{"gene":"PPM1H","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2019,"finding":"PPM1H directly dephosphorylates LRRK2-phosphorylated Rab GTPases (e.g., Rab8A at its Switch-II motif phosphorylation site). siRNA screen identified PPM1H as the phosphatase counteracting LRRK2 signaling; PPM1H knockout increased endogenous Rab phosphorylation; overexpression suppressed LRRK2-mediated Rab phosphorylation; a substrate-trapping mutant (Asp288Ala) bound with high affinity to LRRK2-phosphorylated Rab proteins, blocking dephosphorylation.","method":"siRNA screen of all human phosphatases, PPM1H knockout in A549 cells, overexpression assays, in vitro biochemical dephosphorylation of Rab8A, substrate-trapping mutagenesis (D288A)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution, mutagenesis (active-site trap), KO and OE cellular assays, multiple orthogonal methods in one study","pmids":["31663853"],"is_preprint":false},{"year":2019,"finding":"PPM1H is localized to the Golgi, and its knockdown suppresses primary cilia formation, phenocopying pathogenic LRRK2.","method":"Immunofluorescence localization, siRNA knockdown with ciliogenesis readout","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization experiment with functional ciliogenesis consequence, single lab, two orthogonal methods","pmids":["31663853"],"is_preprint":false},{"year":2011,"finding":"PPM1H dephosphorylates p27 at threonine 187, removing a signal for proteasomal degradation and stabilizing p27 protein levels. Knockdown of PPM1H reduces p27 protein levels and confers trastuzumab resistance.","method":"RNA interference screening, site-specific phosphorylation analysis (pThr187 of p27), western blotting","journal":"Cancer discovery","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — specific phosphosite-directed dephosphorylation demonstrated, RNAi functional phenotype, single lab","pmids":["22586611"],"is_preprint":false},{"year":2014,"finding":"PPM1H directly interacts with Smad1/5/8 through its Smad-binding domain and dephosphorylates phospho-Smad1/5/8 in the cytoplasm, preventing nuclear translocation and attenuating BMP signaling. Loss of PPM1H enhances BMP-dependent gene regulation and mesenchymal differentiation.","method":"Co-immunoprecipitation, domain mapping, in vitro dephosphorylation assay, ectopic expression and loss-of-function studies, BMP reporter assays, mesenchymal differentiation assays","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — direct binding (Co-IP with domain mapping), in vitro dephosphorylation, multiple functional readouts, single lab with multiple orthogonal methods","pmids":["24732009"],"is_preprint":false},{"year":2021,"finding":"Crystal structure of PPM1H reveals a conserved phosphatase fold with a unique 110-residue flap domain adjacent to the active site that encodes the docking motif for phosphorylated Rab GTPases. The flap domain distantly resembles tudor domains. A PPM1J chimera carrying the PPM1H flap domain gains ability to dephosphorylate pThr72 of Rab8a both in vitro and in cellular assays, confirming the flap domain as the determinant of Rab specificity.","method":"X-ray crystallography, domain-swap chimera (PPM1J + PPM1H flap), in vitro dephosphorylation assay, cellular dephosphorylation assay, crosslinking, 3D modelling","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional domain-swap chimera validated in vitro and in cells, multiple orthogonal methods","pmids":["34580980"],"is_preprint":false},{"year":2023,"finding":"PPM1H relies on an N-terminal amphipathic helix for Golgi localization. The amphipathic helix enables PPM1H to bind liposomes in vitro, and small, highly curved liposomes stimulate PPM1H activity. Localization drives substrate selection: PPM1H at the mother centriole is required for Rab10 dephosphorylation and ciliogenesis regulation, while poor colocalization of Rab12 explains why it is a poor PPM1H substrate in cells but not in vitro.","method":"Artificial targeting to Golgi, mitochondria, or mother centriole, liposome-binding assay, in vitro phosphatase activity assay with liposomes of varying curvature, live-cell imaging, Rab phosphorylation readouts","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution (liposome binding/activation), multiple artificial targeting experiments with defined functional readouts, single lab with multiple orthogonal methods","pmids":["37889931"],"is_preprint":false},{"year":2023,"finding":"LRRK2-hyperphosphorylated RABs disrupt axonal autophagosome transport by perturbing coordinated regulation of dynein and kinesin. PPM1H knockout phenocopies hyperactive LRRK2 in iPSC-derived neurons, causing frequent directional reversals and pauses in autophagosome transport. Overexpression of ARF6 (a GTPase switch for dynein/kinesin) attenuates transport defects in both LRRK2-p.R1441H knockin and PPM1H KO neurons, placing PPM1H upstream of ARF6 in this pathway.","method":"iPSC-derived human neurons, LRRK2 knockin (R1441H), PPM1H knockout, live imaging of autophagosome transport, ARF6 overexpression rescue experiments","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in human iPSC-derived neurons with quantitative live-imaging readout, KO phenocopy and rescue by ARF6, multiple orthogonal methods","pmids":["37133994"],"is_preprint":false},{"year":2009,"finding":"PPM1H possesses phosphatase activity toward pNPP, casein, and phosphopeptides and shows substrate-dependent metal preference: Mn²⁺ is preferred with pNPP or phosphopeptide substrates, while Mg²⁺ is preferred with casein. When both cations are added, Mn²⁺ dominates due to greater affinity for PPM1H.","method":"In vitro phosphatase activity assays with pNPP, casein, and phosphopeptides; metal ion substitution experiments","journal":"Biometals","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical assay with multiple substrates, single lab, single study","pmids":["19262998"],"is_preprint":false},{"year":2020,"finding":"PPM1H is phosphorylated by PKA at Ser-123 and by CaMKI at Ser-210. A hierarchical phosphorylation occurs in neuronal cells whereby initial Ser-123 phosphorylation promotes subsequent Ser-210 phosphorylation. The S123A/S210A double mutant of PPM1H fails to dephosphorylate Smad1 in cell-based assays, establishing that dual phosphorylation at these sites is required for PPM1H activity toward Smad1.","method":"In vitro kinase assays, in silico site prediction, phospho-mimetic and non-phosphorylatable PPM1H mutants, cell-based Smad1 dephosphorylation assay in Neuro2a cells, kinase activator/inhibitor treatments","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro kinase assays plus mutagenesis with cellular functional readout, single lab, two orthogonal methods","pmids":["32600616"],"is_preprint":false},{"year":2023,"finding":"PPM1H directly dephosphorylates p-RPS6KB1 (ribosomal protein S6 kinase B1, a component of the BMP/TGF-β pathway). ATF6 transcriptionally downregulates PPM1H expression in hepatoma cells.","method":"Homology modeling/Rosetta substrate docking screen, in vitro dephosphorylation assay, hepatoma cell-based assays, Atf6 knockdown in mice, western blotting","journal":"Molecular therapy. Nucleic acids","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — in vitro dephosphorylation of RPS6KB1 supported by structural modeling, single lab, limited orthogonal validation of the direct dephosphorylation","pmids":["37456776"],"is_preprint":false},{"year":2025,"finding":"PPM1H contains an allosteric binding site for its non-phosphorylated reaction products Rab8A and Rab10. Microscale thermophoresis showed that thiophosphorylated Rab8A binds the active site with KD ~1 µM, while non-phosphorylated Rab8A and Rab10 bind an alternative (allosteric) site at similar affinity; this interaction is not observed for Rab12. Non-phosphorylated Rab8A or Rab10 inhibit PPM1H phosphatase activity (product/end-product inhibition). Rab binding to the allosteric site also requires PPM1H's N-terminal amphipathic helix; removing it decreases affinity ~6-fold. Sucrose gradient co-flotation of non-phosphorylated Rabs with liposome-bound PPM1H provided independent confirmation.","method":"Microscale thermophoresis (binding affinity measurement), in vitro phosphatase activity inhibition assays, L66R mutagenesis, sucrose gradient co-flotation with liposomes","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — quantitative binding assay (MST), in vitro functional inhibition, mutagenesis, and orthogonal co-flotation, single lab with multiple orthogonal methods","pmids":["40912655"],"is_preprint":false},{"year":2026,"finding":"PPM1H knockout in primary neurons causes gene-dose-dependent disruption of axonal autophagosome transport, impaired degradation of axonal alpha-synuclein, and increased alpha-synuclein aggregation upon exposure to preformed fibrils. The aggregation phenotype is dependent on LRRK2 kinase activity, mechanistically linking PPM1H-controlled RAB dephosphorylation to autophagosomal cargo clearance.","method":"PPM1H knockout primary neurons, live imaging of autophagosome transport, preformed fibril seeding assay, LRRK2 kinase inhibitor rescue experiments, alpha-synuclein aggregation quantification","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic KO with quantitative live-imaging, cargo-degradation, and aggregation readouts; LRRK2 inhibitor epistasis; multiple orthogonal methods in one study","pmids":["42166327"],"is_preprint":false}],"current_model":"PPM1H is a Golgi-localized, metal-dependent serine/threonine phosphatase (PP2C/PPM family) that directly dephosphorylates LRRK2-phosphorylated Rab GTPases (particularly Rab8A and Rab10) via a unique 110-residue flap domain that confers Rab specificity; its Golgi targeting depends on an N-terminal amphipathic helix that also enables membrane curvature-stimulated activity and allosteric regulation by non-phosphorylated Rabs; it additionally dephosphorylates phospho-Smad1/5/8 in the cytoplasm to gate BMP signaling, dephosphorylates p27 at Thr187 to protect it from proteasomal degradation, and dephosphorylates RPS6KB1, with its own activity regulated by hierarchical dual phosphorylation at Ser-123 (PKA) and Ser-210 (CaMKI); loss of PPM1H causes impaired axonal autophagosome transport, alpha-synuclein accumulation, and defective ciliogenesis, positioning it as a key counterbalance to LRRK2 in Parkinson's disease-relevant trafficking pathways."