tau phosphorylation/aggregation in HEK293","pmids":["33380426"],"confidence":"High","gaps":["No in vivo or neuronal model","Relevance to disease tauopathies not established"]},{"year":2022,"claim":"Resolved how PPM1B activity is gated spatially, showing 14-3-3ε sequesters PPM1B until leucine deprivation triggers crotonylation-driven release to dephosphorylate ULK1 and initiate autophagy.","evidence":"Crotonylome profiling, MD simulation, Co-IP, crotonylation-deficient mutant, autophagy and ULK1 phospho readouts","pmids":["36543144"],"confidence":"Medium","gaps":["ULK1 dephosphorylation site not mapped","In vivo autophagic relevance untested"]},{"year":2023,"claim":"Identified a regulatory inhibitor (TXLNA) that blocks PPM1B–TBK1 binding, explaining aberrant TBK1 activation in cancer.","evidence":"BioID and APEX2 proximity proteomics, Co-IP, phospho-TBK1 immunoblotting","pmids":["37506885"],"confidence":"Medium","gaps":["Structural basis of competition unknown","In vivo tumor relevance not tested"]},{"year":2023,"claim":"Defined a PPM1B–RBM10–YBX1 triple complex in which RBM10 scaffolds YBX1 dephosphorylation, controlling YBX1 nuclear translocation and tumorigenesis.","evidence":"Co-IP of triple complex, phospho-immunoblotting, nuclear fractionation, xenograft rescue","pmids":["38246397"],"confidence":"Medium","gaps":["YBX1 phospho-site not mapped here","Scaffolding stoichiometry undefined"]},{"year":2024,"claim":"Mapped a specific YBX1-Ser314 dephosphorylation event that destabilizes YBX1 via USP10-coupled ubiquitination, controlling chemoresistance and PANoptosis in gastric cancer.","evidence":"Co-IP, S314 mutagenesis, ubiquitination assays, cell death and oxaliplatin resistance assays","pmids":["38364962"],"confidence":"Medium","gaps":["No in vitro reconstitution of dephosphorylation","Mechanistic link to USP10 indirect"]},{"year":2025,"claim":"Established BRISC/ABRO1-mediated K63 deubiquitination at K326 as a stabilizing regulation, demonstrating in vivo protection against diet-induced arterial stiffness through TGF-β–Smad signaling.","evidence":"siRNA screen, MS, GST pull-down, Co-IP, phase-separation assays, smooth muscle-specific knockout mice, Doppler/telemetry","pmids":["39742393"],"confidence":"High","gaps":["Phosphatase substrate driving arterial phenotype not pinpointed","Mechanism of YAP-dependent phase separation incomplete"]},{"year":2025,"claim":"Identified TRIM25 as a further E3 ligase degrading PPM1B, placing it upstream of CDK2 in a cell-cycle control axis with in vivo tumor suppression.","evidence":"Co-IP, ubiquitination assay, overexpression/knockout with cell cycle and proliferation readouts, in vivo tumor growth","pmids":["39979355"],"confidence":"Medium","gaps":["Whether CDK2 is a direct PPM1B substrate not reconstituted here","Ubiquitination site not mapped"]},{"year":2025,"claim":"Provided structural mechanism: PPM1B uses a trinuclear metal architecture in which the third metal coordinates substrate phosphate for in-line hydrolysis, convergent with the PPP arginine clamp.","evidence":"Structural/biochemical study of M3 catalytic role (preprint)","pmids":["42094482"],"confidence":"Medium","gaps":["Preprint, not peer reviewed","How substrate-specific contacts integrate with the core mechanism unresolved"]},{"year":null,"claim":"It remains unresolved how PPM1B's many reported substrates are prioritized in vivo and which dephosphorylation events drive its tissue-specific roles in inflammation, metabolism, cancer, and vascular biology.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified substrate-targeting code beyond GAS41/RBM10 scaffolds","Limited in vivo substrate-resolution genetics","Several substrate claims rest on single-lab Co-IP without reconstitution"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,4,5,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[18,22]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,6,16]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[0,17]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4,5,6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[14,20]}],"complexes":["GAS41-PPM1B complex","Groucho4 repressor complex","RBM10-YBX1-PPM1B complex","BRISC/ABRO1 complex"],"partners":["RIPK3","IKBKB","TBK1","PPARG","GAS41","DYRK1A","YBX1","YWHAE"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75688","full_name":"Protein phosphatase 1B","aliases":["Protein phosphatase 2C isoform beta","PP2C-beta"],"length_aa":479,"mass_kda":52.6,"function":"Enzyme with a broad specificity. Dephosphorylates CDK2 and CDK6 in vitro. Dephosphorylates PRKAA1 and PRKAA2. Inhibits TBK1-mediated antiviral signaling by dephosphorylating it at 'Ser-172'. Plays an important role in the termination of TNF-mediated NF-kappa-B activation through dephosphorylating and inactivating IKBKB/IKKB","subcellular_location":"Cytoplasm, cytosol; Membrane","url":"https://www.uniprot.org/uniprotkb/O75688/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPM1B","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PPM1B","total_profiled":1310},"omim":[{"mim_id":"620421","title":"DDB1- AND CUL4-ASSOCIATED FACTOR 4-LIKE 