Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Li, Yitong; Balakrishnan, Vijaya Kumar; Rowse, Michael; Wu, Cheng-Guo; Bravos, Anastasia Phoebe; Yadav, Vikash K.; Ivarsson, Ylva; Strack, Stefan; Novikova, Irina V.; Xing, Yongna

doi:10.7554/elife.79736

Title: Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Journal Article · 03 August 2022 · eLife

DOI: https://doi.org/10.7554/elife.79736 · OSTI ID:2471560

^[1]; Balakrishnan, Vijaya Kumar ^[1];

^[1]; Wu, Cheng-Guo ^[1]; Bravos, Anastasia Phoebe ^[1]; Yadav, Vikash K. ^[2]; Ivarsson, Ylva ^[2]; Strack, Stefan ^[3]; Novikova, Irina V. ^[4];

^[1]

University of Wisconsin at Madison, WI (United States)
Uppsala University (Sweden)
University of Iowa, Iowa City, IA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: American Cancer Society; Jordan's Guardian Angels Foundation and Jordan's; National Institute of General Medical Sciences; Syndrome research; USDOE; consortium fund

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2471560

Journal Information:: eLife, Journal Name: eLife Vol. 11; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

References (60)

A stable association with PME‐1 may be dispensable for PP2A demethylation – implications for the detection of PP2A methylation and immunoprecipitation Yabe, Ryotaro; Tsuji, Shunya; Mochida, Satoru FEBS Open Bio, Vol. 8, Issue 9 https://doi.org/10.1002/2211-5463.12485	journal	August 2018
A tumor suppressor role for PP2A-B56α through negative regulation of c-Myc and other key oncoproteins Arnold, Hugh K.; Sears, Rosalie C. Cancer and Metastasis Reviews, Vol. 27, Issue 2 https://doi.org/10.1007/s10555-008-9128-9	journal	February 2008
Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization Wang, Jiao; Wang, Zhizhi; Yu, Tingting Protein & Cell, Vol. 7, Issue 7 https://doi.org/10.1007/s13238-016-0283-4	journal	June 2016
Protein phosphatase 2A catalytic subunit is methyl-esterified at its carboxyl terminus by a novel methyltransferase. Lee, J.; Stock, J. Journal of Biological Chemistry, Vol. 268, Issue 26 https://doi.org/10.1016/S0021-9258(19)36497-X	journal	September 1993
Structure of Protein Phosphatase 2A Core Enzyme Bound to Tumor-Inducing Toxins Xing, Yongna; Xu, Yanhui; Chen, Yu Cell, Vol. 127, Issue 2 https://doi.org/10.1016/j.cell.2006.09.025	journal	October 2006
Structure of the Protein Phosphatase 2A Holoenzyme Xu, Yanhui; Xing, Yongna; Chen, Yu Cell, Vol. 127, Issue 6 https://doi.org/10.1016/j.cell.2006.11.033	journal	December 2006
Structural Mechanism of Demethylation and Inactivation of Protein Phosphatase 2A Xing, Yongna; Li, Zhu; Chen, Yu Cell, Vol. 133, Issue 1 https://doi.org/10.1016/j.cell.2008.02.041	journal	April 2008
Docking Motif-Guided Mapping of the Interactome of Protein Phosphatase-1 Hendrickx, Annick; Beullens, Monique; Ceulemans, Hugo Chemistry & Biology, Vol. 16, Issue 4 https://doi.org/10.1016/j.chembiol.2009.02.012	journal	April 2009
Spindle Checkpoint Silencing: PP1 Tips the Balance Lesage, Bart; Qian, Junbin; Bollen, Mathieu Current Biology, Vol. 21, Issue 21 https://doi.org/10.1016/j.cub.2011.08.063	journal	November 2011
PP2A: the expected tumor suppressor Janssens, Veerle; Goris, Jozef; Van Hoof, Christine Current Opinion in Genetics & Development, Vol. 15, Issue 1 https://doi.org/10.1016/j.gde.2004.12.004	journal	February 2005
Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment Sonntag, Tim; Ostojić, Jelena; Vaughan, Joan M. iScience, Vol. 11 https://doi.org/10.1016/j.isci.2018.12.012	journal	January 2019
