Affinage

PPM1E

Protein phosphatase 1E · UniProt Q8WY54

Length
755 aa
Mass
84.0 kDa
Annotated
2026-06-10
18 papers in source corpus 8 papers cited in narrative 8 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PPM1E (CaMKP-N/POPX1) is a metal-dependent PPM-family Ser/Thr phosphatase that turns off Ca2+/calmodulin- and stress-responsive kinase signaling (PMID:11726284, PMID:11864573). It dephosphorylates and inactivates members of the CaMK cascade, including nuclear CaMKIV and autophosphorylated CaMKII (PMID:11726284, PMID:23991411), and acts as an in-cellulo AMPKα phosphatase, with its knockdown elevating AMPKα-Thr172 phosphorylation (PMID:20801214). In parallel, PPM1E is recruited through the exchange factor PIX to dephosphorylate and inactivate PAK, thereby suppressing Cdc42/Rac-driven actin stress-fiber remodeling (PMID:11864573). The enzyme requires Mn2+/Mg2+ for catalysis, prefers phospho-Thr substrates, and is targeted to the nucleus by two independent C-terminal NLS elements (PMID:11726284, PMID:23991411, PMID:15496589). Its catalytic output is tightly regulated: CaMKI-mediated phosphorylation at Ser-480 stimulates activity (PMID:22627141), ubiquitin-proteasome-dependent C-terminal truncation markedly activates the enzyme while relocating it from nucleus to cytosol and shifting substrate targeting (PMID:22100705, PMID:23991411), and oxidation by H2O2 reversibly inactivates it (PMID:23991411). Evans Blue and Chicago Sky Blue 6B inhibit PPM1E in vitro and in cells (PMID:17897624).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2001 High

    Established PPM1E as a nuclear Mn2+-dependent phosphatase acting on the CaMK cascade, defining its substrate class and compartment.

    Evidence recombinant protein, in vitro phosphatase assay with CaMKIV, transfection localization in COS-7 cells

    PMID:11726284

    Open questions at the time
    • Direct dephosphorylation of nuclear CaMKII inferred from localization rather than measured
    • Physiological substrate selectivity in vivo not established
  2. 2002 High

    Showed PPM1E acts beyond the CaMK cascade by binding PIX and inactivating PAK, linking it to Cdc42/Rac actin-cytoskeleton control.

    Evidence Co-IP of PIX, in vitro phosphatase assay, cell-based PAK/Cdc42(V12) activity and actin readouts

    PMID:11864573

    Open questions at the time
    • PAK residues dephosphorylated not mapped
    • How nuclear localization reconciles with cytoskeletal/PAK function unresolved
  3. 2004 Medium

    Defined the nuclear-targeting determinants, showing two independent C-terminal NLS elements drive nuclear localization.

    Evidence deletion/point mutagenesis of NLS basic residues with fluorescence localization

    PMID:15496589

    Open questions at the time
    • Import receptors mediating NLS recognition unidentified
    • Single-lab characterization
  4. 2007 Medium

    Identified small-molecule inhibitors and the minimal pharmacophore, providing chemical tools and demonstrating in-cell inhibition.

    Evidence in vitro phosphatase inhibition assays and Neuro2a cell dephosphorylation assays

    PMID:17897624

    Open questions at the time
    • Inhibitor selectivity across PPM-family phosphatases unknown
    • No structural basis of inhibition
  5. 2010 High

    Connected PPM1E to energy-sensing signaling by identifying it as an in-cellulo AMPKα-Thr172 phosphatase responsive to biguanides.

    Evidence stable shRNA knockdown, phospho-AMPKα western blot, AMPK Co-IP, phosphatase activity assay in HEK293

    PMID:20801214

    Open questions at the time
    • AMPK-PPM1E interaction was weak
    • Mechanism by which phenformin lowers PPM1E activity not defined
  6. 2011 Medium

    Revealed proteasome-dependent C-terminal processing as a regulatory switch that relocalizes PPM1E, retargets substrates, and activates catalysis.

    Evidence proteasome inhibitors, subcellular fractionation, substrate phosphorylation assays in Neuro2a and brain (zebrafish ortholog)

    PMID:22100705

    Open questions at the time
    • Protease/E3 machinery and cleavage site not identified in human enzyme
    • Demonstrated in zebrafish ortholog
  7. 2012 High

    Identified CaMKI phosphorylation at Ser-480 as an activating post-translational modification, establishing feedback regulation within the CaMK network.