2; DCAF4L2","url":"https://www.omim.org/entry/620421"},{"mim_id":"609557","title":"PROLYL ENDOPEPTIDASE-LIKE; PREPL","url":"https://www.omim.org/entry/609557"},{"mim_id":"606407","title":"HYPOTONIA-CYSTINURIA SYNDROME","url":"https://www.omim.org/entry/606407"},{"mim_id":"603770","title":"PROTEIN PHOSPHATASE, MAGNESIUM/MANGANESE-DEPENDENT, 1B; PPM1B","url":"https://www.omim.org/entry/603770"},{"mim_id":"176916","title":"PROTEIN PHOSPHATASE 2, CATALYTIC SUBUNIT, BETA ISOFORM; PPP2CB","url":"https://www.omim.org/entry/176916"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPM1B"},"hgnc":{"alias_symbol":["PPC2BETAX","PP2CB","PP2CBETA"],"prev_symbol":[]},"alphafold":{"accession":"O75688","domains":[{"cath_id":"3.60.40.10","chopping":"3-88_95-293","consensus_level":"high","plddt":96.9361,"start":3,"end":293},{"cath_id":"1.10.10.430","chopping":"302-372","consensus_level":"medium","plddt":92.2468,"start":302,"end":372}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75688","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75688-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75688-F1-predicted_aligned_error_v6.png","plddt_mean":84.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPM1B","jax_strain_url":"https://www.jax.org/strain/search?query=PPM1B"},"sequence":{"accession":"O75688","fasta_url":"https://rest.uniprot.org/uniprotkb/O75688.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75688/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75688"}},"corpus_meta":[{"pmid":"25751141","id":"PMC_25751141","title":"Ppm1b 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Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/37506885","citation_count":2,"is_preprint":false},{"pmid":"37515673","id":"PMC_37515673","title":"Circ_0090231 knockdown protects vascular smooth muscle cells from ox-LDL-induced proliferation, migration and invasion via miR-942-5p/PPM1B axis during atherosclerosis.","date":"2023","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37515673","citation_count":2,"is_preprint":false},{"pmid":"33520691","id":"PMC_33520691","title":"Ppm1b Negatively Regulates 3-Bromopyruvate Induced Necroptosis in Breast Cancer Cells.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33520691","citation_count":2,"is_preprint":false},{"pmid":"41301499","id":"PMC_41301499","title":"Decreased PPM1B Expression Drives PRMT5-Mediated Histone Modification in Lung Cancer Progression.","date":"2025","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/41301499","citation_count":0,"is_preprint":false},{"pmid":"42094482","id":"PMC_42094482","title":"PPM1B utilizes a trinuclear metal architecture for phosphatase activity.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/42094482","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19881,"output_tokens":7007,"usd":0.082374,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":16061,"output_tokens":5950,"usd":0.114528,"stage2_stop_reason":"end_turn"},"total_usd":0.196902,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"PPM1B (Ppm1b) acts as a direct phosphatase for RIP3 (receptor-interacting protein 3), dephosphorylating its Thr231 and Ser232 auto-phosphorylation sites. This dephosphorylation prevents recruitment of MLKL to the necrosome, thereby suppressing necroptosis both in cultured cells and in vivo (Ppm1b-deficient mice showed enhanced TNF-induced death and elevated RIP3 phosphorylation in a RIP3-dependent manner).\",\n      \"method\": \"Co-immunoprecipitation, in vitro dephosphorylation assay, Ppm1b-deficient mouse model with TNF challenge, phospho-specific immunoblotting\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro phosphatase assay plus in vivo genetic model with multiple orthogonal readouts; replicated in breast cancer context (PMID:33520691)\",\n      \"pmids\": [\"25751141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PPM1B (and PPM1A) function as IKKβ phosphatases, dephosphorylating IKKβ at Ser177 and Ser181 to terminate TNFα-induced NF-κB activation. PPM1B associates with the phosphorylated form of IKKβ, and this interaction is transiently induced by TNFα. Knockdown of PPM1B enhances TNFα-induced IKKβ phosphorylation, NF-κB nuclear translocation, and NF-κB-dependent gene expression.\",\n      \"method\": \"Functional genomic screen, co-immunoprecipitation, overexpression/knockdown, NF-κB reporter assay, immunoblotting for phospho-IKKβ\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, gain- and loss-of-function experiments, multiple orthogonal readouts; consistent with multiple downstream studies\",\n      \"pmids\": [\"18930133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PPM1B acts as a TBK1 phosphatase, dephosphorylating TBK1 at Ser172 both in vivo and in vitro. PPM1B wild-type but not its phosphatase-deficient R179G mutant inhibits TBK1-mediated antiviral signaling and facilitates VSV replication. Viral infection induces transient association of PPM1B with TBK1. Knockdown of PPM1B enhances virus-induced IRF3 phosphorylation and IFNβ production.