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Structures of Down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition.

Soundararajan M, Roos AK, Savitsky P, Filippakopoulos P, Kettenbach AN, Olsen JV, Gerber SA, Eswaran J, Knapp S, Elkins JM
Structure 21 986-96 (2013)
Related entries: 2vx3, 2wo6

Cited: 91 times
EuropePMC logo PMID: 23665168

Abstract

Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinases (DYRKs) play key roles in brain development, regulation of splicing, and apoptosis, and are potential drug targets for neurodegenerative diseases and cancer. We present crystal structures of one representative member of each DYRK subfamily: DYRK1A with an ATP-mimetic inhibitor and consensus peptide, and DYRK2 including NAPA and DH (DYRK homology) box regions. The current activation model suggests that DYRKs are Ser/Thr kinases that only autophosphorylate the second tyrosine of the activation loop YxY motif during protein translation. The structures explain the roles of this tyrosine and of the DH box in DYRK activation and provide a structural model for DYRK substrate recognition. Phosphorylation of a library of naturally occurring peptides identified substrate motifs that lack proline in the P+1 position, suggesting that DYRK1A is not a strictly proline-directed kinase. Our data also show that DYRK1A wild-type and Y321F mutant retain tyrosine autophosphorylation activity.

Reviews - 3k2l mentioned but not cited (2)

  1. Dual-Specificity, Tyrosine Phosphorylation-Regulated Kinases (DYRKs) and cdc2-Like Kinases (CLKs) in Human Disease, an Overview. Lindberg MF, Meijer L. Int J Mol Sci 22 6047 (2021)
  2. Emerging roles of DYRK2 in cancer. Tandon V, de la Vega L, Banerjee S. J Biol Chem 296 100233 (2021)

Articles - 3k2l mentioned but not cited (10)

  1. Structures of Down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition. Soundararajan M, Roos AK, Savitsky P, Filippakopoulos P, Kettenbach AN, Olsen JV, Gerber SA, Eswaran J, Knapp S, Elkins JM. Structure 21 986-996 (2013)
  2. Novel Inverse Binding Mode of Indirubin Derivatives Yields Improved Selectivity for DYRK Kinases. Myrianthopoulos V, Kritsanida M, Gaboriaud-Kolar N, Magiatis P, Ferandin Y, Durieu E, Lozach O, Cappel D, Soundararajan M, Filippakopoulos P, Sherman W, Knapp S, Meijer L, Mikros E, Skaltsounis AL. ACS Med Chem Lett 4 22-26 (2013)
  3. Evaluation of cancer dependence and druggability of PRP4 kinase using cellular, biochemical, and structural approaches. Gao Q, Mechin I, Kothari N, Guo Z, Deng G, Haas K, McManus J, Hoffmann D, Wang A, Wiederschain D, Rocnik J, Czechtizky W, Chen X, McLean L, Arlt H, Harper D, Liu F, Majid T, Patel V, Lengauer C, Garcia-Echeverria C, Zhang B, Cheng H, Dorsch M, Huang SA. J Biol Chem 288 30125-30138 (2013)
  4. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Nat Commun 11 3563 (2020)
  5. Identification of suppressors of mbk-2/DYRK by whole-genome sequencing. Wang Y, Wang JT, Rasoloson D, Stitzel ML, O' Connell KF, Smith HE, Seydoux G. G3 (Bethesda) 4 231-241 (2014)
  6. The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. Agnew C, Liu L, Liu S, Xu W, You L, Yeung W, Kannan N, Jablons D, Jura N. J Biol Chem 294 13545-13559 (2019)
  7. Abemaciclib is a potent inhibitor of DYRK1A and HIP kinases involved in transcriptional regulation. Kaltheuner IH, Anand K, Moecking J, Düster R, Wang J, Gray NS, Geyer M. Nat Commun 12 6607 (2021)
  8. Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry. Wei T, Wang J, Liang R, Chen W, Chen Y, Ma M, He A, Du Y, Zhou W, Zhang Z, Zeng X, Wang C, Lu J, Guo X, Chen XW, Wang Y, Tian R, Xiao J, Lei X. Elife 11 e77696 (2022)
  9. Druggable exosites of the human kino-pocketome. Nicola G, Kufareva I, Ilatovskiy AV, Abagyan R. J Comput Aided Mol Des 34 219-230 (2020)
  10. Murine isoforms of UDP-GlcNAc 2-epimerase/ManNAc kinase: Secondary structures, expression profiles, and response to ManNAc therapy. Yardeni T, Jacobs K, Niethamer TK, Ciccone C, Anikster Y, Kurochkina N, Gahl WA, Huizing M. Glycoconj J 30 609-618 (2013)


