Affinage

PPM1H

Protein phosphatase 1H · UniProt Q9ULR3

Length
514 aa
Mass
56.4 kDa
Annotated
2026-04-28
15 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PPM1H is a metal-dependent PP2C family serine/threonine phosphatase that functions as a key antagonist of LRRK2 kinase signaling by specifically dephosphorylating LRRK2-phosphorylated Rab GTPases at their Switch-II motif, thereby regulating ciliogenesis and axonal autophagosome transport (PMID:31663853, PMID:37133994). Substrate specificity toward Rab proteins is encoded by a unique 110-residue flap domain adjacent to the active site; transplanting this domain into the related phosphatase PPM1J confers Rab-dephosphorylating activity (PMID:34580980). PPM1H localizes to the Golgi through an N-terminal amphipathic helix that also mediates allosteric product inhibition by non-phosphorylated Rab8A/Rab10, coupling membrane association to feedback regulation of catalytic output (PMID:37889931, PMID:40912655). Beyond Rab GTPases, PPM1H dephosphorylates cytoplasmic phospho-Smad1/5/8 to attenuate BMP signaling and p27-pThr187 to stabilize the cell-cycle inhibitor p27, with its activity toward Smad1 requiring hierarchical phosphorylation by PKA (Ser-123) and CaMKI (Ser-210) (PMID:24732009, PMID:22586611, PMID:32600616).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2009 Medium

    Establishing that PPM1H is a catalytically active PP2C phosphatase with metal-dependent activity answered the basic question of whether this gene product possesses intrinsic enzymatic function.

    Evidence In vitro phosphatase activity assays with defined substrates and varying metal cations

    PMID:19262998

    Open questions at the time
    • No physiological substrates identified
    • Metal preference in a cellular context unknown
    • No structural information available
  2. 2011 Medium

    Identifying p27-pThr187 as a cellular substrate demonstrated that PPM1H stabilizes the CDK inhibitor p27 and can influence drug resistance in cancer cells, establishing a first physiological role.

    Evidence RNAi screen and western blotting for p27-pThr187 in HER2-positive breast cancer cells

    PMID:22586611

    Open questions at the time
    • Direct in vitro dephosphorylation of p27-pThr187 not shown
    • Mechanism of PPM1H recruitment to p27 not defined
    • Relevance beyond HER2-positive cell lines not tested
  3. 2014 High

    Showing that PPM1H directly dephosphorylates Smad1/5/8 in the cytoplasm to prevent their nuclear accumulation established PPM1H as a gatekeeper of BMP signaling and mesenchymal differentiation.

    Evidence Co-immunoprecipitation, in vitro dephosphorylation, domain mapping, and gain/loss-of-function experiments

    PMID:24732009

    Open questions at the time
    • How PPM1H discriminates Smad1/5/8 from other Smads structurally unknown
    • Relationship between Smad and Rab substrates in cells not explored
    • Regulation of PPM1H's Smad-directed activity not defined
  4. 2019 High

    A systematic screen identified PPM1H as the phosphatase that counteracts LRRK2 by dephosphorylating Rab GTPases at their Switch-II motif, resolving the long-standing question of which phosphatase opposes LRRK2 signaling and connecting PPM1H to Parkinson's disease-relevant pathways.

    Evidence siRNA screen, KO/overexpression in A549 cells, in vitro dephosphorylation of Rab8A, substrate-trapping mutant D288A, fluorescence localization to Golgi

    PMID:31663853

    Open questions at the time
    • Structural basis of Rab recognition unknown
    • How Golgi localization is achieved molecularly not defined
    • Whether all LRRK2-phosphorylated Rabs are equally good substrates unclear
  5. 2020 Medium

    Demonstrating that PKA phosphorylation at Ser-123 and CaMKI phosphorylation at Ser-210 are required for PPM1H activity toward Smad1 revealed a hierarchical regulatory mechanism coupling upstream kinase signaling to PPM1H function.