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Structure of a Protein Phosphatase 2A Holoenzyme: Insights into B55-Mediated Tau Dephosphorylation Xu, Yanhui; Chen, Yu; Zhang, Ping Molecular Cell, Vol. 31, Issue 6 https://doi.org/10.1016/j.molcel.2008.08.006	journal	September 2008
α4 Is an Essential Regulator of PP2A Phosphatase Activity Kong, Mei; Ditsworth, Dara; Lindsten, Tullia Molecular Cell, Vol. 36, Issue 1 https://doi.org/10.1016/j.molcel.2009.09.025	journal	October 2009
The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1 Stanevich, Vitali; Jiang, Li; Satyshur, Kenneth A. Molecular Cell, Vol. 41, Issue 3 https://doi.org/10.1016/j.molcel.2010.12.030	journal	February 2011
Phosphorylation of p53 by TAF1 Inactivates p53-Dependent Transcription in the DNA Damage Response Wu, Yong; Lin, Joy C.; Piluso, Landon G. Molecular Cell, Vol. 53, Issue 1 https://doi.org/10.1016/j.molcel.2013.10.031	journal	January 2014
A Conserved Motif Provides Binding Specificity to the PP2A-B56 Phosphatase Hertz, Emil Peter Thrane; Kruse, Thomas; Davey, Norman E. Molecular Cell, Vol. 63, Issue 4 https://doi.org/10.1016/j.molcel.2016.06.024	journal	August 2016
Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex Davey, Norman E.; Morgan, David O. Molecular Cell, Vol. 64, Issue 1 https://doi.org/10.1016/j.molcel.2016.09.006	journal	October 2016
A Consensus Binding Motif for the PP4 Protein Phosphatase Ueki, Yumi; Kruse, Thomas; Weisser, Melanie Bianca Molecular Cell, Vol. 76, Issue 6 https://doi.org/10.1016/j.molcel.2019.08.029	journal	December 2019
Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling Wigington, Callie P.; Roy, Jagoree; Damle, Nikhil P. Molecular Cell, Vol. 79, Issue 2 https://doi.org/10.1016/j.molcel.2020.06.029	journal	July 2020
Expanding the PP2A Interactome by Defining a B56-Specific SLiM Wang, Xinru; Bajaj, Rakhi; Bollen, Mathieu Structure, Vol. 24, Issue 12 https://doi.org/10.1016/j.str.2016.09.010	journal	December 2016
Spatial control of protein phosphatase 2A (de)methylation Longin, Sari; Zwaenepoel, Karen; Martens, Ellen Experimental Cell Research, Vol. 314, Issue 1 https://doi.org/10.1016/j.yexcr.2007.07.030	journal	January 2008
Protein phosphatase 2A: a panoply of enzymes Virshup, David M. Current Opinion in Cell Biology, Vol. 12, Issue 2 https://doi.org/10.1016/s0955-0674(99)00074-5	journal	April 2000
Purification of Porcine Brain Protein Phosphatase 2A Leucine Carboxyl Methyltransferase and Cloning of the Human Homologue ^† ^, ^‡ De Baere, I.; Derua, R.; Janssens, V. Biochemistry, Vol. 38, Issue 50 https://doi.org/10.1021/bi991646a	journal	December 1999
PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis Wu, Cheng-Guo; Chen, Hui; Guo, Feng Cell Discovery, Vol. 3, Issue 1 https://doi.org/10.1038/celldisc.2017.27	journal	August 2017
Structural basis of PP2A activation by PTPA, an ATP-dependent activation chaperone Guo, Feng; Stanevich, Vitali; Wlodarchak, Nathan Cell Research, Vol. 24, Issue 2 https://doi.org/10.1038/cr.2013.138	journal	October 2013
Structure of the Ca2+-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation Wlodarchak, Nathan; Guo, Feng; Satyshur, Kenneth A. Cell Research, Vol. 23, Issue 7 https://doi.org/10.1038/cr.2013.77	journal	June 2013
It takes three to find the exit Bollen, Mathieu Nature, Vol. 517, Issue 7532 https://doi.org/10.1038/nature14080	journal	December 2014
Structural basis of protein phosphatase 2A stable latency Jiang, Li; Stanevich, Vitali; Satyshur, Kenneth A. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2663	journal	April 2013
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Structural and biochemical insights into the regulation of protein phosphatase 2A by small t antigen of SV40 Chen, Yu; Xu, Yanhui; Bao, Qing Nature Structural & Molecular Biology, Vol. 14, Issue 6 https://doi.org/10.1038/nsmb1254	journal	May 2007
