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Structural and functional characterization of the phosphorylation-dependent interaction between PML and SUMO1.

Cappadocia L, Mascle XH, Bourdeau V, Tremblay-Belzile S, Chaker-Margot M, Lussier-Price M, Wada J, Sakaguchi K, Aubry M, Ferbeyre G, Omichinski JG
Structure 23 126-138 (2015)
Related entries: 4wjn, 4wjp, 4wjq

Cited: 37 times
EuropePMC logo PMID: 25497731

Abstract

PML and several other proteins localizing in PML-nuclear bodies (PML-NB) contain phosphoSIMs (SUMO-interacting motifs), and phosphorylation of this motif plays a key role in their interaction with SUMO family proteins. We examined the role that phosphorylation plays in the binding of the phosphoSIMs of PML and Daxx to SUMO1 at the atomic level. The crystal structures of SUMO1 bound to unphosphorylated and tetraphosphorylated PML-SIM peptides indicate that three phosphoserines directly contact specific positively charged residues of SUMO1. Surprisingly, the crystal structure of SUMO1 bound to a diphosphorylated Daxx-SIM peptide indicate that the hydrophobic residues of the phosphoSIM bind in a manner similar to that seen with PML, but important differences are observed when comparing the phosphorylated residues. Together, the results provide an atomic level description of how specific acetylation patterns within different SUMO family proteins can work together with phosphorylation of phosphoSIM's regions of target proteins to regulate binding specificity.

Articles - 4wjo mentioned but not cited (5)

  1. A framework for exhaustively mapping functional missense variants. Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP. Mol Syst Biol 13 957 (2017)
  2. SUMO enables substrate selectivity by mitogen-activated protein kinases to regulate immunity in plants. Verma V, Srivastava AK, Gough C, Campanaro A, Srivastava M, Morrell R, Joyce J, Bailey M, Zhang C, Krysan PJ, Sadanandom A. Proc Natl Acad Sci U S A 118 e2021351118 (2021)
  3. A conserved and buried edge-to-face aromatic interaction in small ubiquitin-like modifier (SUMO) has a role in SUMO stability and function. Chatterjee KS, Tripathi V, Das R. J Biol Chem 294 6772-6784 (2019)
  4. Casein kinase-2-mediated phosphorylation increases the SUMO-dependent activity of the cytomegalovirus transactivator IE2. Tripathi V, Chatterjee KS, Das R. J Biol Chem 294 14546-14561 (2019)
  5. An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity. Chatterjee KS, Das R. J Biol Chem 297 100970 (2021)


Reviews citing this publication (13)

  1. Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism. Cappadocia L, Lima CD. Chem Rev 118 889-918 (2018)
  2. PML nuclear bodies and chromatin dynamics: catch me if you can! Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. Nucleic Acids Res 48 11890-11912 (2020)
  3. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. Ishida T, Ciulli A. SLAS Discov 26 484-502 (2021)
  4. Role and Regulation of Myeloid Zinc Finger Protein 1 in Cancer. Eguchi T, Prince T, Wegiel B, Calderwood SK. J Cell Biochem 116 2146-2154 (2015)
  5. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. J Mol Biol 429 3409-3429 (2017)
  6. SUMO Interacting Motifs: Structure and Function. Yau TY, Sander W, Eidson C, Courey AJ. Cells 10 2825 (2021)
  7. SUMO: Glue or Solvent for Phase-Separated Ribonucleoprotein Complexes and Molecular Condensates? Keiten-Schmitz J, Röder L, Hornstein E, Müller-McNicoll M, Müller S. Front Mol Biosci 8 673038 (2021)
  8. Divergent signaling via SUMO modification: potential for CFTR modulation. Ahner A, Gong X, Frizzell RA. Am J Physiol Cell Physiol 310 C175-80 (2016)
  9. Phospho-regulation of intrinsically disordered proteins for actin assembly and endocytosis. Miao Y, Tipakornsaowapak T, Zheng L, Mu Y, Lewellyn E. FEBS J 285 2762-2784 (2018)
  10. Plant SUMO E3 Ligases: Function, Structural Organization, and Connection With DNA. Jmii S, Cappadocia L. Front Plant Sci 12 652170 (2021)
  11. How Does SUMO Participate in Spindle Organization? Abrieu A, Liakopoulos D. Cells 8 E801 (2019)
  12. Regulating the p53 Tumor Suppressor Network at PML Biomolecular Condensates. Liebl MC, Hofmann TG. Cancers (Basel) 14 4549 (2022)
  13. Phase Separation in the Nucleus and at the Nuclear Periphery during Post-Mitotic Nuclear Envelope Reformation. Maccaroni K, La Torre M, Burla R, Saggio I. Cells 11 1749 (2022)