},"narrative":{"mechanistic_narrative":"PPM1H is a metal-dependent serine/threonine phosphatase that serves as the principal cellular counterbalance to LRRK2 kinase signaling by directly dephosphorylating LRRK2-phosphorylated Rab GTPases such as Rab8A at its Switch-II motif [PMID:31663853]. Its specificity for phospho-Rabs is encoded by a unique ~110-residue flap domain adjacent to the active site, since grafting this flap onto the related phosphatase PPM1J confers gain of Rab8A dephosphorylation activity [PMID:34580980]. PPM1H is targeted to the Golgi via an N-terminal amphipathic helix that binds membranes and is stimulated by high curvature, and subcellular localization dictates substrate choice: PPM1H at the mother centriole drives Rab10 dephosphorylation and ciliogenesis [PMID:37889931], and its activity is further tuned by an allosteric site that binds non-phosphorylated Rab8A/Rab10 reaction products to mediate end-product inhibition [PMID:40912655]. Through this LRRK2-Rab axis PPM1H governs membrane trafficking processes: its loss impairs axonal autophagosome transport upstream of ARF6 [PMID:37133994] and, in a LRRK2 kinase-dependent manner, blocks degradation of axonal alpha-synuclein and promotes its aggregation, linking PPM1H to Parkinson's disease-relevant pathways [PMID:42166327]. Independently of Rab signaling, PPM1H dephosphorylates phospho-Smad1/5/8 in the cytoplasm to attenuate BMP signaling [PMID:24732009], stabilizes p27 by removing the Thr187 degradation mark [PMID:22586611], and its activity toward Smad1 requires hierarchical dual phosphorylation at Ser-123 by PKA and Ser-210 by CaMKI [PMID:32600616].","teleology":[{"year":2009,"claim":"Before substrates were known, the basic catalytic identity of PPM1H needed to be established; this defined it as a functional metal-dependent phosphatase with substrate-tunable cation preference.","evidence":"in vitro phosphatase assays against pNPP, casein, and phosphopeptides with Mn2+/Mg2+ substitution","pmids":["19262998"],"confidence":"Medium","gaps":["No physiological substrate identified","Generic substrates do not reveal cellular function"]},{"year":2011,"claim":"The first physiological substrate question was addressed by showing PPM1H dephosphorylates p27 at Thr187, connecting it to cell-cycle control and drug resistance.","evidence":"RNAi screen, site-specific pThr187 analysis, and western blotting in cancer cells","pmids":["22586611"],"confidence":"Medium","gaps":["Single lab","Direct in vitro dephosphorylation of p27 not fully reconstituted","Mechanism of phosphosite recognition unknown"]},{"year":2014,"claim":"A second substrate axis was defined by showing PPM1H binds and dephosphorylates phospho-Smad1/5/8, establishing it as a cytoplasmic brake on BMP signaling.","evidence":"Co-IP with domain mapping, in vitro dephosphorylation, BMP reporter and differentiation assays","pmids":["24732009"],"confidence":"High","gaps":["Structural basis of Smad recognition not resolved","Relationship to Rab substrate specificity unclear"]},{"year":2019,"claim":"The central question of which phosphatase reverses LRRK2 signaling was answered by identifying PPM1H as the direct phospho-Rab phosphatase, and localizing it to the Golgi with a ciliogenesis phenotype.","evidence":"siRNA phosphatase screen, KO/OE in A549 cells, in vitro Rab8A dephosphorylation, D288A substrate-trap, immunofluorescence and ciliogenesis readout","pmids":["31663853"],"confidence":"High","gaps":["Determinant of Rab versus other-substrate specificity not yet defined","Mechanism of Golgi targeting unknown"]},{"year":2020,"claim":"How PPM1H activity itself is regulated was addressed by showing hierarchical dual phosphorylation by PKA (Ser-123) then CaMKI (Ser-210) is required for activity toward Smad1.","evidence":"in vitro kinase assays, phospho-mimetic/non-phosphorylatable mutants, cell-based Smad1 dephosphorylation in Neuro2a","pmids":["32600616"],"confidence":"Medium","gaps":["Whether dual phosphorylation also gates Rab dephosphorylation untested","Structural effect of the modifications unknown"]},{"year":2021,"claim":"The structural basis of Rab specificity was resolved by crystallography revealing a unique flap domain whose transfer to PPM1J confers phospho-Rab activity.","evidence":"X-ray crystallography plus PPM1J+flap domain-swap chimera validated in vitro and in cells","pmids":["34580980"],"confidence":"High","gaps":["Co-structure with a phospho-Rab not captured","How flap reconciles with Smad/p27 substrates unclear"]},{"year":2023,"claim":"How membrane context controls PPM1H was established: an N-terminal amphipathic helix drives curvature-stimulated membrane binding and localization, and localization selects substrates.","evidence":"artificial organelle targeting, liposome-binding and curvature-dependent activity assays, live-cell imaging of Rab phosphorylation","pmids":["37889931"],"confidence":"High","gaps":["In vivo curvature sensing not directly measured","Regulation of helix exposure unknown"]},{"year":2023,"claim":"A new substrate and a transcriptional regulator were added by showing PPM1H dephosphorylates RPS6KB1 and is downregulated by ATF6 in hepatoma cells.","evidence":"Rosetta substrate docking, in vitro dephosphorylation, hepatoma assays, Atf6 knockdown in mice","pmids":["37456776"],"confidence":"Medium","gaps":["Direct dephosphorylation has limited orthogonal validation","Physiological relevance of the RPS6KB1 axis unclear"]},{"year":2023,"claim":"The functional consequence of the LRRK2-Rab axis in neurons was defined by showing PPM1H loss disrupts axonal autophagosome transport upstream of ARF6.","evidence":"iPSC-derived neurons, LRRK2 R1441H knockin, PPM1H KO, live transport imaging, ARF6 overexpression rescue","pmids":["37133994"],"confidence":"High","gaps":["Direct link from phospho-Rab to ARF6 not molecularly resolved","Identity of the relevant Rab in transport unconfirmed"]},{"year":2025,"claim":"An additional regulatory layer was uncovered: an allosteric site binds non-phosphorylated Rab8A/Rab10 products to mediate end-product inhibition, dependent on the amphipathic helix.","evidence":"microscale