Methylation-regulated decommissioning of multimeric PP2A complexes Wu, Cheng-Guo; Zheng, Aiping; Jiang, Li Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02405-3	journal	December 2017
Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression Zhang, Lingdi; Zhou, Hengbo; Li, Xueni Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03327-4	journal	March 2018
A specific PP2A regulatory subunit, B56γ, mediates DNA damage-induced dephosphorylation of p53 at Thr55 Li, Heng-Hong; Cai, Xin; Shouse, Geoffrey P. The EMBO Journal, Vol. 26, Issue 2 https://doi.org/10.1038/sj.emboj.7601519	journal	January 2007
An inactive protein phosphatase 2A population is associated with methylesterase and can be re-activated by the phosphotyrosyl phosphatase activator Longin, Sari; Jordens, Jan; Martens, Ellen Biochemical Journal, Vol. 380, Issue 1 https://doi.org/10.1042/BJ20031643	journal	May 2004
Methylated C-terminal leucine residue of PP2A catalytic subunit is important for binding of regulatory Bα subunit Bryant, Jeffrey C.; Westphal, Ryan S.; Wadzinski, Brian E. Biochemical Journal, Vol. 339, Issue 2 https://doi.org/10.1042/bj3390241	journal	April 1999
Academic cross-fertilization by public screening yields a remarkable class of protein phosphatase methylesterase-1 inhibitors Bachovchin, D. A.; Mohr, J. T.; Speers, A. E. Proceedings of the National Academy of Sciences, Vol. 108, Issue 17 https://doi.org/10.1073/pnas.1015248108	journal	March 2011
PP2A methylation controls sensitivity and resistance to β-amyloid–induced cognitive and electrophysiological impairments Nicholls, Russell E.; Sontag, Jean-Marie; Zhang, Hong Proceedings of the National Academy of Sciences, Vol. 113, Issue 12 https://doi.org/10.1073/pnas.1521018113	journal	March 2016
A specific protein carboxyl methylesterase that demethylates phosphoprotein phosphatase 2A in bovine brain. Lee, J.; Chen, Y.; Tolstykh, T. Proceedings of the National Academy of Sciences, Vol. 93, Issue 12 https://doi.org/10.1073/pnas.93.12.6043	journal	June 1996
Leucine Carboxyl Methyltransferase-1 Is Necessary for Normal Progression through Mitosis in Mammalian Cells Lee, Jocelyn A.; Pallas, David C. Journal of Biological Chemistry, Vol. 282, Issue 42 https://doi.org/10.1074/jbc.M704861200	journal	August 2007
Protein Phosphatase 2A Is Targeted to Cell Division Control Protein 6 by a Calcium-binding Regulatory Subunit Davis, Anthony J.; Yan, Zhen; Martinez, Bobbie Journal of Biological Chemistry, Vol. 283, Issue 23 https://doi.org/10.1074/jbc.M710313200	journal	June 2008
Differential methylation and altered conformation of cytoplasmic and nuclear forms of protein phosphatase 2A during cell cycle progression. Turowski, P.; Fernandez, A.; Favre, B. The Journal of cell biology, Vol. 129, Issue 2 https://doi.org/10.1083/jcb.129.2.397	journal	April 1995
Methylation of the Protein Phosphatase 2A Catalytic Subunit Is Essential for Association of Bα Regulatory Subunit But Not SG2NA, Striatin, or Polyomavirus Middle Tumor Antigen Yu, Xing Xian; Du, Xianxing; Moreno, Carlos S. Molecular Biology of the Cell, Vol. 12, Issue 1 https://doi.org/10.1091/mbc.12.1.185	journal	January 2001
Carboxyl methylation of the phosphoprotein phosphatase 2A catalytic subunit promotes its functional association with regulatory subunits in vivo Wu, J. The EMBO Journal, Vol. 19, Issue 21 https://doi.org/10.1093/emboj/19.21.5672	journal	November 2000
Carboxyl methylation regulates phosphoprotein phosphatase 2A by controlling the association of regulatory B subunits Tolstykh, T. The EMBO Journal, Vol. 19, Issue 21 https://doi.org/10.1093/emboj/19.21.5682	journal	November 2000