Articles citing this publication (19)

  1. Compositional Control of Phase-Separated Cellular Bodies. Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, Rosen MK. Cell 166 651-663 (2016)
  2. Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase. Cappadocia L, Pichler A, Lima CD. Nat Struct Mol Biol 22 968-975 (2015)
  3. Sumoylation regulates FMRP-mediated dendritic spine elimination and maturation. Khayachi A, Gwizdek C, Poupon G, Alcor D, Chafai M, Cassé F, Maurin T, Prieto M, Folci A, De Graeve F, Castagnola S, Gautier R, Schorova L, Loriol C, Pronot M, Besse F, Brau F, Deval E, Bardoni B, Martin S. Nat Commun 9 757 (2018)
  4. C-terminal motifs in promyelocytic leukemia protein isoforms critically regulate PML nuclear body formation. Li C, Peng Q, Wan X, Sun H, Tang J. J Cell Sci 130 3496-3506 (2017)
  5. Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80. Anamika, Spyracopoulos L. J Biol Chem 291 4417-4428 (2016)
  6. Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO. Diehl C, Akke M, Bekker-Jensen S, Mailand N, Streicher W, Wikström M. J Biol Chem 291 12658-12672 (2016)
  7. A high throughput mutagenic analysis of yeast sumo structure and function. Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ. PLoS Genet 13 e1006612 (2017)
  8. The Role of Non-Specific Interactions in Canonical and ALT-Associated PML-Bodies Formation and Dynamics. Fonin AV, Silonov SA, Shpironok OG, Antifeeva IA, Petukhov AV, Romanovich AE, Kuznetsova IM, Uversky VN, Turoverov KK. Int J Mol Sci 22 5821 (2021)
  9. Anticancer effects of valproic acid on oral squamous cell carcinoma via SUMOylation in vivo and in vitro. Sang Z, Sun Y, Ruan H, Cheng Y, Ding X, Yu Y. Exp Ther Med 12 3979-3987 (2016)
  10. Opposing biological functions of the cytoplasm and nucleus DAXX modified by SUMO-2/3 in gastric cancer. Chen C, Sun X, Xie W, Chen S, Hu Y, Xing D, Xu J, Chen X, Zhao Z, Han Z, Xue X, Shen X, Lin K. Cell Death Dis 11 514 (2020)
  11. Functional impairment of the HIPK2 small ubiquitin-like modifier (SUMO)-interacting motif in acute myeloid leukemia. Sung KS, Kim SJ, Cho SW, Park YJ, Tae K, Choi CY. Am J Cancer Res 9 94-107 (2019)
  12. Phosphorylable tyrosine residue 162 in the double-stranded RNA-dependent kinase PKR modulates its interaction with SUMO. de la Cruz-Herrera CF, Baz-Martínez M, Motiam AE, Vidal S, Collado M, Vidal A, Rodríguez MS, Esteban M, Rivas C. Sci Rep 7 14055 (2017)
  13. Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations. Kötter A, Mootz HD, Heuer A. Biophys J 119 1558-1567 (2020)
  14. Promyelocytic leukemia nuclear body-like structures can assemble in mouse oocytes. Udagawa O, Kato-Udagawa A, Hirano S. Biol Open 11 bio059130 (2022)
  15. Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1. Lussier-Price M, Wahba HM, Mascle XH, Cappadocia L, Bourdeau V, Gagnon C, Igelmann S, Sakaguchi K, Ferbeyre G, Omichinski JG. Nucleic Acids Res 50 8331-8348 (2022)
  16. A CK2 and SUMO-dependent, PML NB-involved regulatory mechanism controlling BLM ubiquitination and G-quadruplex resolution. Liu S, Atkinson E, Paulucci-Holthauzen A, Wang B. Nat Commun 14 6111 (2023)
  17. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Elife 12 e80156 (2023)
  18. MAVS deSUMOylation by SENP1 inhibits its aggregation and antagonizes IRF3 activation. Dai T, Zhang L, Ran Y, Zhang M, Yang B, Lu H, Lin S, Zhang L, Zhou F. Nat Struct Mol Biol 30 785-799 (2023)
  19. SUMO-mediated recruitment allows timely function of the Yen1 nuclease in mitotic cells. Dorison H, Talhaoui I, Mazón G. PLoS Genet 18 e1009860 (2022)


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