Skip to main content

Advertisement

Log in

The activation mechanisms of master kinases in the DNA damage response

  • Review Article
  • Published:
Genome Instability & Disease Aims and scope Submit manuscript

Abstract

DNA damage can be introduced by intrinsic or extrinsic stimuli and threaten the transmission of genetic information and ultimately, survival. Eukaryotes have evolved a sophisticated mechanism, DNA damage response (DDR), to counteract this threat posed by DNA damage. The DDR requires a series of proteins involved in multiple DNA repair pathways, of which ATM, ATR and DNA–PK serve as the three most critical kinases. The signaling mechanisms underlying these pathways have been extensively studied and these three master kinases structures determined by cryo-electron microscopy (cryo-EM) have led to tremendous progress in understanding the molecular mechanism of the DDR. In this review, we discuss the recent advances made in understanding the structures of ATM, ATR, and DNA–PK. We highlight the implications of these structures in terms of their function and regulation, and speculate on the critical role of PIKK regulatory domain (PRD) in their activation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Adamowicz, M. (2018). Breaking up with ATM. Journal of Immunology Science, 2, 26–31.

    Article  Google Scholar 

  • Adamowicz, M., Vermezovic, J., & di Fagagna, F. D. (2016). NOTCH1 inhibits activation of ATM by impairing the formation of an ATM-FOXO3a-KAT5/Tip60 complex. Cell Reports, 16, 2068–2076.

    Article  CAS  PubMed  Google Scholar 

  • Aparicio, T., Baer, R., & Gautier, J. (2014). DNA double-strand break repair pathway choice and cancer. DNA Repair (amst), 19, 169–175.

    Article  CAS  Google Scholar 

  • Bakkenist, C. J., & Kastan, M. B. (2003). DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature, 421, 499–506.

    Article  CAS  PubMed  Google Scholar 

  • Baretic, D., Maia de Oliveira, T., Niess, M., Wan, P., Pollard, H., Johnson, C. M., Truman, C., McCall, E., Fisher, D., Williams, R., et al. (2019). Structural insights into the critical DNA damage sensors DNA-PKcs, ATM and ATR. Progress in Biophysics and Molecular Biology, 147, 4–16.

    Article  CAS  PubMed  Google Scholar 

  • Baretic, D., Pollard, H.K., Fisher, D.I., Johnson, C.M., Santhanam, B., Truman, C.M., Kouba, T., Fersht, A.R., Phillips, C., and Williams, R.L. (2017). Structures of closed and open conformations of dimeric human ATM. Science Advances, 3, e1700933

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baretic, D., & Williams, R. L. (2014). PIKKs–the solenoid nest where partners and kinases meet. Current Opinion in Structural Biology, 29, 134–142.

    Article  CAS  PubMed  Google Scholar 

  • Bass, T.E., Luzwick, J.W., Kavanaugh, G., Carroll, C., Dungrawala, H., Glick, G.G., Feldkamp, M.D., Putney, R., Chazin, W.J., and Cortez, D. (2016). ETAA1 acts at stalled replication forks to maintain genome integrity. Nature Cell Biology, 18, 1185–1195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berkovich, E., Monnat, R. J., Jr., & Kastan, M. B. (2007). Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nature Cell Biology, 9, 683–690.

    Article  CAS  PubMed  Google Scholar 

  • Bhatti, S., Kozlov, S., Farooqi, A. A., Naqi, A., Lavin, M., & Khanna, K. K. (2011). ATM protein kinase: The linchpin of cellular defenses to stress. Cellular and Molecular Life Sciences, 68, 2977–3006.

    Article  CAS  PubMed  Google Scholar 

  • Blackford, A. N., & Jackson, S. P. (2017). ATM, ATR, and DNA-PK: The trinity at the heart of the DNA damage response. Molecular Cell, 66, 801–817.

    Article  CAS  PubMed  Google Scholar 

  • Boskovic, J., Rivera-Calzada, A., Maman, J. D., Chacon, P., Willison, K. R., Pearl, L. H., & Llorca, O. (2003). Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. EMBO Journal, 22, 5875–5882.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown, E. J., & Baltimore, D. (2000). ATR disruption leads to chromosomal fragmentation and early embryonic lethality. Gene Development, 14, 397–402.

    CAS  Google Scholar 

  • Callen, E., Jankovic, M., Wong, N., Zha, S., Chen, H. T., Difilippantonio, S., Di Virgilio, M., Heidkamp, G., Alt, F. W., Nussenzweig, A., et al. (2009). Essential role for DNA-PKcs in DNA double-strand break repair and apoptosis in ATM-deficient lymphocytes. Molecular Cell, 34, 285–297.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carter, T. H., Kopman, C. R., & James, C. B. (1988). DNA-stimulated protein phosphorylation in HeLa whole cell and nuclear extracts. Biochemical and Biophysical Research Communications, 157, 535–540.