    Evidence in vitro phosphorylation with CaMKI, S480A/D/E mutagenesis, phosphatase and cellular CaMKII autophosphorylation assays (zebrafish ortholog)

    PMID:22627141

    Open questions at the time
    • Mechanism by which Ser-480 phosphorylation enhances activity unknown
    • Validation in human PPM1E pending
  8. 2013 Medium

    Characterized the activated truncated human enzyme biochemically, defining metal/substrate preferences, PSD binding, and reversible redox inactivation.

    Evidence cell-free expressed PPM1E(1-559), phosphopeptide and CaMKII dephosphorylation assays, PSD binding, H2O2/DTT redox treatment

    PMID:23991411

    Open questions at the time
    • Oxidized residue(s) mediating redox control not mapped
    • Single-lab in vitro reconstitution

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the distinct regulatory inputs (Ser-480 phosphorylation, proteasomal truncation, oxidation, localization) are integrated to govern substrate choice across CaMK, AMPK, and PAK pathways in vivo remains unresolved.
  • No structural model of the holoenzyme or substrate-bound state
  • Physiological contexts selecting each substrate not defined
  • No in vivo loss-of-function phenotype reported

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 4 GO:0016787 hydrolase activity 3
Localization
GO:0005634 nucleus 2 GO:0005829 cytosol 1
Pathway
GO:0140096 catalytic activity, acting on a protein 2
Partners
ARHGEF6CAMK1CAMK2ACAMK4PAK1PRKAA1

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 PPM1E (POPX1) was isolated as a binding partner for the PAK-interacting guanine nucleotide exchange factor PIX, and was shown to dephosphorylate and inactivate PAK (p21-activated kinase) in vitro and in vivo; its dephosphorylating activity correlated with blockade of active PAK effects, and it inhibited actin stress fiber breakdown and morphological changes driven by active Cdc42(V12). Co-immunoprecipitation (PIX binding), in vitro phosphatase assay, cell-based overexpression with PAK/Cdc42 activity readouts Current biology : CB High 11864573
2001 CaMKP-N (PPM1E) was identified as a nuclear Ser/Thr phosphatase that dephosphorylates CaMKIV; its activity requires Mn2+ ions and is stimulated by polycations; when transiently expressed in COS-7 cells it localizes to the nucleus, suggesting it dephosphorylates nuclear CaMKIV and nuclear CaMKII. Recombinant protein expression, in vitro phosphatase assay with CaMKIV substrate, transient transfection with subcellular localization imaging Journal of biochemistry High 11726284
2010 Stable lentiviral knockdown of Ppm1E (but not Ppm1A) in HEK293 cells increased AMPKα-Thr172 phosphorylation approximately 3-fold; Ppm1E and Ppm1F interact weakly with AMPK, identifying Ppm1E as an in-cellulo AMPK phosphatase; phenformin treatment decreased Ppm1E phosphatase activity, connecting Ppm1E inhibition to biguanide-induced AMPK activation. Stable lentiviral shRNA knockdown, phospho-AMPKα-Thr172 western blot, co-immunoprecipitation of AMPK with Ppm1E, phosphatase activity assay with specific antibodies Cellular signalling High 20801214
2004 CaMKP-N (PPM1E) contains two independent nuclear localization signals (NLS1 and NLS2) at its C-terminus; a cluster of basic residues in the NLSs is required for nuclear targeting; NLS1 and NLS2 function independently but mutagenesis suggests they interact with each other. Deletion and point mutagenesis of NLS sequences, subcellular localization assay by fluorescence microscopy Journal of biochemistry Medium 15496589
2007 Evans Blue and Chicago Sky Blue 6B were identified as inhibitors of CaMKP-N (PPM1E) and CaMKP; the minimum inhibitory structure is 1-amino-8-naphthol-4-sulfonic acid; in Neuro2a cells co-transfected with CaMKIV and CaMKP-N, these compounds suppressed CaMKIV dephosphorylation, demonstrating in-cell inhibitory activity. In vitro phosphatase assay with inhibitor compounds, cell-based dephosphorylation assay in Neuro2a cells Biochemical and biophysical research communications Medium 17897624
2011 Zebrafish CaMKP-N (PPM1E ortholog) undergoes proteolytic processing via the ubiquitin-proteasome pathway in brain and Neuro2a cells; this processing relocates the protein from the nucleus to the cytosol, changes its substrate targeting, and markedly activates its catalytic activity by removal of the C-terminal domain. Proteasome inhibitor treatment (MG-132, Epoxomicin, Lactacystin), subcellular fractionation, substrate phosphorylation assays in Neuro2a cells Archives of biochemistry and biophysics Medium 22100705
2012 CaMKI phosphorylates zebrafish CaMKP-N (PPM1E ortholog) at Ser-480; phosphorylation-mimic mutants (S480D/S480E) showed higher phosphatase activities than wild-type or non-phosphorylatable (S480A) mutants; in Neuro2a cells, phosphorylation-mimic CaMKP-N more strongly attenuated CaMKII autophosphorylation after ionomycin treatment, demonstrating that CaMKI-mediated phosphorylation activates CaMKP-N. In vitro phosphorylation assay with CaMKI, site-directed mutagenesis (S480A, S480D, S480E), solution-based phosphatase assay, cell-based CaMKII autophosphorylation assay in Neuro2a cells Biochemical and biophysical research communications High 22627141
2013 A C-terminally truncated form of human CaMKP-N/PPM1E (residues 1-559) exhibits much higher Vmax than full-length enzyme; it displays Mn2+/Mg2+-dependent phosphatase activity with preference for phospho-Thr residues, binds postsynaptic density, dephosphorylates autophosphorylated CaMKII, and is reversibly inactivated by H2O2 (oxidation), indicating redox regulation. Wheat-embryo cell-free protein expression, phosphopeptide phosphatase assay, postsynaptic density binding assay, CaMKII dephosphorylation assay, H2O2/DTT redox treatment BioMed research international Medium 23991411