thermophoresis, in vitro inhibition assays, L66R mutagenesis, sucrose gradient co-flotation with liposomes","pmids":["40912655"],"confidence":"High","gaps":["Structural location of the allosteric site undefined","Physiological set-point of product inhibition in cells untested"]},{"year":2026,"claim":"The disease-relevant endpoint was demonstrated: PPM1H loss impairs alpha-synuclein clearance and promotes aggregation in a LRRK2-kinase-dependent manner, linking phospho-Rab control to proteostasis.","evidence":"PPM1H KO primary neurons, autophagosome transport imaging, preformed fibril seeding, LRRK2 kinase inhibitor rescue","pmids":["42166327"],"confidence":"High","gaps":["In vivo Parkinson's model validation absent","Quantitative contribution relative to other LRRK2 effectors unknown"]},{"year":null,"claim":"How PPM1H integrates its multiple substrate axes (phospho-Rabs, Smad1/5/8, p27, RPS6KB1) and whether a single regulatory logic governs substrate selection across compartments remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of how flap domain, localization, and dual phosphorylation jointly select substrates","No co-crystal structures with non-Rab substrates","In vivo physiological hierarchy of substrates undetermined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,3,4,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[7]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[5,10]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1,5]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[5]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6,11]}],"complexes":[],"partners":["LRRK2","RAB8A","RAB10","SMAD1","P27"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9ULR3","full_name":"Protein phosphatase 1H","aliases":[],"length_aa":514,"mass_kda":56.4,"function":"Dephosphorylates CDKN1B at 'Thr-187', thus removing a signal for proteasomal degradation","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9ULR3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPM1H","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/PPM1H","total_profiled":1310},"omim":[{"mim_id":"620260","title":"TRANSMEMBRANE PROTEIN 132B; TMEM132B","url":"https://www.omim.org/entry/620260"},{"mim_id":"616016","title":"PROTEIN PHOSPHATASE, MAGNESIUM/MANGANESE-DEPENDENT, 1H; PPM1H","url":"https://www.omim.org/entry/616016"},{"mim_id":"609007","title":"LEUCINE-RICH REPEAT KINASE 2; LRRK2","url":"https://www.omim.org/entry/609007"},{"mim_id":"600778","title":"CYCLIN-DEPENDENT KINASE INHIBITOR 1B; CDKN1B","url":"https://www.omim.org/entry/600778"},{"mim_id":"179490","title":"RAS-ASSOCIATED PROTEIN RAB3A; RAB3A","url":"https://www.omim.org/entry/179490"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":34.8},{"tissue":"parathyroid gland","ntpm":39.8}],"url":"https://www.proteinatlas.org/search/PPM1H"},"hgnc":{"alias_symbol":["KIAA1157","FLJ13253","NERPP-2C"],"prev_symbol":["ARHCL1"]},"alphafold":{"accession":"Q9ULR3","domains":[{"cath_id":"3.60.40.10","chopping":"40-104_142-186_235-306_411-511","consensus_level":"high","plddt":95.4851,"start":40,"end":511},{"cath_id":"-","chopping":"311-387","consensus_level":"high","plddt":96.4655,"start":311,"end":387}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULR3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULR3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULR3-F1-predicted_aligned_error_v6.png","plddt_mean":83.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPM1H","jax_strain_url":"https://www.jax.org/strain/search?query=PPM1H"},"sequence":{"accession":"Q9ULR3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULR3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULR3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULR3"}},"corpus_meta":[{"pmid":"31663853","id":"PMC_31663853","title":"PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins.","date":"2019","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/31663853","citation_count":100,"is_preprint":false},{"pmid":"22586611","id":"PMC_22586611","title":"PPM1H is a p27 phosphatase implicated in trastuzumab resistance.","date":"2011","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/22586611","citation_count":41,"is_preprint":false},{"pmid":"24732009","id":"PMC_24732009","title":"Specific control of BMP signaling and mesenchymal differentiation by cytoplasmic phosphatase PPM1H.","date":"2014","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/24732009","citation_count":31,"is_preprint":false},{"pmid":"37133994","id":"PMC_37133994","title":"Regulatory imbalance between LRRK2 kinase, PPM1H phosphatase, and ARF6 GTPase disrupts the axonal transport of autophagosomes.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37133994","citation_count":30,"is_preprint":false},{"pmid":"34580980","id":"PMC_34580980","title":"Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.","date":"2021","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/34580980","citation_count":23,"is_preprint":false},{"pmid":"37889931","id":"PMC_37889931","title":"Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37889931","citation_count":20,"is_preprint":false},{"pmid":"27599670","id":"PMC_27599670","title":"Effect of PPM1H on malignant phenotype of human pancreatic cancer cells.","date":"2016","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/27599670","citation_count":15,"is_preprint":false},{"pmid":"19262998","id":"PMC_19262998","title":"Substrate-dependent metal preference of PPM1H, a cancer-associated protein phosphatase 