Review Special Issues

Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy

  • Received: 02 January 2015 Accepted: 19 March 2015 Published: 29 March 2015
  • The phosphatidylinositol 3-kinase-like kinases (PIKKs) are large serine-threonine protein kinases with a catalytic domain homologous to the phosphatidylinositol 3-kinase (PI3K). All PIKK family members share a general organization comprising a conserved C-terminus that contains the PI3K domain, which is preceded by a large N-terminal region made of helical HEAT repeats. In humans, the PIKK family includes six members, which play essential roles in various processes including DNA repair and DNA damage signalling (ATM, ATR, DNA-PKcs), control of cell growth (mTOR), nonsense-mediated mRNA decay (SMG1) and transcriptional regulation (TRRAP). High-resolution structural information is limited due to the large size (approx. 280-470 kDa) and structural complexity of these kinases. Adding further complexity, PIKKs work as part of larger assemblies with accessory subunits. These complexes are dynamic in composition and protein-protein and protein-DNA interactions regulate the kinase activity and functions of PIKKs. Moreover, recent findings have shown that the maturation and correct assembly of the PIKKs require a large chaperon machinery, containing RuvBL1 and RuvBL2 ATPases and the HSP90 chaperon. Single-particle electron microscopy (EM) is making key contributions to our understanding of the architecture of PIKKs and their complex regulation. This review summarizes the findings on the structure of these kinases, focusing mainly on medium-low resolution structures of several PIKKs obtained using EM, combined with X-ray crystallography of DNA-PKcs and mTOR. In addition, EM studies on higher-order complexes have revealed some of the mechanisms regulating the PIKKs, which will also be addressed. The model that emerges is that PIKKs, through their extensive interacting surfaces, integrate the information provided by multiple accessory subunits and nucleic acids to regulate their kinase activity in response to diverse stimuli.

    Citation: Angel Rivera-Calzada, Andrés López-Perrote, Roberto Melero, Jasminka Boskovic, Hugo Muñoz-Hernández, Fabrizio Martino, Oscar Llorca. Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy[J]. AIMS Biophysics, 2015, 2(2): 36-57. doi: 10.3934/biophy.2015.2.36

    Related Papers:

  • The phosphatidylinositol 3-kinase-like kinases (PIKKs) are large serine-threonine protein kinases with a catalytic domain homologous to the phosphatidylinositol 3-kinase (PI3K). All PIKK family members share a general organization comprising a conserved C-terminus that contains the PI3K domain, which is preceded by a large N-terminal region made of helical HEAT repeats. In humans, the PIKK family includes six members, which play essential roles in various processes including DNA repair and DNA damage signalling (ATM, ATR, DNA-PKcs), control of cell growth (mTOR), nonsense-mediated mRNA decay (SMG1) and transcriptional regulation (TRRAP). High-resolution structural information is limited due to the large size (approx. 280-470 kDa) and structural complexity of these kinases. Adding further complexity, PIKKs work as part of larger assemblies with accessory subunits. These complexes are dynamic in composition and protein-protein and protein-DNA interactions regulate the kinase activity and functions of PIKKs. Moreover, recent findings have shown that the maturation and correct assembly of the PIKKs require a large chaperon machinery, containing RuvBL1 and RuvBL2 ATPases and the HSP90 chaperon. Single-particle electron microscopy (EM) is making key contributions to our understanding of the architecture of PIKKs and their complex regulation. This review summarizes the findings on the structure of these kinases, focusing mainly on medium-low resolution structures of several PIKKs obtained using EM, combined with X-ray crystallography of DNA-PKcs and mTOR. In addition, EM studies on higher-order complexes have revealed some of the mechanisms regulating the PIKKs, which will also be addressed. The model that emerges is that PIKKs, through their extensive interacting surfaces, integrate the information provided by multiple accessory subunits and nucleic acids to regulate their kinase activity in response to diverse stimuli.