    Evidence In vitro kinase assays, phospho-site mutagenesis, cell-based Smad1 dephosphorylation in neuron-like cells

    PMID:32600616

    Open questions at the time
    • Whether PKA/CaMKI phosphorylation also regulates Rab dephosphorylation not tested
    • Structural mechanism by which phosphorylation activates PPM1H unknown
    • Single lab, awaits independent confirmation
  6. 2021 High

    Solving the crystal structure of PPM1H and identifying the unique 110-residue flap domain as the molecular determinant of Rab substrate selectivity explained why PPM1H, but not related PP2C phosphatases, dephosphorylates Rab proteins.

    Evidence X-ray crystallography, chimeric flap-swap between PPM1H and PPM1J, in vitro and cellular dephosphorylation assays

    PMID:34580980

    Open questions at the time
    • No co-crystal structure of PPM1H–phosphoRab complex
    • Whether the flap domain contributes to Smad or p27 recognition unknown
    • Catalytic mechanism at atomic resolution not fully resolved
  7. 2023 High

    Demonstrating that PPM1H's cellular substrate selectivity is governed by colocalization—requiring its N-terminal amphipathic helix for Golgi targeting and proximity to the mother centriole for Rab10 dephosphorylation—resolved why in vitro substrates like Rab12 are poor cellular substrates.

    Evidence Artificial anchoring constructs, liposome binding and activity assays, live imaging, cellular Rab phosphorylation measurements

    PMID:37889931

    Open questions at the time
    • Whether membrane curvature sensing is physiologically relevant in vivo not established
    • How PPM1H accesses the mother centriole from the Golgi unclear
    • Quantitative contribution of localization vs. intrinsic selectivity not separated
  8. 2023 High

    Showing that PPM1H knockout phenocopies LRRK2-hyperactive mutations in disrupting axonal autophagosome transport placed PPM1H in a functional LRRK2/Rab/ARF6 axis controlling motor coordination in human neurons.

    Evidence iPSC-derived neuron knockouts and knockins, live autophagosome transport imaging, genetic epistasis with ARF6

    PMID:37133994

    Open questions at the time
    • Which specific phosphoRab(s) mediate the transport defect not determined
    • Whether PPM1H loss contributes to Parkinson's disease in vivo not tested
    • Mechanism by which ARF6 rescues transport downstream of Rab phosphorylation unknown
  9. 2025 High

    Identifying an allosteric binding site where non-phosphorylated Rab8A/Rab10 inhibit PPM1H activity revealed a product-inhibition feedback mechanism dependent on the membrane-targeting amphipathic helix, providing a new layer of catalytic regulation.

    Evidence Microscale thermophoresis, in vitro phosphatase inhibition, L66R mutagenesis, sucrose gradient co-flotation with liposomes

    PMID:40912655

    Open questions at the time
    • Structural basis of the allosteric site not determined
    • Physiological significance of product inhibition in cells or neurons not tested
    • Whether allosteric regulation extends to non-Rab substrates unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include whether PPM1H dysfunction contributes to Parkinson's disease pathogenesis in vivo, the structural basis of the allosteric Rab-binding site, and how PPM1H coordinates its multiple substrates (Rabs, Smads, p27) in different cell types.
  • No in vivo animal model of PPM1H loss-of-function published
  • No co-crystal structure with any physiological substrate
  • Integration of PKA/CaMKI regulation with Rab dephosphorylation not tested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 7
Localization
GO:0005794 Golgi apparatus 2 GO:0005815 microtubule organizing center 1 GO:0005829 cytosol 1
Pathway
R-HSA-162582 Signal Transduction 4 R-HSA-1852241 Organelle biogenesis and maintenance 2 R-HSA-1640170 Cell Cycle 1 R-HSA-9612973 Autophagy 1
Partners
ARF6CDKN1BLRRK2RAB10RAB8ASMAD1