    Article  CAS  PubMed  Google Scholar 

  • Chan, D. W., Chen, B. P., Prithivirajsingh, S., Kurimasa, A., Story, M. D., Qin, J., & Chen, D. J. (2002). Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks. Genes & Development, 16, 2333–2338.

    Article  CAS  Google Scholar 

  • Chan, D. W., & Lees-Miller, S. P. (1996). The DNA-dependent protein kinase is inactivated by autophosphorylation of the catalytic subunit. Journal of Biological Chemistry, 271, 8936–8941.

    Article  CAS  PubMed  Google Scholar 

  • Chaplin, A. K., Hardwick, S. W., Liang, S., Kefala Stavridi, A., Hnizda, A., Cooper, L. R., De Oliveira, T. M., Chirgadze, D. Y., & Blundell, T. L. (2021). Dimers of DNA-PK create a stage for DNA double-strand break repair. Nature Structural & Molecular Biology, 28, 13–19.

    Article  CAS  Google Scholar 

  • Chen, S., Lee, L., Naila, T., Fishbain, S., Wang, A., Tomkinson, A. E., Lees-Miller, S. P., & He, Y. (2021a). Structural basis of long-range to short-range synaptic transition in NHEJ. Nature, 593, 294–298.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen, X., Xu, X., Chen, Y., Cheung, J.C., Wang, H., Jiang, J., de Val, N., Fox, T., Gellert, M., and Yang, W. (2021b). Structure of an activated DNA-PK and its implications for NHEJ. Molecular Cell, 81, 801–810.

  • Chi, X., Li, Y., & Qiu, X. (2020). V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: Mechanism and regulation. Immunology, 160, 233–247.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chiu, C. Y., Cary, R. B., Chen, D. J., Peterson, S. R., & Stewart, P. L. (1998). Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase. Journal of Molecular Biology, 284, 1075–1081.

    Article  CAS  PubMed  Google Scholar 

  • Ciccia, A., & Elledge, S. J. (2010). The DNA damage response: making it safe to play with knives. Molecular Cell, 40, 179–204.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cimprich, K. A., & Cortez, D. (2008). ATR: an essential regulator of genome integrity. Nature Reviews Molecular Cell Biology, 9, 616–627.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cortez, D., Guntuku, S., Qin, J., & Elledge, S. J. (2001). ATR and ATRIP: partners in checkpoint signaling. Science, 294, 1713–1716.

    Article  CAS  PubMed  Google Scholar 

  • Cotta-Ramusino, C., McDonald, E. R., 3rd., Hurov, K., Sowa, M. E., Harper, J. W., & Elledge, S. J. (2011). A DNA damage response screen identifies RHINO, a 9-1-1 and TopBP1 interacting protein required for ATR signaling. Science, 332, 1313–1317.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davis, A. J., Chen, B. P., & Chen, D. J. (2014). DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (amst), 17, 21–29.

    Article  CAS  Google Scholar 

  • de Klein, A., Muijtjens, M., van Os, R., Verhoeven, Y., Smit, B., Carr, A. M., Lehmann, A. R., & Hoeijmakers, J. H. J. (2000). Targeted disruption of the cell-cycle checkpoint gene ATR leads to early embryonic lethality in mice. Current Biology, 10, 479–482.

    Article  PubMed  Google Scholar 

  • DeFazio, L. G., Stansel, R. M., Griffith, J. D., & Chu, G. (2002). Synapsis of DNA ends by DNA-dependent protein kinase. EMBO Journal, 21, 3192–3200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delacroix, S., Wagner, J. M., Kobayashi, M., Yamamoto, K., & Karnitz, L. M. (2007). The Rad9-Hus1-Rad1 (9-1-1) clamp activates checkpoint signaling via TopBP1. Genes & Development, 21, 1472–1477.

    Article  CAS  Google Scholar 

  • Ding, Q., Reddy, Y. V., Wang, W., Woods, T., Douglas, P., Ramsden, D. A., Lees-Miller, S. P., & Meek, K. (2003). Autophosphorylation of the catalytic subunit of the DNA-dependent protein kinase is required for efficient end processing during DNA double-strand break repair. Molecular and Cellular Biology, 23, 5836–5848.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dobbs, T. A., Tainer, J. A., & Lees-Miller, S. P. (2010). A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (amst), 9, 1307–1314.

    Article  CAS  PubMed Central  Google Scholar 

  • Dupre, A., Boyer-Chatenet, L., & Gautier, J. (2006). Two-step activation of ATM by DNA and the Mre11-Rad50-Nbs1 complex. Nature Structural & Molecular Biology, 13, 451–457.