    加载中
    [1] Baretic D, Williams RL (2014) PIKKs - the solenoid nest where partners and kinases meet. Curr Opin Struct Biol 29C: 134-142.
    [2] Lovejoy CA, Cortez D (2009) Common mechanisms of PIKK regulation. DNA Repair (Amst) 8: 1004-1008. doi: 10.1016/j.dnarep.2009.04.006
    [3] Lempiainen H, Halazonetis TD (2009) Emerging common themes in regulation of PIKKs and PI3Ks. EMBO J 28: 3067-3073. doi: 10.1038/emboj.2009.281
    [4] van der Burg M, van Dongen JJ, van Gent DC (2009) DNA-PKcs deficiency in human: long predicted, finally found. Curr Opin Allergy Clin Immunol 9: 503-509. doi: 10.1097/ACI.0b013e3283327e41
    [5] Savitsky K, Bar-Shira A, Gilad S, et al. (1995) A single ataxia telangiectasia gene with a product similar to PI-3 kinase. Science 268: 1749-1753. doi: 10.1126/science.7792600
    [6] Weber AM, Ryan AJ (2014) ATM and ATR as therapeutic targets in cancer. Pharmacol Ther.
    [7] Roberts TL, Ho U, Luff J, et al. (2013) Smg1 haploinsufficiency predisposes to tumor formation and inflammation. Proc Natl Acad Sci U S A 110: E285-294. doi: 10.1073/pnas.1215696110
    [8] Zoncu R, Efeyan A, Sabatini DM (2011) mTOR: from growth signal integration to cancer, diabetes and ageing. Nat Rev Mol Cell Biol 12: 21-35. doi: 10.1038/nrm3025
    [9] Kong X, Shen Y, Jiang N, et al. (2011) Emerging roles of DNA-PK besides DNA repair. Cell Signal 23: 1273-1280. doi: 10.1016/j.cellsig.2011.04.005
    [10] Kruger A, Ralser M (2011) ATM is a redox sensor linking genome stability and carbon metabolism. Sci Signal 4: pe17.
    [11] Oliveira V, Romanow WJ, Geisen C, et al. (2008) A protective role for the human SMG-1 kinase against tumor necrosis factor-alpha-induced apoptosis. J Biol Chem 283: 13174-13184. doi: 10.1074/jbc.M708008200
    [12] Bosotti R, Isacchi A, Sonnhammer EL (2000) FAT: a novel domain in PIK-related kinases. Trends Biochem Sci 25: 225-227. doi: 10.1016/S0968-0004(00)01563-2
    [13] Keith CT, Schreiber SL (1995) PIK-related kinases: DNA repair, recombination, and cell cycle checkpoints. Science 270: 50-51. doi: 10.1126/science.270.5233.50
    [14] Brewerton SC, Dore AS, Drake AC, et al. (2004) Structural analysis of DNA-PKcs: modelling of the repeat units and insights into the detailed molecular architecture. J Struct Biol 145: 295-306. doi: 10.1016/j.jsb.2003.11.024
    [15] Perry J, Kleckner N (2003) The ATRs, ATMs, and TORs are giant HEAT repeat proteins. Cell 112: 151-155. doi: 10.1016/S0092-8674(03)00033-3
    [16] Sommer LA, Schaad M, Dames SA (2013) NMR- and circular dichroism-monitored lipid binding studies suggest a general role for the FATC domain as membrane anchor of phosphatidylinositol 3-kinase-related kinases (PIKK). J Biol Chem 288: 20046-20063. doi: 10.1074/jbc.M113.467233
    [17] Lucero H, Gae D, Taccioli GE (2003) Novel localization of the DNA-PK complex in lipid rafts: a putative role in the signal transduction pathway of the ionizing radiation response. J Biol Chem 278: 22136-22143. doi: 10.1074/jbc.M301579200
    [18] Dames SA (2010) Structural basis for the association of the redox-sensitive target of rapamycin FATC domain with membrane-mimetic micelles. J Biol Chem 285: 7766-7775. doi: 10.1074/jbc.M109.058404
    [19] Sancak Y, Bar-Peled L, Zoncu R, et al. (2010) Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141: 290-303. doi: 10.1016/j.cell.2010.02.024
    [20] Morita T, Yamashita A, Kashima I, et al. (2007) Distant N- and C-terminal domains are required for intrinsic kinase activity of SMG-1, a critical component of nonsense-mediated mRNA decay. J Biol Chem 282: 7799-7808. doi: 10.1074/jbc.M610159200
    [21] Yang H, Rudge DG, Koos JD, et al. (2013) mTOR kinase structure, mechanism and regulation. Nature 497: 217-223. doi: 10.1038/nature12122