\",\n      \"method\": \"Functional genomics, in vitro dephosphorylation assay, phosphatase-dead mutant (R179G), co-immunoprecipitation, viral infection assay, siRNA knockdown with IRF3/IFNβ readouts\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro phosphatase assay with active-site mutagenesis plus Co-IP and cellular gain/loss-of-function, single lab\",\n      \"pmids\": [\"22750291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PPM1B is N-myristoylated (at Gly2), and this modification is essential for its ability to dephosphorylate AMPKα in cells. The non-myristoylated G2A mutant prevents membrane association and shows reduced activity toward AMPKα in vitro, though it retains higher specific activity against an artificial substrate (PNPP), suggesting N-myristoylation is required for physiological substrate recognition rather than catalysis per se.\",\n      \"method\": \"N-myristoylation assay, G2A mutant analysis, membrane fractionation, in vitro phosphatase assay with AMPKα and PNPP\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and multiple substrates, single lab with orthogonal methods\",\n      \"pmids\": [\"23088624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PPM1B directly interacts with and dephosphorylates PPARγ at Ser112 (and Ser273), increasing PPARγ-mediated transcription. Endogenous PPM1B is localized in the nucleus of mature adipocytes where it binds PPARγ. Knockdown of PPM1B blunts expression of some PPARγ target genes.\",\n      \"method\": \"Immunoprecipitation coupled to tandem MS, in vitro dephosphorylation assay, nuclear localization by fractionation/immunofluorescence, knockdown in 3T3-L1 adipocytes with transcriptional readout\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro dephosphorylation assay plus Co-IP, nuclear localization, and functional transcriptional readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"23320500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The GAS41–PP2Cβ (PPM1B) complex, but not PPM1B alone, specifically dephosphorylates p53 at Ser366, reducing UV-induced p53 stabilization and increasing cell survival after genotoxic damage. GAS41 acts as a regulatory subunit controlling substrate specificity of PPM1B.\",\n      \"method\": \"Co-immunoprecipitation, in vitro dephosphorylation assay, ectopic expression, UV irradiation with p53 phosphorylation readout, cell survival assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro dephosphorylation assay plus Co-IP and cellular functional validation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"21317290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PPM1B is an essential component of the Groucho4 repressor complex recruited by Pax2 to chromatin. PPM1B dephosphorylates the Pax2 activation domain, displacing the adaptor PTIP, thereby inhibiting H3K4 methylation and switching Pax2 from a transcriptional activator to a repressor. Loss of PPM1B prevents Groucho-mediated gene repression.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation, loss-of-function (PPM1B knockout/depletion) with gene expression and histone methylation readouts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ChIP, and loss-of-function with histone modification readout, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"25631048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PPM1B interacts with EKLF (KLF1) via the EKLF PEST1 sequence. PPM1B superactivates EKLF at the β-globin and BKLF promoters in an erythroid cell line, dependent on intact PPM1B phosphatase activity. Conversely, depletion of PPM1B in CD34+ cells leads to higher endogenous β-globin gene activation after differentiation, indicating a complex, context-dependent regulatory role.\",\n      \"method\": \"Co-immunoprecipitation, promoter-reporter assay, PPM1B phosphatase-dead mutant, shRNA knockdown in CD34+ cells with gene expression readout\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP with mutant validation and functional reporter, but complex/contradictory phenotypic outcome across assay systems, single lab\",\n      \"pmids\": [\"22393050\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PKA phosphorylates PPM1B (PP2Cβ) at Ser195, promoting its ubiquitin-dependent proteasomal degradation and thereby activating NF-κB-mediated inflammatory signaling. PKA inhibition (by H89) stabilizes PPM1B and restores its anti-inflammatory function.\",\n      \"method\": \"Mutagenesis of serine residues, PKA kinase assay, proteasome inhibitor experiments, H89 PKA inhibitor, immunoblotting for PPM1B stability and NF-κB pathway\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — site-directed mutagenesis with kinase and degradation assays, single lab, single study\",\n      \"pmids\": [\"23756813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PPM1B directly dephosphorylates DYRK1A at Ser258 (a DYRK1A autophosphorylation site), thereby inhibiting DYRK1A kinase activity. PPM1B-mediated dephosphorylation of DYRK1A subsequently reduces tau phosphorylation at Thr212 and inhibits toxic tau oligomerization and aggregation.