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Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression.

Tereshko V, Teplova M, Brunzelle J, Watterson DM, Egli M
Nat Struct Biol 8 899-907 (2001)
Related entries: 1ig1, 1jkk, 1jkl, 1jkt

Cited: 70 times
EuropePMC logo PMID: 11573098

Abstract

We have determined X-ray crystal structures with up to 1.5 A resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. The geometry of the active site was studied in the apo form, in a complex with nonhydrolyzable AMPPnP and in a ternary complex consisting of kinase, AMPPnP and either Mg2+ or Mn2+. The structures revealed a previously undescribed water-mediated stabilization of the interaction between the lysine that is conserved in protein kinases and the beta- and gamma-phosphates of ATP, as well as conformational changes at the active site upon ion binding. Comparison between these structures and nucleotide triphosphate complexes of several other kinases disclosed a number of unique features of the DAPK catalytic domain, among which is a highly ordered basic loop in the N-terminal domain that may participate in enzyme regulation.

Reviews - 1jks mentioned but not cited (2)

  1. Substrate and docking interactions in serine/threonine protein kinases. Goldsmith EJ, Akella R, Min X, Zhou T, Humphreys JM. Chem Rev 107 5065-5081 (2007)
  2. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)

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  1. Death-associated protein kinase controls STAT3 activity in intestinal epithelial cells. Chakilam S, Gandesiri M, Rau TT, Agaimy A, Vijayalakshmi M, Ivanovska J, Wirtz RM, Schulze-Luehrmann J, Benderska N, Wittkopf N, Chellappan A, Ruemmele P, Vieth M, Rave-Fränk M, Christiansen H, Hartmann A, Neufert C, Atreya R, Becker C, Steinberg P, Schneider-Stock R. Am J Pathol 182 1005-1020 (2013)
  2. Protein flexibility: coordinate uncertainties and interpretation of structural differences. Rashin AA, Rashin AH, Jernigan RL. Acta Crystallogr D Biol Crystallogr 65 1140-1161 (2009)
  3. Structural insight into nucleotide recognition by human death-associated protein kinase. McNamara LK, Watterson DM, Brunzelle JS. Acta Crystallogr D Biol Crystallogr 65 241-248 (2009)
  4. Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein⁻Peptide Docking and Molecular Dynamics Simulation. Tu G, Fu T, Yang F, Yao L, Xue W, Zhu F. Molecules 23 E3018 (2018)
  5. Crystal structure of death-associated protein kinase 1 in complex with the dietary compound resveratrol. Yokoyama T, Suzuki R, Mizuguchi M. IUCrJ 8 131-138 (2021)
  6. Site-directed mutagenesis of the glycine-rich loop of death associated protein kinase (DAPK) identifies it as a key structure for catalytic activity. McNamara LK, Brunzelle JS, Schavocky JP, Watterson DM, Grum-Tokars V. Biochim Biophys Acta 1813 1068-1073 (2011)
  7. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. Hernandez Garcia A, Nair SK. ACS Cent Sci 9 1944-1956 (2023)