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2019 PPM1H is a Rab GTPase phosphatase that counteracts LRRK2 signaling by specifically dephosphorylating LRRK2-phosphorylated Rab proteins within their Switch-II motif. PPM1H knockout increased endogenous Rab phosphorylation, overexpression suppressed LRRK2-mediated Rab phosphorylation, and PPM1H directly dephosphorylated Rab8A in biochemical assays. A substrate-trapping mutant (Asp288Ala) binds endogenous LRRK2-phosphorylated Rabs with high affinity. PPM1H localizes to the Golgi, and its knockdown suppresses primary cilia formation. siRNA screen, KO/overexpression in human A549 cells, in vitro phosphatase assay, substrate-trapping mutagenesis, fluorescence localization eLife High 31663853
2011 PPM1H dephosphorylates p27 at threonine 187, thereby removing a proteasomal degradation signal and stabilizing p27 protein levels. RNAi knockdown of PPM1H reduces p27 protein and confers trastuzumab resistance in HER2-positive cancer cells. RNA interference screen, western blotting for p27-pThr187, cell-based trastuzumab resistance assay Cancer discovery Medium 22586611
2014 PPM1H is a cytoplasm-localized Smad1/5/8-specific phosphatase that directly interacts with Smad1/5/8 through a Smad-binding domain, dephosphorylates phospho-Smad1/5/8 in the cytoplasm, and thereby gates BMP signaling and mesenchymal differentiation by preventing nuclear accumulation of P-Smad1/5/8. Co-immunoprecipitation, in vitro dephosphorylation assay, ectopic expression and loss-of-function, nuclear/cytoplasmic fractionation, domain mapping Cell research High 24732009
2009 PPM1H is a catalytically active PP2C family phosphatase that dephosphorylates pNPP, casein, and phosphopeptides in a metal cation-dependent manner; it shows substrate-dependent metal preference, preferring Mn2+ for pNPP and phosphopeptides and Mg2+ for casein, with Mn2+ having greater affinity for PPM1H than Mg2+. In vitro phosphatase activity assays with defined substrates and metal cations Biometals Medium 19262998
2021 Crystal structure of PPM1H reveals a conserved phosphatase fold containing a unique 110-residue 'flap domain' adjacent to the active site that distantly resembles tudor domains. The flap domain encodes a Rab-specific docking motif: transplanting the PPM1H flap domain into PPM1J (which lacks Rab activity) confers dephosphorylation of pThr72-Rab8A both in vitro and in cells, establishing the flap domain as the molecular determinant of Rab substrate specificity. X-ray crystallography, chimeric phosphatase construction, in vitro dephosphorylation assay, cellular assays, crosslinking and 3D modelling EMBO reports High 34580980
2020 PPM1H is directly phosphorylated by PKA at Ser-123 and by CaMKI at Ser-210. A hierarchical dual phosphorylation occurs in neuron-like cells where phosphorylation at Ser-123 promotes subsequent phosphorylation at Ser-210. The double phosphorylation-null mutant (S123A/S210A) fails to dephosphorylate endogenous Smad1, indicating that these phosphorylation events are required for PPM1H phosphatase activity toward Smad1 in cellulo. In vitro kinase assay, in silico site prediction, phospho-site mutagenesis, cell-based Smad1 dephosphorylation assay, kinase activator/inhibitor treatments Biochemical and biophysical research communications Medium 32600616
2023 PPM1H localizes to the Golgi via an N-terminal amphipathic helix that enables membrane binding. PPM1H's substrate selectivity in cells is driven by colocalization: Rab10 dephosphorylation requires PPM1H access at or near the mother centriole, while poor colocalization with Rab12 explains why Rab12 is a poor cellular substrate despite being dephosphorylated efficiently in vitro. Small, highly curved liposomes stimulate PPM1H activity in vitro. Live imaging with artificial Golgi/mitochondria/centriole anchoring constructs, liposome binding assay, in vitro phosphatase assay with liposomes, cellular Rab phosphorylation measurements Proceedings of the National Academy of Sciences of the United States of America High 37889931
2023 LRRK2 hyperphosphorylated Rab GTPases disrupt axonal autophagosome transport by perturbing the coordinated regulation of dynein and kinesin; PPM1H knockout phenocopies the transport defect of hyperactive LRRK2 in iPSC-derived neurons, and overexpression of ARF6 GTPase rescues transport in both PPM1H KO and LRRK2 p.R1441H knockin neurons, placing PPM1H in a regulatory axis with LRRK2/Rab/ARF6 that controls motor coordination. iPSC-derived neuron knockin/knockout, live imaging of autophagosome transport, genetic epistasis with ARF6 overexpression Cell reports High 37133994
2023 PPM1H can directly dephosphorylate phospho-RPS6KB1 (p70 S6 kinase) in the BMP/TGF-β pathway, identified by homology-based substrate screening and confirmed by direct dephosphorylation assay. Rosetta-based substrate prediction, 3D homology modelling, direct in vitro dephosphorylation assay, cell-based assay Molecular therapy. Nucleic acids Medium 37456776
2025 PPM1H contains an allosteric binding site for its non-phosphorylated reaction products Rab8A and Rab10 (KD ~1 μM), distinct from the active site where thiophosphorylated Rab8A binds. Non-phosphorylated Rab8A or Rab10 inhibit PPM1H phosphatase activity, and this inhibition and binding require the N-terminal amphipathic helix (PPM1H L66R mutant abrogates the effect). Rab12 does not bind the allosteric site. Co-flotation with liposomes confirmed non-phosphorylated Rab binding to membrane-associated PPM1H. Microscale thermophoresis, in vitro phosphatase inhibition assay, site-directed mutagenesis (L66R), sucrose gradient co-flotation The Journal of biological chemistry High 40912655