2C: comparison with other family members.","date":"2009","source":"Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19262998","citation_count":12,"is_preprint":false},{"pmid":"32600616","id":"PMC_32600616","title":"Dual phosphorylation of protein phosphatase PPM1H promotes dephosphorylation of Smad1 in cellulo.","date":"2020","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/32600616","citation_count":9,"is_preprint":false},{"pmid":"37456776","id":"PMC_37456776","title":"PPM1H is down-regulated by ATF6 and dephosphorylates p-RPS6KB1 to inhibit progression of hepatocellular carcinoma.","date":"2023","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/37456776","citation_count":9,"is_preprint":false},{"pmid":"34712356","id":"PMC_34712356","title":"FAM87A as a Competing Endogenous RNA of miR-424-5p Suppresses Glioma Progression by Regulating PPM1H.","date":"2021","source":"Computational and mathematical methods in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34712356","citation_count":7,"is_preprint":false},{"pmid":"22586608","id":"PMC_22586608","title":"On the road to combinations of targeted therapies: PPM1H phosphatase as a suppressor of trastuzumab resistance.","date":"2011","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/22586608","citation_count":4,"is_preprint":false},{"pmid":"40912655","id":"PMC_40912655","title":"Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson's disease.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40912655","citation_count":0,"is_preprint":false},{"pmid":"40463289","id":"PMC_40463289","title":"End-product inhibition of the LRRK2-counteracting PPM1H phosphatase.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40463289","citation_count":0,"is_preprint":false},{"pmid":"42166327","id":"PMC_42166327","title":"Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.","date":"2026","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/42166327","citation_count":0,"is_preprint":false},{"pmid":"37811266","id":"PMC_37811266","title":"Retracted: FAM87A as a Competing Endogenous RNA of miR-424-5p Suppresses Glioma Progression by Regulating PPM1H.","date":"2023","source":"Computational and mathematical methods in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37811266","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.17.676758","title":"Proteomic and Kinetic Characterization of Prion Seeding in Distinct Human CJD Strains Unveils Early Diagnostic Biomarkers","date":"2025-09-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.17.676758","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.19.644182","title":"PPM1M, a LRRK2-counteracting, phosphoRab12-preferring phosphatase with potential link to Parkinson’s disease","date":"2025-03-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.19.644182","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10830,"output_tokens":3636,"usd":0.043515,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11166,"output_tokens":3686,"usd":0.07399,"stage2_stop_reason":"end_turn"},"total_usd":0.117505,"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\": 2019,\n      \"finding\": \"PPM1H directly dephosphorylates LRRK2-phosphorylated Rab GTPases (e.g., Rab8A at its Switch-II motif phosphorylation site). siRNA screen identified PPM1H as the phosphatase counteracting LRRK2 signaling; PPM1H knockout increased endogenous Rab phosphorylation; overexpression suppressed LRRK2-mediated Rab phosphorylation; a substrate-trapping mutant (Asp288Ala) bound with high affinity to LRRK2-phosphorylated Rab proteins, blocking dephosphorylation.\",\n      \"method\": \"siRNA screen of all human phosphatases, PPM1H knockout in A549 cells, overexpression assays, in vitro biochemical dephosphorylation of Rab8A, substrate-trapping mutagenesis (D288A)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution, mutagenesis (active-site trap), KO and OE cellular assays, multiple orthogonal methods in one study\",\n      \"pmids\": [\"31663853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PPM1H is localized to the Golgi, and its knockdown suppresses primary cilia formation, phenocopying pathogenic LRRK2.\",\n      \"method\": \"Immunofluorescence localization, siRNA knockdown with ciliogenesis readout\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization experiment with functional ciliogenesis consequence, single lab, two orthogonal methods\",\n      \"pmids\": [\"31663853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"PPM1H dephosphorylates p27 at threonine 187, removing a signal for proteasomal degradation and stabilizing p27 protein levels. Knockdown of PPM1H reduces p27 protein levels and confers trastuzumab resistance.\",\n      \"method\": \"RNA interference screening, site-specific phosphorylation analysis (pThr187 of p27), western blotting\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — specific phosphosite-directed dephosphorylation demonstrated, RNAi functional phenotype, single lab\",\n      \"pmids\": [\"22586611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PPM1H directly interacts with Smad1/5/8 through its Smad-binding domain and dephosphorylates phospho-Smad1/5/8 in the cytoplasm, preventing nuclear translocation and attenuating BMP signaling. Loss of PPM1H enhances BMP-dependent gene regulation and mesenchymal differentiation.