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  1. Regulation of protein kinases; controlling activity through activation segment conformation. Nolen B, Taylor S, Ghosh G. Mol Cell 15 661-675 (2004)
  2. Long Noncoding RNA in Cancer: Wiring Signaling Circuitry. Lin C, Yang L. Trends Cell Biol 28 287-301 (2018)
  3. The death-associated protein kinases: structure, function, and beyond. Bialik S, Kimchi A. Annu Rev Biochem 75 189-210 (2006)
  4. Plant innate immunity: perception of conserved microbial signatures. Schwessinger B, Ronald PC. Annu Rev Plant Biol 63 451-482 (2012)
  5. A decision between life and death during TNF-alpha-induced signaling. Gupta S. J Clin Immunol 22 185-194 (2002)
  6. Death Associated Protein Kinase 1 (DAPK1): A Regulator of Apoptosis and Autophagy. Singh P, Ravanan P, Talwar P. Front Mol Neurosci 9 46 (2016)
  7. The DAPK family: a structure-function analysis. Shiloh R, Bialik S, Kimchi A. Apoptosis 19 286-297 (2014)
  8. Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. Diamantopoulos MA, Tsiakanikas P, Scorilas A. Ann Transl Med 6 241 (2018)
  9. ZIP kinase, a key regulator of myosin protein phosphatase 1. Haystead TA. Cell Signal 17 1313-1322 (2005)
  10. Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes. Farag AK, Roh EJ. Med Res Rev 39 349-385 (2019)
  11. New insights into the interplay between long non-coding RNAs and RNA-binding proteins in cancer. Yao ZT, Yang YM, Sun MM, He Y, Liao L, Chen KS, Li B. Cancer Commun (Lond) 42 117-140 (2022)
  12. The function of ROCO proteins in health and disease. Lewis PA. Biol Cell 101 183-191 (2009)
  13. Proteus in the world of proteins: conformational changes in protein kinases. Rabiller M, Getlik M, Klüter S, Richters A, Tückmantel S, Simard JR, Rauh D. Arch Pharm (Weinheim) 343 193-206 (2010)
  14. Death-Associated Protein Kinase 1 as a Promising Drug Target in Cancer and Alzheimer's Disease. Chen D, Zhou XZ, Lee TH. Recent Pat Anticancer Drug Discov 14 144-157 (2019)
  15. DAPK1 Signaling Pathways in Stroke: from Mechanisms to Therapies. Wang S, Shi X, Li H, Pang P, Pei L, Shen H, Lu Y. Mol Neurobiol 54 4716-4722 (2017)
  16. Death associated protein kinases: molecular structure and brain injury. Nair S, Hagberg H, Krishnamurthy R, Thornton C, Mallard C. Int J Mol Sci 14 13858-13872 (2013)
  17. Death-Associated Protein Kinase 1 Phosphorylation in Neuronal Cell Death and Neurodegenerative Disease. Kim N, Chen D, Zhou XZ, Lee TH. Int J Mol Sci 20 E3131 (2019)
  18. Death-associated protein kinase as a potential therapeutic target. Schumacher AM, Velentza AV, Watterson DM. Expert Opin Ther Targets 6 497-506 (2002)
  19. Structural and functional diversity in the activity and regulation of DAPK-related protein kinases. Temmerman K, Simon B, Wilmanns M. FEBS J 280 5533-5550 (2013)
  20. Biochemical and functional characterization of the ROC domain of DAPK establishes a new paradigm of GTP regulation in ROCO proteins. Bialik S, Kimchi A. Biochem Soc Trans 40 1052-1057 (2012)
  21. Role and mechanism of action of leucine-rich repeat kinase 1 in bone. Xing WR, Goodluck H, Zeng C, Mohan S. Bone Res 5 17003 (2017)
  22. Structure and enzymology of a death-associated protein kinase. Van Eldik LJ. Trends Pharmacol Sci 23 302-304 (2002)
  23. Structure, activity, regulation, and inhibitor discovery for a protein kinase associated with apoptosis and neuronal death. Velentza AV, Schumacher AM, Watterson DM. Pharmacol Ther 93 217-224 (2002)
  24. Architecture and mechanism of the central gear in an ancient molecular timer. Egli M. J R Soc Interface 14 20161065 (2017)
  25. Death-associated protein kinase 1 as a therapeutic target for Alzheimer's disease. Zhang T, Kim BM, Lee TH. Transl Neurodegener 13 4 (2024)