    [22] Sirbu BM, Cortez D (2013) DNA damage response: three levels of DNA repair regulation. Cold Spring Harb Perspect Biol 5: a012724.
    [23] Ochi T, Wu Q, Blundell TL (2014) The spatial organization of non-homologous end joining: from bridging to end joining. DNA Repair (Amst) 17: 98-109. doi: 10.1016/j.dnarep.2014.02.010
    [24] Spagnolo L, Rivera-Calzada A, Pearl LH, et al. (2006) Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. Mol Cell 22: 511-519. doi: 10.1016/j.molcel.2006.04.013
    [25] Hammel M, Yu Y, Mahaney BL, et al. (2010) Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem 285: 1414-1423. doi: 10.1074/jbc.M109.065615
    [26] Lee JH, Paull TT (2005) ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 308: 551-554. doi: 10.1126/science.1108297
    [27] Zou L, Elledge SJ (2003) Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science 300: 1542-1548. doi: 10.1126/science.1083430
    [28] Heitman J, Movva NR, Hall MN (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253: 905-909. doi: 10.1126/science.1715094
    [29] Laplante M, Sabatini DM (2012) mTOR signaling in growth control and disease. Cell 149: 274-293. doi: 10.1016/j.cell.2012.03.017
    [30] Shimobayashi M, Hall MN (2014) Making new contacts: the mTOR network in metabolism and signalling crosstalk. Nat Rev Mol Cell Biol 15: 155-162. doi: 10.1038/nrm3757
    [31] Yamashita A (2013) Role of SMG-1-mediated Upf1 phosphorylation in mammalian nonsense-mediated mRNA decay. Genes Cells 18: 161-175. doi: 10.1111/gtc.12033
    [32] Yamashita A, Izumi N, Kashima I, et al. (2009) SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. Genes Dev 23: 1091-1105. doi: 10.1101/gad.1767209
    [33] Ivanov PV, Gehring NH, Kunz JB, et al. (2008) Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. Embo J 27: 736-747. doi: 10.1038/emboj.2008.17
    [34] Kashima I, Yamashita A, Izumi N, et al. (2006) Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. Genes Dev 20: 355-367. doi: 10.1101/gad.1389006
    [35] Murr R, Vaissiere T, Sawan C, et al. (2007) Orchestration of chromatin-based processes: mind the TRRAP. Oncogene 26: 5358-5372. doi: 10.1038/sj.onc.1210605
    [36] McMahon SB, Wood MA, Cole MD (2000) The essential cofactor TRRAP recruits the histone acetyltransferase hGCN5 to c-Myc. Mol Cell Biol 20: 556-562. doi: 10.1128/MCB.20.2.556-562.2000
    [37] Sibanda BL, Chirgadze DY, Blundell TL (2010) Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats. Nature 463: 118-121. doi: 10.1038/nature08648
    [38] Stark H (2010) GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol 481: 109-126. doi: 10.1016/S0076-6879(10)81005-5
    [39] Boskovic J, Rivera-Calzada A, Maman JD, et al. (2003) Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. EMBO J 22: 5875-5882. doi: 10.1093/emboj/cdg555
    [40] Melero R, Uchiyama A, Castano R, et al. (2014) Structures of SMG1-UPFs complexes: SMG1 contributes to regulate UPF2-dependent activation of UPF1 in NMD. Structure 22: 1105-1119. doi: 10.1016/j.str.2014.05.015
    [41] Dames SA, Mulet JM, Rathgeb-Szabo K, et al. (2005) The solution structure of the FATC domain of the protein kinase target of rapamycin suggests a role for redox-dependent structural and cellular stability. J Biol Chem 280: 20558-20564. doi: 10.1074/jbc.M501116200
    [42] Leone M, Crowell KJ, Chen J, et al. (2006) The FRB domain of mTOR: NMR solution structure and inhibitor design. Biochemistry 45: 10294-10302.
    [43] Yip CK, Murata K, Walz T, et al. (2010) Structure of the human mTOR complex I and its implications for rapamycin inhibition. Mol Cell 38: 768-774. doi: 10.1016/j.molcel.2010.05.017
    [44] Williams DR, Lee KJ, Shi J, et al. (2008) Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding. Structure 16: 468-477. doi: 10.1016/j.str.2007.12.014