Reviews citing this publication (17)

  1. DYRK1A, a Dosage-Sensitive Gene Involved in Neurodevelopmental Disorders, Is a Target for Drug Development in Down Syndrome. Duchon A, Herault Y. Front Behav Neurosci 10 104 (2016)
  2. Therapeutic strategies targeting FOXO transcription factors. Calissi G, Lam EW, Link W. Nat Rev Drug Discov 20 21-38 (2021)
  3. The DYRK Family of Kinases in Cancer: Molecular Functions and Therapeutic Opportunities. Boni J, Rubio-Perez C, López-Bigas N, Fillat C, de la Luna S. Cancers (Basel) 12 E2106 (2020)
  4. Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature. Luco SM, Pohl D, Sell E, Wagner JD, Dyment DA, Daoud H. BMC Med Genet 17 15 (2016)
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  6. GSK-3β, FYN, and DYRK1A: Master Regulators in Neurodegenerative Pathways. Demuro S, Di Martino RMC, Ortega JA, Cavalli A. Int J Mol Sci 22 9098 (2021)
  7. Structure and function of RET in multiple endocrine neoplasia type 2. Plaza-Menacho I. Endocr Relat Cancer 25 T79-T90 (2018)
  8. Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases. Correa-Sáez A, Jiménez-Izquierdo R, Garrido-Rodríguez M, Morrugares R, Muñoz E, Calzado MA. Cell Mol Life Sci 77 4747-4763 (2020)
  9. Dyrk1a from Gene Function in Development and Physiology to Dosage Correction across Life Span in Down Syndrome. Atas-Ozcan H, Brault V, Duchon A, Herault Y. Genes (Basel) 12 1833 (2021)
  10. Emerging Roles of DYRK Kinases in Embryogenesis and Hedgehog Pathway Control. Singh R, Lauth M. J Dev Biol 5 E13 (2017)
  11. Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. Yeung W, Ruan Z, Kannan N. IUBMB Life 72 1189-1202 (2020)
  12. The chromosome 21 kinase DYRK1A: emerging roles in cancer biology and potential as a therapeutic target. Rammohan M, Harris E, Bhansali RS, Zhao E, Li LS, Crispino JD. Oncogene 41 2003-2011 (2022)
  13. Diabetic Kinome Inhibitors-A New Opportunity for β-Cells Restoration. Pucelik B, Barzowska A, Dąbrowski JM, Czarna A. Int J Mol Sci 22 9083 (2021)
  14. DYRK1A pathogenic variants in two patients with syndromic intellectual disability and a review of the literature. Meissner LE, Macnamara EF, D'Souza P, Yang J, Vezina G, Undiagnosed Diseases Network, Ferreira CR, Zein WM, Tifft CJ, Adams DR. Mol Genet Genomic Med 8 e1544 (2020)
  15. Insights from the protein interaction Universe of the multifunctional "Goldilocks" kinase DYRK1A. Ananthapadmanabhan V, Shows KH, Dickinson AJ, Litovchick L. Front Cell Dev Biol 11 1277537 (2023)
  16. New insights into the roles for DYRK family in mammalian development and congenital diseases. Yoshida S, Yoshida K. Genes Dis 10 758-770 (2023)
  17. Regulation of CMGC kinases by hypoxia. Kim K, Lee SB. BMB Rep 56 584-593 (2023)

Articles citing this publication (62)