Downregulation of Protein Phosphatase 2A Carboxyl Methylation and Methyltransferase May Contribute to Alzheimer Disease Pathogenesis Sontag, Estelle; Hladik, Christa; Montgomery, Lisa Journal of Neuropathology & Experimental Neurology, Vol. 63, Issue 10 https://doi.org/10.1093/jnen/63.10.1080	journal	October 2004
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Regulation of protein phosphatase 2A methylation by LCMT1 and PME‐1 plays a critical role in differentiation of neuroblastoma cells Sontag, Jean‐Marie; Nunbhakdi‐Craig, Viyada; Mitterhuber, Martina Journal of Neurochemistry, Vol. 115, Issue 6 https://doi.org/10.1111/j.1471-4159.2010.07049.x	journal	November 2010
The PP1 binding code: a molecular-lego strategy that governs specificity: The PP1 binding code Heroes, Ewald; Lesage, Bart; Görnemann, Janina FEBS Journal, Vol. 280, Issue 2 https://doi.org/10.1111/j.1742-4658.2012.08547.x	journal	March 2012
Cracking the Phosphatase Code: Docking Interactions Determine Substrate Specificity Roy, Jagoree; Cyert, Martha S. Science Signaling, Vol. 2, Issue 100 https://doi.org/10.1126/scisignal.2100re9	journal	December 2009
Aurora B opposes PP1 function in mitosis by phosphorylating the conserved PP1-binding RVxF motif in PP1 regulatory proteins Nasa, Isha; Rusin, Scott F.; Kettenbach, Arminja N. Science Signaling, Vol. 11, Issue 530 https://doi.org/10.1126/scisignal.aai8669	journal	May 2018
PME-1 Modulates Protein Phosphatase 2A Activity to Promote the Malignant Phenotype of Endometrial Cancer Cells Wandzioch, Ewa; Pusey, Michelle; Werda, Amy Cancer Research, Vol. 74, Issue 16 https://doi.org/10.1158/0008-5472.CAN-13-3130	journal	August 2014
PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells Kaur, Amanpreet; Denisova, Oxana V.; Qiao, Xi Cancer Research, Vol. 76, Issue 23 https://doi.org/10.1158/0008-5472.CAN-16-1134	journal	November 2016
Short linear motifs – ex nihilo evolution of protein regulation Davey, Norman E.; Cyert, Martha S.; Moses, Alan M. Cell Communication and Signaling, Vol. 13, Issue 1 https://doi.org/10.1186/s12964-015-0120-z	journal	November 2015
Targeted Disruption of the PME-1 Gene Causes Loss of Demethylated PP2A and Perinatal Lethality in Mice Ortega-Gutiérrez, Silvia; Leung, Donmienne; Ficarro, Scott PLoS ONE, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pone.0002486	journal	July 2008
Mechanisms of the Scaffold Subunit in Facilitating Protein Phosphatase 2A Methylation Stanevich, Vitali; Zheng, Aiping; Guo, Feng PLoS ONE, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pone.0086955	journal	January 2014
PP2A as a master regulator of the cell cycle Wlodarchak, Nathan; Xing, Yongna Critical Reviews in Biochemistry and Molecular Biology, Vol. 51, Issue 3 https://doi.org/10.3109/10409238.2016.1143913	journal	February 2016

Similar Records

Structural Mechanism of Demethylation and Inactivation of Protein Phosphatase 2A

Journal Article · 2007 · Cell · OSTI ID:959560

Xing, Y; Li, Z; Chen, Y; +3 more

Structure of the Protein Phosphatase 2A Holoenzyme

Journal Article · 2005 · Cell · OSTI ID:930171

Xu, Y; Xing, Y; Chen, Y; +7 more

B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations

Journal Article · 2023 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:2470213

Wu, Cheng-Guo; Balakrishnan, Vijaya K.; Merrill, Ronald A.; +16 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Life Sciences & Biomedicine - Other Topics

Title: Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Citation Formats

References (60)

Similar Records

Related Subjects