    [45] Rivera-Calzada A, Maman JD, Spagnolo L, et al. (2005) Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Structure 13: 243-255. doi: 10.1016/j.str.2004.12.006
    [46] Kuhlbrandt W (2014) Cryo-EM enters a new era. Elife 3: e03678.
    [47] Llorca O, Rivera-Calzada A, Grantham J, et al. (2003) Electron microscopy and 3D reconstructions reveal that human ATM kinase uses an arm-like domain to clamp around double-stranded DNA. Oncogene 22: 3867-3874. doi: 10.1038/sj.onc.1206649
    [48] Arias-Palomo E, Yamashita A, Fernandez IS, et al. (2011) The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8. Genes Dev 25: 153-164. doi: 10.1101/gad.606911
    [49] Adami A, Garcia-Alvarez B, Arias-Palomo E, et al. (2007) Structure of TOR and its complex with KOG1. Mol Cell 27: 509-516. doi: 10.1016/j.molcel.2007.05.040
    [50] Chiu CY, Cary RB, Chen DJ, et al. (1998) Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase. J Mol Biol 284: 1075-1081. doi: 10.1006/jmbi.1998.2212
    [51] Leuther KK, Hammarsten O, Kornberg RD, et al. (1999) Structure of DNA-dependent protein kinase: implications for its regulation by DNA. EMBO J 18: 1114-1123. doi: 10.1093/emboj/18.5.1114
    [52] Grinthal A, Adamovic I, Weiner B, et al. (2010) PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis. Proc Natl Acad Sci USA 107: 2467-2472. doi: 10.1073/pnas.0914073107
    [53] Forwood JK, Lange A, Zachariae U, et al. (2010) Quantitative structural analysis of importin-beta flexibility: paradigm for solenoid protein structures. Structure 18: 1171-1183. doi: 10.1016/j.str.2010.06.015
    [54] Knutson BA (2010) Insights into the domain and repeat architecture of target of rapamycin. J Struct Biol 170: 354-363. doi: 10.1016/j.jsb.2010.01.002
    [55] Spagnolo L, Barbeau J, Curtin NJ, et al. (2012) Visualization of a DNA-PK/PARP1 complex. Nucleic Acids Res 40: 4168-4177. doi: 10.1093/nar/gkr1231
    [56] Morris EP, Rivera-Calzada A, da Fonseca PC, et al. (2011) Evidence for a remodelling of DNA-PK upon autophosphorylation from electron microscopy studies. Nucleic Acids Res 39: 5757-5767. doi: 10.1093/nar/gkr146
    [57] Bakkenist CJ, Kastan MB (2003) DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421: 499-506. doi: 10.1038/nature01368
    [58] Perry JJ, Tainer JA (2011) All stressed out without ATM kinase. Sci Signal 4: pe18.
    [59] Guo Z, Kozlov S, Lavin MF, et al. (2010) ATM activation by oxidative stress. Science 330: 517-521. doi: 10.1126/science.1192912
    [60] Shiloh Y, Ziv Y (2013) The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 14: 197-210. doi: 10.1038/nrm3546
    [61] Dynan WS, Yoo S (1998) Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res 26: 1551-1559. doi: 10.1093/nar/26.7.1551
    [62] Neal JA, Sugiman-Marangos S, VanderVere-Carozza P, et al. (2014) Unraveling the complexities of DNA-dependent protein kinase autophosphorylation. Mol Cell Biol 34: 2162-2175. doi: 10.1128/MCB.01554-13
    [63] Meek K, Douglas P, Cui X, et al. (2007) trans Autophosphorylation at DNA-dependent protein kinase's two major autophosphorylation site clusters facilitates end processing but not end joining. Mol Cell Biol 27: 3881-3890. doi: 10.1128/MCB.02366-06
    [64] Dobbs TA, Tainer JA, Lees-Miller SP (2010) A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (Amst) 9: 1307-1314. doi: 10.1016/j.dnarep.2010.09.019
    [65] Villarreal SA, Stewart PL (2014) CryoEM and image sorting for flexible protein/DNA complexes. J Struct Biol 187: 76-83. doi: 10.1016/j.jsb.2013.12.002
    [66] Wu PY, Ruhlmann C, Winston F, et al. (2004) Molecular architecture of the S. cerevisiae SAGA complex. Mol Cell 15: 199-208.
    [67] Chittuluru JR, Chaban Y, Monnet-Saksouk J, et al. (2011) Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes. Nat Struct Mol Biol 18: 1196-1203. doi: 10.1038/nsmb.2128