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, in vitro dephosphorylation assay, ectopic expression and loss-of-function studies, BMP reporter assays, mesenchymal differentiation assays\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — direct binding (Co-IP with domain mapping), in vitro dephosphorylation, multiple functional readouts, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"24732009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal structure of PPM1H reveals a conserved phosphatase fold with a unique 110-residue flap domain adjacent to the active site that encodes the docking motif for phosphorylated Rab GTPases. The flap domain distantly resembles tudor domains. A PPM1J chimera carrying the PPM1H flap domain gains ability to dephosphorylate pThr72 of Rab8a both in vitro and in cellular assays, confirming the flap domain as the determinant of Rab specificity.\",\n      \"method\": \"X-ray crystallography, domain-swap chimera (PPM1J + PPM1H flap), in vitro dephosphorylation assay, cellular dephosphorylation assay, crosslinking, 3D modelling\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional domain-swap chimera validated in vitro and in cells, multiple orthogonal methods\",\n      \"pmids\": [\"34580980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPM1H relies on an N-terminal amphipathic helix for Golgi localization. The amphipathic helix enables PPM1H to bind liposomes in vitro, and small, highly curved liposomes stimulate PPM1H activity. Localization drives substrate selection: PPM1H at the mother centriole is required for Rab10 dephosphorylation and ciliogenesis regulation, while poor colocalization of Rab12 explains why it is a poor PPM1H substrate in cells but not in vitro.\",\n      \"method\": \"Artificial targeting to Golgi, mitochondria, or mother centriole, liposome-binding assay, in vitro phosphatase activity assay with liposomes of varying curvature, live-cell imaging, Rab phosphorylation readouts\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution (liposome binding/activation), multiple artificial targeting experiments with defined functional readouts, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37889931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LRRK2-hyperphosphorylated RABs disrupt axonal autophagosome transport by perturbing coordinated regulation of dynein and kinesin. PPM1H knockout phenocopies hyperactive LRRK2 in iPSC-derived neurons, causing frequent directional reversals and pauses in autophagosome transport. Overexpression of ARF6 (a GTPase switch for dynein/kinesin) attenuates transport defects in both LRRK2-p.R1441H knockin and PPM1H KO neurons, placing PPM1H upstream of ARF6 in this pathway.\",\n      \"method\": \"iPSC-derived human neurons, LRRK2 knockin (R1441H), PPM1H knockout, live imaging of autophagosome transport, ARF6 overexpression rescue experiments\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in human iPSC-derived neurons with quantitative live-imaging readout, KO phenocopy and rescue by ARF6, multiple orthogonal methods\",\n      \"pmids\": [\"37133994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PPM1H possesses phosphatase activity toward pNPP, casein, and phosphopeptides and shows substrate-dependent metal preference: Mn²⁺ is preferred with pNPP or phosphopeptide substrates, while Mg²⁺ is preferred with casein. When both cations are added, Mn²⁺ dominates due to greater affinity for PPM1H.\",\n      \"method\": \"In vitro phosphatase activity assays with pNPP, casein, and phosphopeptides; metal ion substitution experiments\",\n      \"journal\": \"Biometals\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical assay with multiple substrates, single lab, single study\",\n      \"pmids\": [\"19262998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PPM1H is phosphorylated by PKA at Ser-123 and by CaMKI at Ser-210. A hierarchical phosphorylation occurs in neuronal cells whereby initial Ser-123 phosphorylation promotes subsequent Ser-210 phosphorylation. The S123A/S210A double mutant of PPM1H fails to dephosphorylate Smad1 in cell-based assays, establishing that dual phosphorylation at these sites is required for PPM1H activity toward Smad1.\",\n      \"method\": \"In vitro kinase assays, in silico site prediction, phospho-mimetic and non-phosphorylatable PPM1H mutants, cell-based Smad1 dephosphorylation assay in Neuro2a cells, kinase activator/inhibitor treatments\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro kinase assays plus mutagenesis with cellular functional readout, single lab, two orthogonal methods\",\n      \"pmids\": [\"32600616\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPM1H directly dephosphorylates p-RPS6KB1 (ribosomal protein S6 kinase B1, a component of the BMP/TGF-β pathway). ATF6 transcriptionally downregulates PPM1H expression in hepatoma cells.\",\n      \"method\": \"Homology modeling/Rosetta substrate docking screen, in vitro dephosphorylation assay, hepatoma cell-based assays, Atf6 knockdown in mice, western blotting\",\n      \"journal\": \"Molecular therapy. Nucleic acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — in vitro dephosphorylation of RPS6KB1 supported by structural modeling, single lab, limited orthogonal validation of the direct dephosphorylation\",\n      \"pmids\": [\"37456776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPM1H contains an allosteric binding site for its non-phosphorylated reaction products Rab8A and Rab10. Microscale thermophoresis showed that thiophosphorylated Rab8A binds the active site with KD ~1 µM, while non-phosphorylated Rab8A and Rab10 bind an alternative (allosteric) site at similar affinity; this interaction is not observed for Rab12. Non-phosphorylated Rab8A or Rab10 inhibit PPM1H phosphatase activity (product/end-product inhibition). Rab binding to the allosteric site also requires PPM1H's N-terminal amphipathic helix; removing it decreases affinity ~6-fold. Sucrose gradient co-flotation of non-phosphorylated Rabs with liposome-bound PPM1H provided independent confirmation.