\",\n      \"method\": \"LC-MS/MS identification of DYRK1A-PPM1B interaction, Co-immunoprecipitation, in vitro dephosphorylation assay, tau phosphorylation and aggregation readouts in HEK293 cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro dephosphorylation assay with MS identification of interaction, downstream tau phosphorylation and aggregation validated, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"33380426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PPM1B is sequestered by 14-3-3ε under basal conditions; leucine deprivation induces crotonylation of 14-3-3ε (regulated by HDAC7), disrupting the 14-3-3ε amphipathic pocket and releasing PPM1B. Free PPM1B then dephosphorylates ULK1, initiating autophagy.\",\n      \"method\": \"Crotonylome profiling, molecular dynamics simulation, co-immunoprecipitation, 14-3-3ε crotonylation-deficient mutant, autophagy assays, ULK1 phosphorylation immunoblotting\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP showing 14-3-3ε–PPM1B interaction and release, crotonylation mutant with functional autophagy readout, single lab\",\n      \"pmids\": [\"36543144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PPM1B is a substrate of the Cul4A-DDB1-DCAF4L2 E3 ubiquitin ligase complex; DCAF4L2 overexpression promotes PPM1B degradation, leading to NF-κB pathway activation and increased colorectal cancer invasion and metastasis. Knockdown of PPM1B abrogates the shDCAF4L2-mediated inhibition of cell invasion.\",\n      \"method\": \"Mass spectrometry identification of E3 complex components, co-immunoprecipitation, knockdown/overexpression with invasion assay, immunoblotting for NF-κB\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — MS identification of complex plus functional rescue experiments, single lab\",\n      \"pmids\": [\"27158335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPM1B directly interacts with YBX1 and dephosphorylates YBX1 at Ser314. This dephosphorylation affects USP10-mediated deubiquitination of YBX1, reducing YBX1 protein stability, which suppresses PANoptosis inhibition and decreases oxaliplatin resistance in gastric cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/silencing experiments, phosphorylation site mutagenesis (S314), ubiquitination assays, cell death and drug resistance assays\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP with mutagenesis and functional readout, single lab\",\n      \"pmids\": [\"38364962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TXLNA interacts with TBK1 and impairs PPM1B binding to TBK1, thereby inhibiting PPM1B-mediated dephosphorylation of TBK1 at Ser172 and contributing to aberrant TBK1 activation in cancer cells.\",\n      \"method\": \"BioID biotinylation with TMT quantitative proteomics, APEX2 proximity labeling with TMT proteomics, co-immunoprecipitation, phospho-TBK1 immunoblotting\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — proximity labeling proteomics plus Co-IP, single lab, single study\",\n      \"pmids\": [\"37506885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TRIM25 physically interacts with PPM1B and promotes its ubiquitin-dependent degradation, leading to increased CDK2 phosphorylation and gastric cancer cell proliferation. PPM1B overexpression induces G1 phase cell cycle arrest and suppresses tumor growth, placing PPM1B upstream of CDK2 in the TRIM25/PPM1B/CDK2 signaling axis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown/knockout with cell cycle and proliferation readouts, in vivo tumor growth assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP with ubiquitination assay and functional cell cycle readout, single lab\",\n      \"pmids\": [\"39979355\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"BRISC complex component ABRO1 directly binds YAP and undergoes liquid-liquid phase separation with YAP and PPM1B in a YAP-dependent manner, promoting K63-linked deubiquitination of PPM1B at K326. Smooth muscle cell-specific PPM1B overexpression attenuates high-fat/high-sucrose diet-induced arterial stiffness in a K326 K63-polyubiquitination-dependent manner. ABRO1 or BRCC3 knockout attenuates arterial stiffness and TGF-β–Smad signaling activation.\",\n      \"method\": \"siRNA screening, mass spectrometry, GST pull-down, co-immunoprecipitation, protein purification, immunofluorescence, Doppler ultrasound, telemetry, smooth muscle cell-specific knockout mice\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — GST pull-down, Co-IP, in vivo genetic models with multiple orthogonal methods, multiple mechanistic layers validated\",\n      \"pmids\": [\"39742393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPM1B forms a triple complex with RBM10 and YBX1, in which PPM1B serves as the phosphatase for YBX1. RBM10 knockdown attenuates the YBX1–PPM1B association, elevating YBX1 phosphorylation and nuclear translocation; these tumorigenic phenotypes are reversed by PPM1B overexpression.\",\n      \"method\": \"Co-immunoprecipitation (triple complex), phosphorylation immunoblotting, overexpression/knockdown, nuclear-cytoplasmic fractionation, xenograft rescue experiment\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP of triple complex with functional rescue in vivo, single lab\",\n      \"pmids\": [\"38246397\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Ppm1b negatively regulates 3-bromopyruvate (3-BP)-induced necroptosis in breast cancer cells through dephosphorylation of RIP3, consistent with the established Ppm1b–RIP3 phosphatase relationship.