Source papers

Stage 0 corpus · 15 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2019 PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins. eLife 99 31663853
2011 PPM1H is a p27 phosphatase implicated in trastuzumab resistance. Cancer discovery 41 22586611
2014 Specific control of BMP signaling and mesenchymal differentiation by cytoplasmic phosphatase PPM1H. Cell research 31 24732009
2023 Regulatory imbalance between LRRK2 kinase, PPM1H phosphatase, and ARF6 GTPase disrupts the axonal transport of autophagosomes. Cell reports 29 37133994
2021 Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. EMBO reports 23 34580980
2023 Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis. Proceedings of the National Academy of Sciences of the United States of America 20 37889931
2016 Effect of PPM1H on malignant phenotype of human pancreatic cancer cells. Oncology reports 15 27599670
2009 Substrate-dependent metal preference of PPM1H, a cancer-associated protein phosphatase 2C: comparison with other family members. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 12 19262998
2023 PPM1H is down-regulated by ATF6 and dephosphorylates p-RPS6KB1 to inhibit progression of hepatocellular carcinoma. Molecular therapy. Nucleic acids 9 37456776
2020 Dual phosphorylation of protein phosphatase PPM1H promotes dephosphorylation of Smad1 in cellulo. Biochemical and biophysical research communications 9 32600616
2021 FAM87A as a Competing Endogenous RNA of miR-424-5p Suppresses Glioma Progression by Regulating PPM1H. Computational and mathematical methods in medicine 7 34712356
2011 On the road to combinations of targeted therapies: PPM1H phosphatase as a suppressor of trastuzumab resistance. Cancer discovery 4 22586608
2025 End-product inhibition of the LRRK2-counteracting PPM1H phosphatase. bioRxiv : the preprint server for biology 0 40463289
2025 Allosteric regulation of the Golgi-localized PPM1H phosphatase by Rab GTPases modulates LRRK2 substrate dephosphorylation in Parkinson's disease. The Journal of biological chemistry 0 40912655
2023 Retracted: FAM87A as a Competing Endogenous RNA of miR-424-5p Suppresses Glioma Progression by Regulating PPM1H. Computational and mathematical methods in medicine 0 37811266