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  16. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Elife 8 e44635 (2019)
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  20. Structural assembly of the signaling competent ERK2-RSK1 heterodimeric protein kinase complex. Alexa A, Gógl G, Glatz G, Garai Á, Zeke A, Varga J, Dudás E, Jeszenői N, Bodor A, Hetényi C, Reményi A. Proc Natl Acad Sci U S A 112 2711-2716 (2015)
  21. Identification of a DYRK1A Inhibitor that Induces Degradation of the Target Kinase using Co-chaperone CDC37 fused with Luciferase nanoKAZ. Sonamoto R, Kii I, Koike Y, Sumida Y, Kato-Sumida T, Okuno Y, Hosoya T, Hagiwara M. Sci Rep 5 12728 (2015)
  22. Inhibitors of dual-specificity tyrosine phosphorylation-regulated kinases (DYRK) exert a strong anti-herpesviral activity. Hutterer C, Milbradt J, Hamilton S, Zaja M, Leban J, Henry C, Vitt D, Steingruber M, Sonntag E, Zeitträger I, Bahsi H, Stamminger T, Rawlinson W, Strobl S, Marschall M. Antiviral Res 143 113-121 (2017)
  23. Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38. Kirsch K, Zeke A, Tőke O, Sok P, Sethi A, Sebő A, Kumar GS, Egri P, Póti ÁL, Gooley P, Peti W, Bento I, Alexa A, Reményi A. Nat Commun 11 5769 (2020)
  24. Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells. Recasens A, Humphrey SJ, Ellis M, Hoque M, Abbassi RH, Chen B, Longworth M, Needham EJ, James DE, Johns TG, Day BW, Kassiou M, Yang P, Munoz L. Cell Death Discov 7 81 (2021)
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  26. Functional characterization of DYRK1A missense variants associated with a syndromic form of intellectual deficiency and autism. Widowati EW, Ernst S, Hausmann R, Müller-Newen G, Becker W. Biol Open 7 bio032862 (2018)
  27. DYRK1B mutations associated with metabolic syndrome impair the chaperone-dependent maturation of the kinase domain. Abu Jhaisha S, Widowati EW, Kii I, Sonamoto R, Knapp S, Papadopoulos C, Becker W. Sci Rep 7 6420 (2017)
  28. Identification of DYRK1B as a substrate of ERK1/2 and characterisation of the kinase activity of DYRK1B mutants from cancer and metabolic syndrome. Ashford AL, Dunkley TP, Cockerill M, Rowlinson RA, Baak LM, Gallo R, Balmanno K, Goodwin LM, Ward RA, Lochhead PA, Guichard S, Hudson K, Cook SJ. Cell Mol Life Sci 73 883-900 (2016)
  29. Synthesis and optimization of an original V-shaped collection of 4-7-disubstituted pyrido[3,2-d]pyrimidines as CDK5 and DYRK1A inhibitors. Dehbi O, Tikad A, Bourg S, Bonnet P, Lozach O, Meijer L, Aadil M, Akssira M, Guillaumet G, Routier S. Eur J Med Chem 80 352-363 (2014)
  30. Proline Hydroxylation Primes Protein Kinases for Autophosphorylation and Activation. Lee SB, Ko A, Oh YT, Shi P, D'Angelo F, Frangaj B, Koller A, Chen EI, Cardozo T, Iavarone A, Lasorella A. Mol Cell 79 376-389.e8 (2020)
  31. Synthesis and Biological Validation of a Harmine-Based, Central Nervous System (CNS)-Avoidant, Selective, Human β-Cell Regenerative Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase A (DYRK1A) Inhibitor. Kumar K, Wang P, Wilson J, Zlatanic V, Berrouet C, Khamrui S, Secor C, Swartz EA, Lazarus M, Sanchez R, Stewart AF, Garcia-Ocana A, DeVita RJ. J Med Chem 63 2986-3003 (2020)
  32. The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine. Alexeeva M, Åberg E, Engh RA, Rothweiler U. Acta Crystallogr D Biol Crystallogr 71 1207-1215 (2015)
  33. Synthesis of new pyridazino[4,5-b]indol-4-ones and pyridazin-3(2H)-one analogs as DYRK1A inhibitors. Bruel A, Bénéteau R, Chabanne M, Lozach O, Le Guevel R, Ravache M, Bénédetti H, Meijer L, Logé C, Robert JM. Bioorg Med Chem Lett 24 5037-5040 (2014)
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