\",\n      \"method\": \"Immunoblotting for phospho-RIP3, cell viability assay, overexpression/knockdown, mouse xenograft model\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single study replicating established RIP3 dephosphorylation mechanism in a new cellular context without in vitro reconstitution\",\n      \"pmids\": [\"33520691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Recombinant human PP2Cβ (PPM1B) expressed in E. coli exhibits metal ion-dependent (Mg2+/Mn2+) serine/threonine phosphatase activity that is insensitive to okadaic acid, similar to PP2Cα.\",\n      \"method\": \"Cloning from human liver cDNA library, recombinant protein expression in E. coli, phosphatase activity assay with cation dependence and okadaic acid inhibition tests\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro enzymatic characterization, single study, foundational biochemistry\",\n      \"pmids\": [\"9684878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In Clostridium difficile toxin B (TcdB)-induced colonic inflammation, PPM1B expression is transcriptionally regulated by the AKT/FOXO3 signaling pathway; PPM1B acts as a key mediator promoting phosphorylation of NF-κB p65 and pro-inflammatory cytokine production.\",\n      \"method\": \"Dual-luciferase reporter assay, chromatin immunoprecipitation, lentiviral overexpression/knockdown, ELISA for cytokines, mouse model with PI3K/AKT inhibitor\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic direction is somewhat unclear (PPM1B reported to promote p65 phosphorylation here, contrasting with established NF-κB inhibitory role), single study\",\n      \"pmids\": [\"33194024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PPM1B depletion in U2OS cells suppresses cell growth accompanied by hyper-phosphorylation of RB1 and up-regulation of E2F1 target genes (p27 and caspase 7), placing PPM1B as a negative regulator of the p38-RB1-E2F1 pathway. PPM1B depletion also sensitizes cells to bleomycin-induced cell death.\",\n      \"method\": \"Lentiviral shRNA knockdown, immunoblotting for phospho-RB1, qRT-PCR for E2F1 targets, colony/proliferation assay, bleomycin cell death assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — clean knockdown with defined molecular readouts, single lab, single study\",\n      \"pmids\": [\"29654756\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HN252, a p-terphenyl derivative, was identified as a potent PPM1B inhibitor (Ki = 0.52 µM). Using this inhibitor, five proteins were validated as PPM1B substrates by immunoprecipitation: CDK2 (known) and AKT1, HSP90B, β-catenin, and BRCA1 (novel).\",\n      \"method\": \"In vitro phosphatase inhibition assay (Ki determination), cellular target engagement, immunoprecipitation validation of phosphorylated substrates\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — in vitro Ki measurement plus Co-IP substrate validation, single lab, single study; substrate validation limited to Co-IP without in vitro reconstitution\",\n      \"pmids\": [\"33048454\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPM1B utilizes a trinuclear metal (Mg2+/Mn2+) architecture for phosphatase activity. The third metal ion (M3) directly coordinates the substrate phosphate, positioning it for in-line SN2 hydrolysis, and also positions a water molecule to protonate the departing alkoxide. This M3 function is mechanistically convergent with the arginine clamp in phosphoprotein phosphatases (PPP), but achieved through a fundamentally different catalytic architecture.\",\n      \"method\": \"Structural/biochemical studies of PPM1B in the context of Pseudomonas aeruginosa infection; trinuclear metal center characterized; functional studies of M3 role in catalysis (preprint)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structural and mechanistic catalytic study, but preprint without peer review; single study\",\n      \"pmids\": [\"42094482\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In lung cancer cells, decreased PPM1B expression leads to increased inhibitory phosphorylation of MYPT1 (regulatory subunit of myosin phosphatase) at Thr853, which activates PRMT5 (via phospho-Thr80), resulting in symmetric dimethylation of histone H2A and decreased retinoblastoma protein expression, driving tumor progression.\",\n      \"method\": \"Western blotting, PCR, immunohistochemistry in patient tissues; correlation of PPM1B loss with MYPT1 phospho-Thr853, PRMT5 phospho-Thr80, and H2A symmetric dimethylation levels\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3-4 / Weak — correlative immunoblotting/IHC in tissues without direct in vitro reconstitution of the PPM1B–MYPT1 dephosphorylation step, single lab\",\n      \"pmids\": [\"41301499\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"YAP regulates PPM1B ubiquitination and nuclear translocation in astrocytes; knockdown of PPM1B in astrocytes inhibits TGF-β signaling. Icariin treatment inhibits YAP, thereby affecting PPM1B ubiquitination and nuclear translocation to suppress reactive astrocyte activation.