Source papers

Stage 0 corpus · 18 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 The p21-activated kinase PAK is negatively regulated by POPX1 and POPX2, a pair of serine/threonine phosphatases of the PP2C family. Current biology : CB 110 11864573
2010 Ppm1E is an in cellulo AMP-activated protein kinase phosphatase. Cellular signalling 81 20801214
2016 miR-135b expression downregulates Ppm1e to activate AMPK signaling and protect osteoblastic cells from dexamethasone. Oncotarget 52 27661114
2016 miR-135b-5p inhibits LPS-induced TNFα production via silencing AMPK phosphatase Ppm1e. Oncotarget 37 27793001
2001 Identification and characterization of CaMKP-N, nuclear calmodulin-dependent protein kinase phosphatase. Journal of biochemistry 36 11726284
2018 Long Non-Coding RNA MALAT1 Protects Human Osteoblasts from Dexamethasone-Induced Injury via Activation of PPM1E-AMPK Signaling. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 31 30439702
2007 Inhibitors of the Ca(2+)/calmodulin-dependent protein kinase phosphatase family (CaMKP and CaMKP-N). Biochemical and biophysical research communications 24 17897624
2017 AMPKα phosphatase Ppm1E upregulation in human gastric cancer is required for cell proliferation. Oncotarget 23 28423719
2018 Functions and dysfunctions of Ca2+/calmodulin-dependent protein kinase phosphatase (CaMKP/PPM1F) and CaMKP-N/PPM1E. Archives of biochemistry and biophysics 19 29317228
2021 CircHAS2 promotes the proliferation, migration, and invasion of gastric cancer cells by regulating PPM1E mediated by hsa-miR-944. Cell death & disease 12 34556632
2017 microRNA-135b expression silences Ppm1e to provoke AMPK activation and inhibit osteoblastoma cell proliferation. Oncotarget 12 28460435
2004 Identification and characterization of nuclear localization signals of CaMKP-N. Journal of biochemistry 11 15496589
2012 Phosphorylation and activation of nuclear Ca2+/calmodulin-dependent protein kinase phosphatase (CaMKP-N/PPM1E) by Ca2+/calmodulin-dependent protein kinase I (CaMKI). Biochemical and biophysical research communications 10 22627141
2011 Functional processing of nuclear Ca2+/calmodulin-dependent protein kinase phosphatase (CaMKP-N): evidence for a critical role of proteolytic processing in the regulation of its catalytic activity, subcellular localization and substrate targeting in vivo. Archives of biochemistry and biophysics 9 22100705
2025 The PP2CH- and PBL27-mediated phosphorylation switch of aluminium ion receptor PSKR1/ALR1 controls plant aluminum sensing ability. Nature plants 8 40216985
2013 An active C-terminally truncated form of Ca (2+) /calmodulin-dependent protein kinase phosphatase-N (CaMKP-N/PPM1E). BioMed research international 6 23991411
2022 LINC01087 Promotes the Proliferation, Migration, and Invasion of Thyroid Cancer Cells by Upregulating PPM1E. Journal of oncology 5 35368894
2024 [miR-342-3p Promotes the Proliferation, Migration, and Invasion of Clear Cell Renal Cell Carcinoma Cells by Targeted Inhibition of PPM1E]. Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition 0 38948282

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