    Article  CAS  Google Scholar 

  • Duursma, A. M., Driscoll, R., Elias, J. E., & Cimprich, K. A. (2013). A role for the MRN complex in ATR activation via TOPBP1 recruitment. Molecular Cell, 50, 116–122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernandes, N., Sun, Y., Chen, S., Paul, P., Shaw, R. J., Cantley, L. C., & Price, B. D. (2005). DNA damage-induced association of ATM with its target proteins requires a protein interaction domain in the N terminus of ATM. Journal of Biological Chemistry, 280, 15158–15164.

    Article  CAS  PubMed  Google Scholar 

  • Gottlieb, T. M., & Jackson, S. P. (1993). The DNA-dependent protein kinase: Requirement for DNA ends and association with Ku antigen. Cell, 72, 131–142.

    Article  CAS  PubMed  Google Scholar 

  • Graham, T. G., Walter, J. C., & Loparo, J. J. (2016). Two-stage synapsis of DNA ends during non-homologous end joining. Molecular Cell, 61, 850–858.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greenwell, P. W., Kronmal, S. L., Porter, S. E., Gassenhuber, J., Obermaier, B., & Petes, T. D. (1995). TEL1, a gene involved in controlling telomere length in S. cerevisiae, is homologous to the human ataxia telangiectasia gene. Cell, 82, 823–829.

    Article  CAS  PubMed  Google Scholar 

  • Guo, Z., Deshpande, R., & Paull, T. T. (2010a). ATM activation in the presence of oxidative stress. Cell Cycle, 9, 4805–4811.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo, Z., Kozlov, S., Lavin, M. F., Person, M. D., & Paull, T. T. (2010b). ATM activation by oxidative stress. Science, 330, 517–521.

    Article  CAS  PubMed  Google Scholar 

  • Haahr, P., Hoffmann, S., Tollenaere, M. A., Ho, T., Toledo, L. I., Mann, M., Bekker-Jensen, S., Raschle, M., & Mailand, N. (2016). Activation of the ATR kinase by the RPA-binding protein ETAA1. Nature Cell Biology, 18, 1196–1207.

    Article  CAS  PubMed  Google Scholar 

  • Hailemariam, S., Kumar, S., & Burgers, P. M. (2019). Activation of Tel1(ATM) kinase requires Rad50 ATPase and long nucleosome-free DNA but no DNA ends. Journal of Biological Chemistry, 294, 10120–10130.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hammel, M., Yu, Y., Mahaney, B. L., Cai, B., Ye, R., Phipps, B. M., Rambo, R. P., Hura, G. L., Pelikan, M., So, S., et al. (2010). Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. Journal of Biological Chemistry, 285, 1414–1423.

    Article  PubMed  Google Scholar 

  • Harper, J. W., & Elledge, S. J. (2007). The DNA damage response: ten years after. Molecular Cell, 28, 739–745.

    Article  CAS  PubMed  Google Scholar 

  • Hartlerode, A. J., Morgan, M. J., Wu, Y., Buis, J., & Ferguson, D. O. (2015). Recruitment and activation of the ATM kinase in the absence of DNA-damage sensors. Nature Structural & Molecular Biology, 22, 736–743.

    Article  CAS  Google Scholar 

  • Hartley, K. O., Gell, D., Smith, G. C., Zhang, H., Divecha, N., Connelly, M. A., Admon, A., Lees-Miller, S. P., Anderson, C. W., & Jackson, S. P. (1995). DNA-dependent protein kinase catalytic subunit: a relative of phosphatidylinositol 3-kinase and the ataxia telangiectasia gene product. Cell, 82, 849–856.

    Article  CAS  PubMed  Google Scholar 

  • Hoeijmakers, J. H. (2009). DNA damage, aging, and cancer. New England Journal of Medicine, 361, 1475–1485.

    Article  CAS  PubMed  Google Scholar 

  • Iijima, S., Teraoka, H., Date, T., & Tsukada, K. (1992). DNA-activated protein kinase in Raji Burkitt’s lymphoma cells. Phosphorylation of c-Myc oncoprotein. European Journal of Biochemistry, 206, 595–603.

    Article  CAS  PubMed  Google Scholar 

  • Jackson, S. P., & Bartek, J. (2009). The DNA-damage response in human biology and disease. Nature, 461, 1071–1078.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jackson, S. P., MacDonald, J. J., Lees-Miller, S., & Tjian, R. (1990). GC box binding induces phosphorylation of Sp1 by a DNA-dependent protein kinase. Cell, 63, 155–165.