\",\n      \"method\": \"Microscale thermophoresis (binding affinity measurement), in vitro phosphatase activity inhibition assays, L66R mutagenesis, sucrose gradient co-flotation with liposomes\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — quantitative binding assay (MST), in vitro functional inhibition, mutagenesis, and orthogonal co-flotation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40912655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PPM1H knockout in primary neurons causes gene-dose-dependent disruption of axonal autophagosome transport, impaired degradation of axonal alpha-synuclein, and increased alpha-synuclein aggregation upon exposure to preformed fibrils. The aggregation phenotype is dependent on LRRK2 kinase activity, mechanistically linking PPM1H-controlled RAB dephosphorylation to autophagosomal cargo clearance.\",\n      \"method\": \"PPM1H knockout primary neurons, live imaging of autophagosome transport, preformed fibril seeding assay, LRRK2 kinase inhibitor rescue experiments, alpha-synuclein aggregation quantification\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with quantitative live-imaging, cargo-degradation, and aggregation readouts; LRRK2 inhibitor epistasis; multiple orthogonal methods in one study\",\n      \"pmids\": [\"42166327\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPM1H is a Golgi-localized, metal-dependent serine/threonine phosphatase (PP2C/PPM family) that directly dephosphorylates LRRK2-phosphorylated Rab GTPases (particularly Rab8A and Rab10) via a unique 110-residue flap domain that confers Rab specificity; its Golgi targeting depends on an N-terminal amphipathic helix that also enables membrane curvature-stimulated activity and allosteric regulation by non-phosphorylated Rabs; it additionally dephosphorylates phospho-Smad1/5/8 in the cytoplasm to gate BMP signaling, dephosphorylates p27 at Thr187 to protect it from proteasomal degradation, and dephosphorylates RPS6KB1, with its own activity regulated by hierarchical dual phosphorylation at Ser-123 (PKA) and Ser-210 (CaMKI); loss of PPM1H causes impaired axonal autophagosome transport, alpha-synuclein accumulation, and defective ciliogenesis, positioning it as a key counterbalance to LRRK2 in Parkinson's disease-relevant trafficking pathways.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPM1H is a metal-dependent serine/threonine phosphatase that serves as the principal cellular counterbalance to LRRK2 kinase signaling by directly dephosphorylating LRRK2-phosphorylated Rab GTPases such as Rab8A at its Switch-II motif [#0]. Its specificity for phospho-Rabs is encoded by a unique ~110-residue flap domain adjacent to the active site, since grafting this flap onto the related phosphatase PPM1J confers gain of Rab8A dephosphorylation activity [#4]. PPM1H is targeted to the Golgi via an N-terminal amphipathic helix that binds membranes and is stimulated by high curvature, and subcellular localization dictates substrate choice: PPM1H at the mother centriole drives Rab10 dephosphorylation and ciliogenesis [#5], and its activity is further tuned by an allosteric site that binds non-phosphorylated Rab8A/Rab10 reaction products to mediate end-product inhibition [#10]. Through this LRRK2-Rab axis PPM1H governs membrane trafficking processes: its loss impairs axonal autophagosome transport upstream of ARF6 [#6] and, in a LRRK2 kinase-dependent manner, blocks degradation of axonal alpha-synuclein and promotes its aggregation, linking PPM1H to Parkinson's disease-relevant pathways [#11]. Independently of Rab signaling, PPM1H dephosphorylates phospho-Smad1/5/8 in the cytoplasm to attenuate BMP signaling [#3], stabilizes p27 by removing the Thr187 degradation mark [#2], and its activity toward Smad1 requires hierarchical dual phosphorylation at Ser-123 by PKA and Ser-210 by CaMKI [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Before substrates were known, the basic catalytic identity of PPM1H needed to be established; this defined it as a functional metal-dependent phosphatase with substrate-tunable cation preference.\",\n      \"evidence\": \"in vitro phosphatase assays against pNPP, casein, and phosphopeptides with Mn2+/Mg2+ substitution\",\n      \"pmids\": [\"19262998\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No physiological substrate identified\", \"Generic substrates do not reveal cellular function\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The first physiological substrate question was addressed by showing PPM1H dephosphorylates p27 at Thr187, connecting it to cell-cycle control and drug resistance.\",\n      \"evidence\": \"RNAi screen, site-specific pThr187 analysis, and western blotting in cancer cells\",\n      \"pmids\": [\"22586611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Direct in vitro dephosphorylation of p27 not fully reconstituted\", \"Mechanism of phosphosite recognition unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"A second substrate axis was defined by showing PPM1H binds and dephosphorylates phospho-Smad1/5/8, establishing it as a cytoplasmic brake on BMP signaling.