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  1. CASK Functions as a Mg2+-independent neurexin kinase. Mukherjee K, Sharma M, Urlaub H, Bourenkov GP, Jahn R, Südhof TC, Wahl MC. Cell 133 328-339 (2008)
  2. Structural evolution of the protein kinase-like superfamily. Scheeff ED, Bourne PE. PLoS Comput Biol 1 e49 (2005)
  3. Crystal structure of aurora-2, an oncogenic serine/threonine kinase. Cheetham GM, Knegtel RM, Coll JT, Renwick SB, Swenson L, Weber P, Lippke JA, Austen DA. J Biol Chem 277 42419-42422 (2002)
  4. Pim-1 ligand-bound structures reveal the mechanism of serine/threonine kinase inhibition by LY294002. Jacobs MD, Black J, Futer O, Swenson L, Hare B, Fleming M, Saxena K. J Biol Chem 280 13728-13734 (2005)
  5. Structurally sophisticated octahedral metal complexes as highly selective protein kinase inhibitors. Feng L, Geisselbrecht Y, Blanck S, Wilbuer A, Atilla-Gokcumen GE, Filippakopoulos P, Kräling K, Celik MA, Harms K, Maksimoska J, Marmorstein R, Frenking G, Knapp S, Essen LO, Meggers E. J Am Chem Soc 133 5976-5986 (2011)
  6. Death-associated protein kinase phosphorylates ZIP kinase, forming a unique kinase hierarchy to activate its cell death functions. Shani G, Marash L, Gozuacik D, Bialik S, Teitelbaum L, Shohat G, Kimchi A. Mol Cell Biol 24 8611-8626 (2004)
  7. Proteomic analysis of CA1 and CA3 regions of rat hippocampus and differential susceptibility to intermittent hypoxia. Gozal E, Gozal D, Pierce WM, Thongboonkerd V, Scherzer JA, Sachleben LR, Brittian KR, Guo SZ, Cai J, Klein JB. J Neurochem 83 331-345 (2002)
  8. Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. Mao L, Wang Y, Liu Y, Hu X. J Mol Biol 336 787-807 (2004)
  9. Three new isoforms of Caenorhabditis elegans UNC-89 containing MLCK-like protein kinase domains. Small TM, Gernert KM, Flaherty DB, Mercer KB, Borodovsky M, Benian GM. J Mol Biol 342 91-108 (2004)
  10. An aminopyridazine-based inhibitor of a pro-apoptotic protein kinase attenuates hypoxia-ischemia induced acute brain injury. Velentza AV, Wainwright MS, Zasadzki M, Mirzoeva S, Schumacher AM, Haiech J, Focia PJ, Egli M, Watterson DM. Bioorg Med Chem Lett 13 3465-3470 (2003)
  11. The tumor suppressor DAPK is reciprocally regulated by tyrosine kinase Src and phosphatase LAR. Wang WJ, Kuo JC, Ku W, Lee YR, Lin FC, Chang YL, Lin YM, Chen CH, Huang YP, Chiang MJ, Yeh SW, Wu PR, Shen CH, Wu CT, Chen RH. Mol Cell 27 701-716 (2007)
  12. Phosphoryl transfer by protein kinase A is captured in a crystal lattice. Bastidas AC, Deal MS, Steichen JM, Guo Y, Wu J, Taylor SS. J Am Chem Soc 135 4788-4798 (2013)
  13. Control of death-associated protein kinase (DAPK) activity by phosphorylation and proteasomal degradation. Jin Y, Blue EK, Gallagher PJ. J Biol Chem 281 39033-39040 (2006)
  14. Protein structural ensembles are revealed by redefining X-ray electron density noise. Lang PT, Holton JM, Fraser JS, Alber T. Proc Natl Acad Sci U S A 111 237-242 (2014)
  15. Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment. Jauch R, Cho MK, Jäkel S, Netter C, Schreiter K, Aicher B, Zweckstetter M, Jäckle H, Wahl MC. EMBO J 25 4020-4032 (2006)
  16. Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line. Bogomolovas J, Gasch A, Simkovic F, Rigden DJ, Labeit S, Mayans O. Open Biol 4 140041 (2014)
  17. Conservation, variability and the modeling of active protein kinases. Knight JD, Qian B, Baker D, Kothary R. PLoS One 2 e982 (2007)