    [68] Kozlov SV, Graham ME, Jakob B, et al. (2011) Autophosphorylation and ATM activation: additional sites add to the complexity. J Biol Chem 286: 9107-9119. doi: 10.1074/jbc.M110.204065
    [69] Zhao R, Davey M, Hsu YC, et al. (2005) Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell 120: 715-727. doi: 10.1016/j.cell.2004.12.024
    [70] Boulon S, Bertrand E, Pradet-Balade B (2012) HSP90 and the R2TP co-chaperone complex: building multi-protein machineries essential for cell growth and gene expression. RNA Biol 9: 148-154. doi: 10.4161/rna.18494
    [71] Hurov KE, Cotta-Ramusino C, Elledge SJ (2010) A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability. Genes Dev 24: 1939-1950. doi: 10.1101/gad.1934210
    [72] Takai H, Wang RC, Takai KK, et al. (2007) Tel2 regulates the stability of PI3K-related protein kinases. Cell 131: 1248-1259. doi: 10.1016/j.cell.2007.10.052
    [73] Horejsi Z, Takai H, Adelman CA, et al. (2010) CK2 phospho-dependent binding of R2TP complex to TEL2 is essential for mTOR and SMG1 stability. Mol Cell 39: 839-850. doi: 10.1016/j.molcel.2010.08.037
    [74] Izumi N, Yamashita A, Iwamatsu A, et al. (2010) AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay. Sci Signal 3: ra27.
    [75] Pal M, Morgan M, Phelps SE, et al. (2014) Structural basis for phosphorylation-dependent recruitment of Tel2 to Hsp90 by Pih1. Structure 22: 805-818. doi: 10.1016/j.str.2014.04.001
    [76] Torreira E, Jha S, Lopez-Blanco JR, et al. (2008) Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes. Structure 16: 1511-1520. doi: 10.1016/j.str.2008.08.009
    [77] Lopez-Perrote A, Munoz-Hernandez H, Gil D, et al. (2012) Conformational transitions regulate the exposure of a DNA-binding domain in the RuvBL1-RuvBL2 complex. Nucleic Acids Res 40: 11086-11099. doi: 10.1093/nar/gks871
    [78] Matias PM, Gorynia S, Donner P, et al. (2006) Crystal structure of the human AAA+ protein RuvBL1. J Biol Chem 281: 38918-38929. doi: 10.1074/jbc.M605625200
    [79] Gorynia S, Bandeiras TM, Pinho FG, et al. (2011) Structural and functional insights into a dodecameric molecular machine - the RuvBL1/RuvBL2 complex. J Struct Biol 176: 279-291. doi: 10.1016/j.jsb.2011.09.001
    [80] Huen J, Kakihara Y, Ugwu F, et al. (2010) Rvb1-Rvb2: essential ATP-dependent helicases for critical complexes. Biochem Cell Biol 88: 29-40. doi: 10.1139/O09-122
    [81] Tosi A, Haas C, Herzog F, et al. (2013) Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 154: 1207-1219. doi: 10.1016/j.cell.2013.08.016
    [82] Nguyen VQ, Ranjan A, Stengel F, et al. (2013) Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell 154: 1220-1231. doi: 10.1016/j.cell.2013.08.018
    [83] Jha S, Dutta A (2009) RVB1/RVB2: running rings around molecular biology. Mol Cell 34: 521-533. doi: 10.1016/j.molcel.2009.05.016
    [84] Melero R, Buchwald G, Castano R, et al. (2012) The cryo-EM structure of the UPF-EJC complex shows UPF1 poised toward the RNA 3' end. Nat Struct Mol Biol 19: 498-505, S491-492. doi: 10.1038/nsmb.2287
    [85] Chakrabarti S, Jayachandran U, Bonneau F, et al. (2011) Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2. Mol Cell 41: 693-703. doi: 10.1016/j.molcel.2011.02.010
    [86] Ali MM, Roe SM, Vaughan CK, et al. (2006) Crystal structure of an Hsp90-nucleotide-p23/Sba1 closed chaperone complex. Nature 440: 1013-1017. doi: 10.1038/nature04716
    [87] Takai H, Xie Y, de Lange T, et al. (2010) Tel2 structure and function in the Hsp90-dependent maturation of mTOR and ATR complexes. Genes Dev 24: 2019-2030. doi: 10.1101/gad.1956410
  • Reader Comments
  • © 2015 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Metrics

Article views(7959) PDF downloads(1528) Cited by(10)

Article outline

Figures and Tables

Figures(7)

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return

Catalog