\",\n      \"evidence\": \"Co-IP with domain mapping, in vitro dephosphorylation, BMP reporter and differentiation assays\",\n      \"pmids\": [\"24732009\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of Smad recognition not resolved\", \"Relationship to Rab substrate specificity unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The central question of which phosphatase reverses LRRK2 signaling was answered by identifying PPM1H as the direct phospho-Rab phosphatase, and localizing it to the Golgi with a ciliogenesis phenotype.\",\n      \"evidence\": \"siRNA phosphatase screen, KO/OE in A549 cells, in vitro Rab8A dephosphorylation, D288A substrate-trap, immunofluorescence and ciliogenesis readout\",\n      \"pmids\": [\"31663853\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinant of Rab versus other-substrate specificity not yet defined\", \"Mechanism of Golgi targeting unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"How PPM1H activity itself is regulated was addressed by showing hierarchical dual phosphorylation by PKA (Ser-123) then CaMKI (Ser-210) is required for activity toward Smad1.\",\n      \"evidence\": \"in vitro kinase assays, phospho-mimetic/non-phosphorylatable mutants, cell-based Smad1 dephosphorylation in Neuro2a\",\n      \"pmids\": [\"32600616\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether dual phosphorylation also gates Rab dephosphorylation untested\", \"Structural effect of the modifications unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The structural basis of Rab specificity was resolved by crystallography revealing a unique flap domain whose transfer to PPM1J confers phospho-Rab activity.\",\n      \"evidence\": \"X-ray crystallography plus PPM1J+flap domain-swap chimera validated in vitro and in cells\",\n      \"pmids\": [\"34580980\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Co-structure with a phospho-Rab not captured\", \"How flap reconciles with Smad/p27 substrates unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"How membrane context controls PPM1H was established: an N-terminal amphipathic helix drives curvature-stimulated membrane binding and localization, and localization selects substrates.\",\n      \"evidence\": \"artificial organelle targeting, liposome-binding and curvature-dependent activity assays, live-cell imaging of Rab phosphorylation\",\n      \"pmids\": [\"37889931\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo curvature sensing not directly measured\", \"Regulation of helix exposure unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"A new substrate and a transcriptional regulator were added by showing PPM1H dephosphorylates RPS6KB1 and is downregulated by ATF6 in hepatoma cells.\",\n      \"evidence\": \"Rosetta substrate docking, in vitro dephosphorylation, hepatoma assays, Atf6 knockdown in mice\",\n      \"pmids\": [\"37456776\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct dephosphorylation has limited orthogonal validation\", \"Physiological relevance of the RPS6KB1 axis unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The functional consequence of the LRRK2-Rab axis in neurons was defined by showing PPM1H loss disrupts axonal autophagosome transport upstream of ARF6.\",\n      \"evidence\": \"iPSC-derived neurons, LRRK2 R1441H knockin, PPM1H KO, live transport imaging, ARF6 overexpression rescue\",\n      \"pmids\": [\"37133994\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct link from phospho-Rab to ARF6 not molecularly resolved\", \"Identity of the relevant Rab in transport unconfirmed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"An additional regulatory layer was uncovered: an allosteric site binds non-phosphorylated Rab8A/Rab10 products to mediate end-product inhibition, dependent on the amphipathic helix.\",\n      \"evidence\": \"microscale thermophoresis, in vitro inhibition assays, L66R mutagenesis, sucrose gradient co-flotation with liposomes\",\n      \"pmids\": [\"40912655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural location of the allosteric site undefined\", \"Physiological set-point of product inhibition in cells untested\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The disease-relevant endpoint was demonstrated: PPM1H loss impairs alpha-synuclein clearance and promotes aggregation in a LRRK2-kinase-dependent manner, linking phospho-Rab control to proteostasis.\",\n      \"evidence\": \"PPM1H KO primary neurons, autophagosome transport imaging, preformed fibril seeding, LRRK2 kinase inhibitor rescue\",\n      \"pmids\": [\"42166327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo Parkinson's model validation absent\", \"Quantitative contribution relative to other LRRK2 effectors unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PPM1H integrates its multiple substrate axes (phospho-Rabs, Smad1/5/8, p27, RPS6KB1) and whether a single regulatory logic governs substrate selection across compartments remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of how flap domain, localization, and dual phosphorylation jointly select substrates\", \"No co-crystal structures with non-Rab substrates\", \"In vivo physiological hierarchy of substrates undetermined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 3, 4, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [5, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"LRRK2\", \"RAB8A\", \"RAB10\", \"SMAD1\", \"p27\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}