\",\n      \"method\": \"Immunoprecipitation-Western blot for ubiquitination, cytoplasm-nuclear separation fractionation, PPM1B knockdown with TGF-β signaling readout\",\n      \"journal\": \"Frontiers in pharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/fractionation study, mechanism linking YAP to PPM1B ubiquitination not fully characterized, single lab\",\n      \"pmids\": [\"39439899\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PPM1B depletion induces premature senescence in IMR-90 fibroblasts, with senescence partially rescued by p38 MAPK inactivation, identifying PPM1B as a regulator of both p38 MAPK-dependent and p38 MAPK-independent senescence pathways.\",\n      \"method\": \"Lentiviral shRNA knockdown, senescence markers (β-galactosidase, growth arrest), p38 MAPK inhibitor rescue\",\n      \"journal\": \"Mechanisms of ageing and development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — clean knockdown with senescence phenotype and pharmacological pathway rescue, single lab\",\n      \"pmids\": [\"24674756\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPM1B is a metal ion (Mg2+/Mn2+)-dependent, N-myristoylated serine/threonine phosphatase that operates through a trinuclear metal catalytic mechanism and negatively regulates multiple signaling pathways by dephosphorylating key substrates including RIP3 (suppressing necroptosis), IKKβ (terminating NF-κB activation), TBK1 (limiting antiviral/interferon responses), AMPKα, ULK1 (initiating autophagy upon release from 14-3-3ε), DYRK1A (reducing tau hyperphosphorylation), PPARγ, p53-Ser366 (in complex with GAS41), YBX1-Ser314, and Pax2; its activity and stability are regulated by PKA-mediated phosphorylation at Ser195 (promoting proteasomal degradation), K63-linked ubiquitination (regulated by the BRISC/ABRO1 complex), and ubiquitin-dependent degradation mediated by E3 ligases DCAF4L2-Cul4A-DDB1, TRIM25, and PLEK2, while substrate specificity can be conferred by associated regulatory subunits such as GAS41.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPM1B is a metal ion-dependent (Mg2+/Mn2+), okadaic acid-insensitive serine/threonine protein phosphatase that broadly terminates phosphorylation-driven signaling by dephosphorylating activated kinases and transcriptional regulators [#18, #22]. Catalysis proceeds through a trinuclear metal center in which a third metal ion coordinates the substrate phosphate for in-line hydrolysis [#22]. A dominant theme is the restraint of inflammatory and innate-immune signaling: PPM1B dephosphorylates IKK\\u03b2 at Ser177/Ser181 to extinguish TNF\\u03b1-induced NF-\\u03baB activation [#1] and dephosphorylates TBK1 at Ser172 to limit IRF3-driven antiviral interferon responses [#2]. It also dephosphorylates RIP3 at Thr231/Ser232 to block MLKL recruitment and suppress necroptosis [#0, #17]. Beyond immune control, PPM1B targets metabolic and growth regulators including AMPK\\u03b1 (an interaction requiring N-myristoylation at Gly2 for membrane association and physiological substrate recognition) [#3], ULK1 to trigger autophagy upon release from a sequestering 14-3-3\\u03b5 pool [#10], DYRK1A at Ser258 to reduce downstream tau phosphorylation and aggregation [#9], and several transcriptional regulators (PPAR\\u03b3 at Ser112/Ser273, p53-Ser366 as part of a GAS41 complex that confers substrate specificity, and Pax2 within the Groucho corepressor module) [#4, #5, #6]. PPM1B abundance and activity are themselves tightly controlled: PKA phosphorylation at Ser195 and the E3 ligases DCAF4L2-Cul4A-DDB1 and TRIM25 drive its proteasomal degradation, whereas the BRISC/ABRO1 complex stabilizes it via K63-linked deubiquitination at K326 in a YAP-coupled phase-separated assembly [#8, #11, #14, #15]. Through these activities PPM1B functions as a tumor- and disease-relevant brake on NF-\\u03baB-driven cancer invasion, cell-cycle progression via CDK2, and diet-induced arterial stiffness through TGF-\\u03b2\\u2013Smad signaling [#11, #14, #15].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Established the basic biochemical identity of PPM1B as a phosphatase, answering whether the cloned gene product had catalytic activity and what cofactors it required.\",\n      \"evidence\": \"Recombinant human PP2C\\u03b2 expressed in E. coli assayed for cation dependence and okadaic acid sensitivity\",\n      \"pmids\": [\"9684878\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No physiological substrate identified\", \"No structural basis for catalysis defined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified IKK\\u03b2 as a physiological substrate, defining PPM1B's role in terminating TNF\\u03b1-induced NF-\\u03baB signaling rather than acting only on artificial substrates.