  18. Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site. Jauch R, Jäkel S, Netter C, Schreiter K, Aicher B, Jäckle H, Wahl MC. Structure 13 1559-1568 (2005)
  19. Evolution of CASK into a Mg2+-sensitive kinase. Mukherjee K, Sharma M, Jahn R, Wahl MC, Südhof TC. Sci Signal 3 ra33 (2010)
  20. The MDM2 ubiquitination signal in the DNA-binding domain of p53 forms a docking site for calcium calmodulin kinase superfamily members. Craig AL, Chrystal JA, Fraser JA, Sphyris N, Lin Y, Harrison BJ, Scott MT, Dornreiter I, Hupp TR. Mol Cell Biol 27 3542-3555 (2007)
  21. The role of conserved water molecules in the catalytic domain of protein kinases. Knight JD, Hamelberg D, McCammon JA, Kothary R. Proteins 76 527-535 (2009)
  22. Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites. Simon B, Huart AS, Temmerman K, Vahokoski J, Mertens HD, Komadina D, Hoffmann JE, Yumerefendi H, Svergun DI, Kursula P, Schultz C, McCarthy AA, Hart DJ, Wilmanns M. Structure 24 851-861 (2016)
  23. Structure of the dimeric autoinhibited conformation of DAPK2, a pro-apoptotic protein kinase. Patel AK, Yadav RP, Majava V, Kursula I, Kursula P. J Mol Biol 409 369-383 (2011)
  24. The regulation of CHK2 in human cancer. Craig AL, Hupp TR. Oncogene 23 8411-8418 (2004)
  25. ZIPK: a unique case of murine-specific divergence of a conserved vertebrate gene. Shoval Y, Pietrokovski S, Kimchi A. PLoS Genet 3 1884-1893 (2007)
  26. Homodimerization of the death-associated protein kinase catalytic domain: development of a new small molecule fluorescent reporter. Zimmermann M, Atmanene C, Xu Q, Fouillen L, Van Dorsselaer A, Bonnet D, Marsol C, Hibert M, Sanglier-Cianferani S, Pigault C, McNamara LK, Watterson DM, Haiech J, Kilhoffer MC. PLoS One 5 e14120 (2010)
  27. GTP binding and intramolecular regulation by the ROC domain of Death Associated Protein Kinase 1. Jebelli JD, Dihanich S, Civiero L, Manzoni C, Greggio E, Lewis PA. Sci Rep 2 695 (2012)
  28. Targeting Pim Kinases and DAPK3 to Control Hypertension. Carlson DA, Singer MR, Sutherland C, Redondo C, Alexander LT, Hughes PF, Knapp S, Gurley SB, Sparks MA, MacDonald JA, Haystead TAJ. Cell Chem Biol 25 1195-1207.e32 (2018)
  29. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2″)-Ia. Caldwell SJ, Huang Y, Berghuis AM. Structure 24 935-945 (2016)
  30. Exploring Obscurin and SPEG Kinase Biology. Fleming JR, Rani A, Kraft J, Zenker S, Börgeson E, Lange S. J Clin Med 10 984 (2021)
  31. Link of Dlk/ZIP kinase to cell apoptosis and tumor suppression. Wu Y, Yan Q, Zuo J, Saiyin H, Jiang W, Qiao S, Yu L. Biochem Biophys Res Commun 392 510-515 (2010)
  32. Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+ and Sr2+: a QM/MM study. Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Phys Chem Chem Phys 19 10377-10394 (2017)
  33. PKD autoinhibition in trans regulates activation loop autophosphorylation in cis. Reinhardt R, Hirzel K, Link G, Eisler SA, Hägele T, Parson MAH, Burke JE, Hausser A, Leonard TA. Proc Natl Acad Sci U S A 120 e2212909120 (2023)
  34. Triple resonance EPR spectroscopy determines the Mn2+ coordination to ATP. Litvinov A, Feintuch A, Un S, Goldfarb D. J Magn Reson 294 143-152 (2018)
  35. Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study. Wang L, Yan F. Protein Sci 26 2010-2020 (2017)
  36. Overall protein structure quality assessment using hydrogen-bonding parameters. Afonine PV, Sobolev OV, Moriarty NW, Terwilliger TC, Adams PD. Acta Crystallogr D Struct Biol 79 684-693 (2023)


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