\",\n      \"evidence\": \"Functional genomic screen, reciprocal Co-IP, gain/loss-of-function with NF-\\u03baB reporter and phospho-IKK\\u03b2 readouts\",\n      \"pmids\": [\"18930133\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No in vivo genetic confirmation in this study\", \"Dynamics of TNF\\u03b1-induced association not structurally defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated that a regulatory subunit (GAS41) confers substrate specificity, answering how PPM1B selects targets such as p53-Ser366 that it cannot dephosphorylate alone.\",\n      \"evidence\": \"Co-IP, in vitro dephosphorylation assay, UV-induced p53 phosphorylation and cell survival readouts\",\n      \"pmids\": [\"21317290\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for GAS41-conferred specificity unknown\", \"Generality of subunit-directed targeting to other substrates not established\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended PPM1B's immune-regulatory role to antiviral signaling by identifying TBK1-Ser172 as a substrate, using a phosphatase-dead mutant to prove catalytic dependence.\",\n      \"evidence\": \"In vitro dephosphorylation, R179G active-site mutant, viral infection assays, siRNA with IRF3/IFN\\u03b2 readouts\",\n      \"pmids\": [\"22750291\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance to antiviral defense not tested\", \"Recruitment mechanism to TBK1 undefined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed context-dependent transcriptional regulation through EKLF/KLF1, complicating a purely repressive model.\",\n      \"evidence\": \"Co-IP via PEST1 sequence, promoter-reporter with phosphatase-dead mutant, shRNA in CD34+ cells\",\n      \"pmids\": [\"22393050\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Opposite outcomes across assay systems unresolved\", \"Direct EKLF dephosphorylation site not mapped\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed N-myristoylation is required for physiological substrate recognition (AMPK\\u03b1) rather than catalysis itself, explaining membrane targeting of an otherwise soluble phosphatase.\",\n      \"evidence\": \"N-myristoylation assay, G2A mutant, membrane fractionation, in vitro assays with AMPK\\u03b1 and PNPP\",\n      \"pmids\": [\"23088624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which membranes PPM1B associates with not defined\", \"Whether myristoylation gates other substrates untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Expanded PPM1B into transcriptional/metabolic control by identifying nuclear PPAR\\u03b3 dephosphorylation in adipocytes.\",\n      \"evidence\": \"IP-MS, in vitro dephosphorylation, nuclear localization, knockdown in 3T3-L1 with transcriptional readout\",\n      \"pmids\": [\"23320500\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo metabolic consequence not tested\", \"Relative contribution of Ser112 vs Ser273 unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified PKA-Ser195 phosphorylation as a degradation switch, answering how upstream signaling can inactivate PPM1B to license inflammation.\",\n      \"evidence\": \"Serine mutagenesis, PKA kinase assay, proteasome inhibitor and H89 experiments, stability immunoblotting\",\n      \"pmids\": [\"23756813\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Responsible E3 ligase not identified in this study\", \"Single lab, no in vivo validation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined PPM1B as the RIP3 phosphatase that suppresses necroptosis, establishing a direct cell-death control function validated in vivo.\",\n      \"evidence\": \"Co-IP, in vitro dephosphorylation of Thr231/Ser232, Ppm1b-deficient mice with TNF challenge\",\n      \"pmids\": [\"25751141\", \"33520691\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulation of PPM1B\\u2013RIP3 association dynamics incomplete\", \"Tissue-specific necroptosis contributions not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed PPM1B acts within the Groucho/Pax2 corepressor complex to switch a transcriptional activator to a repressor, linking phosphatase activity to chromatin state.\",\n      \"evidence\": \"Co-IP, ChIP, loss-of-function with gene expression and H3K4 methylation readouts\",\n      \"pmids\": [\"25631048\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Pax2 dephosphorylation site not precisely mapped\", \"Generality to other Groucho-recruited factors unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified DCAF4L2-Cul4A-DDB1 as an E3 ligase degrading PPM1B, mechanistically connecting PPM1B loss to NF-\\u03baB-driven cancer invasion.\",\n      \"evidence\": \"MS of E3 complex, Co-IP, knockdown/overexpression with invasion assay and NF-\\u03baB readout\",\n      \"pmids\": [\"27158335\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination site on PPM1B not mapped\", \"In vivo metastasis dependence on PPM1B not fully isolated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placed PPM1B as a negative regulator of the p38-RB1-E2F1 growth axis, linking it to proliferation control.\",\n      \"evidence\": \"shRNA knockdown in U2OS, phospho-RB1 immunoblotting, E2F1 target qRT-PCR, bleomycin sensitivity\",\n      \"pmids\": [\"29654756\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrate in the pathway not identified\", \"Single lab, single cell line\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked PPM1B to neurodegeneration-relevant signaling by showing it dephosphorylates DYRK1A-Ser258 to reduce tau hyperphosphorylation and aggregation.\",\n      \"evidence\": \"LC-MS/MS interaction mapping, Co-IP, in vitro dephosphorylation, tau phosphorylation/aggregation in HEK293\",\n      \"pmids\": [\"33380426\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No in vivo or neuronal model\", \"Relevance to disease tauopathies not established\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved how PPM1B activity is gated spatially, showing 14-3-3\\u03b5 sequesters PPM1B until leucine deprivation triggers crotonylation-driven release to dephosphorylate ULK1 and initiate autophagy.\",\n      \"evidence\": \"Crotonylome profiling, MD simulation, Co-IP, crotonylation-deficient mutant, autophagy and ULK1 phospho readouts\",\n      \"pmids\": [\"36543144\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ULK1 dephosphorylation site not mapped\", \"In vivo autophagic relevance untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified a regulatory inhibitor (TXLNA) that blocks PPM1B\\u2013TBK1 binding, explaining aberrant TBK1 activation in cancer.\",\n      \"evidence\": \"BioID and APEX2 proximity proteomics, Co-IP, phospho-TBK1 immunoblotting\",\n      \"pmids\": [\"37506885\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of competition unknown\", \"In vivo tumor relevance not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a PPM1B\\u2013RBM10\\u2013YBX1 triple complex in which RBM10 scaffolds YBX1 dephosphorylation, controlling YBX1 nuclear translocation and tumorigenesis.\",\n      \"evidence\": \"Co-IP of triple complex, phospho-immunoblotting, nuclear fractionation, xenograft rescue\",\n      \"pmids\": [\"38246397\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"YBX1 phospho-site not mapped here\", \"Scaffolding stoichiometry undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Mapped a specific YBX1-Ser314 dephosphorylation event that destabilizes YBX1 via USP10-coupled ubiquitination, controlling chemoresistance and PANoptosis in gastric cancer.\",\n      \"evidence\": \"Co-IP, S314 mutagenesis, ubiquitination assays, cell death and oxaliplatin resistance assays\",\n      \"pmids\": [\"38364962\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstitution of dephosphorylation\", \"Mechanistic link to USP10 indirect\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established BRISC/ABRO1-mediated K63 deubiquitination at K326 as a stabilizing regulation, demonstrating in vivo protection against diet-induced arterial stiffness through TGF-\\u03b2\\u2013Smad signaling.\",\n      \"evidence\": \"siRNA screen, MS, GST pull-down, Co-IP, phase-separation assays, smooth muscle-specific knockout mice, Doppler/telemetry\",\n      \"pmids\": [\"39742393\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phosphatase substrate driving arterial phenotype not pinpointed\", \"Mechanism of YAP-dependent phase separation incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified TRIM25 as a further E3 ligase degrading PPM1B, placing it upstream of CDK2 in a cell-cycle control axis with in vivo tumor suppression.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, overexpression/knockout with cell cycle and proliferation readouts, in vivo tumor growth\",\n      \"pmids\": [\"39979355\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether CDK2 is a direct PPM1B substrate not reconstituted here\", \"Ubiquitination site not mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided structural mechanism: PPM1B uses a trinuclear metal architecture in which the third metal coordinates substrate phosphate for in-line hydrolysis, convergent with the PPP arginine clamp.\",\n      \"evidence\": \"Structural/biochemical study of M3 catalytic role (preprint)\",\n      \"pmids\": [\"42094482\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer reviewed\", \"How substrate-specific contacts integrate with the core mechanism unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how PPM1B's many reported substrates are prioritized in vivo and which dephosphorylation events drive its tissue-specific roles in inflammation, metabolism, cancer, and vascular biology.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified substrate-targeting code beyond GAS41/RBM10 scaffolds\", \"Limited in vivo substrate-resolution genetics\", \"Several substrate claims rest on single-lab Co-IP without reconstitution\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [18, 22]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 6, 16]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [0, 17]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4, 5, 6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [14, 20]}\n    ],\n    \"complexes\": [\n      \"GAS41-PPM1B complex\",\n      \"Groucho4 repressor complex\",\n      \"RBM10-YBX1-PPM1B complex\",\n      \"BRISC/ABRO1 complex\"\n    ],\n    \"partners\": [\n      \"RIPK3\",\n      \"IKBKB\",\n      \"TBK1\",\n      \"PPARG\",\n      \"GAS41\",\n      \"DYRK1A\",\n      \"YBX1\",\n      \"YWHAE\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}