    Article  CAS  PubMed  Google Scholar 

  • Jansma, M., Linke-Winnebeck, C., Eustermann, S., Lammens, K., Kostrewa, D., Stakyte, K., Litz, C., Kessler, B., and Hopfner, K.P. (2020). Near-Complete Structure and Model of Tel1ATM from Chaetomium thermophilum Reveals a Robust Autoinhibited ATP State. Structure, 28, 83–95

    Article  CAS  PubMed  Google Scholar 

  • Jeggo, P. A., Taccioli, G. E., & Jackson, S. P. (1995). Menage a trois: double strand break repair, V(D)J recombination and DNA-PK. BioEssays, 17, 949–957.

    Article  CAS  PubMed  Google Scholar 

  • Jette, N., & Lees-Miller, S. P. (2015). The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis. Progress in Biophysics and Molecular Biology, 117, 194–205.

    Article  CAS  PubMed  Google Scholar 

  • Kanu, N., & Behrens, A. (2007). ATMIN defines an NBS1-independent pathway of ATM signalling. EMBO Journal, 26, 2933–2941.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanu, N., & Behrens, A. (2008). ATMINistrating ATM signalling: regulation of ATM by ATMIN. Cell Cycle, 7, 3483–3486.

    Article  CAS  PubMed  Google Scholar 

  • Kumagai, A., Lee, J., Yoo, H. Y., & Dunphy, W. G. (2006). TopBP1 activates the ATR-ATRIP complex. Cell, 124, 943–955.

    Article  CAS  PubMed  Google Scholar 

  • Kumar, S., & Burgers, P. M. (2013). Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery. Gene Development, 27, 313–321.

    Article  CAS  Google Scholar 

  • Kumar, V., Alt, F.W. (2016). NHEJ and Other Repair Factors in V(D)J Recombination. In Encyclopedia of Immunobiology, pp. 107–114

  • Kurimasa, A., Kumano, S., Boubnov, N. V., Story, M. D., Tung, C. S., Peterson, S. R., & Chen, D. J. (1999). Requirement for the kinase activity of human DNA-dependent protein kinase catalytic subunit in DNA strand break rejoining. Molecular and Cellular Biology, 19, 3877–3884.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langer, L.M., Gat, Y., Bonneau, F., Conti, E. (2020). Structure of substrate-bound SMG1–8–9 kinase complex reveals molecular basis for phosphorylation specificity. Elife, 57127

  • Lau, W. C., Li, Y., Liu, Z., Gao, Y., Zhang, Q., & Huen, M. S. (2016). Structure of the human dimeric ATM kinase. Cell Cycle, 15, 1117–1124.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lavin, M. F. (2008). Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer. Nature Reviews Molecular Cell Biology, 9, 759–769.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J., Kumagai, A., & Dunphy, W. G. (2007). The Rad9-Hus1-Rad1 checkpoint clamp regulates interaction of TopBP1 with ATR. Journal of Biological Chemistry, 282, 28036–28044.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J.H., Mand, M.R., Kao, C.H., Zhou, Y., Ryu, S.W., Richards, A.L., Coon, J.J., and Paull, T.T. (2018). ATM directs DNA damage responses and proteostasis via genetically separable pathways. Science Signal, 11, eaan5598.

  • Lee, J. H., & Paull, T. T. (2004). Direct activation of the ATM protein kinase by the Mre11/Rad50/Nbs1 complex. Science, 304, 93–96.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J. H., & Paull, T. T. (2005). ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science, 308, 551–554.

    Article  CAS  PubMed  Google Scholar 

  • Lee, Y. C., Zhou, Q., Chen, J. J., & Yuan, J. S. (2016). RPA-binding protein ETAA1 Is an ATR activator involved in DNA replication stress response. Current Biology, 26, 3257–3268.

    Article  CAS  PubMed  Google Scholar 

  • Lees-Miller, S. P., & Anderson, C. W. (1989). The human double-stranded DNA-activated protein kinase phosphorylates the 90-kDa heat-shock protein, hsp90 alpha at two NH2-terminal threonine residues. Journal of Biological Chemistry, 264, 17275–17280.

    Article  CAS  PubMed  Google Scholar 

  • Lees-Miller, S. P., Chen, Y. R., & Anderson, C. W. (1990). Human cells contain a DNA-activated protein kinase that phosphorylates simian virus 40 T antigen, mouse p53, and the human Ku autoantigen. Molecular and Cellular Biology, 10, 6472–6481.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lempiainen, H., & Halazonetis, T. D. (2009). Emerging common themes in regulation of PIKKs and PI3Ks. EMBO Journal, 28, 3067–3073.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lieber, M. R. (2010). The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annual Review of Biochemistry, 79, 181–211.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Little, A.J., Matthews, A., Oettinger, M., Roth, D.B., Schatz, D.G. (2015). The Mechanism of V(D)J Recombination. In Molecular Biology of B Cells, pp. 13–34.  

    Google Scholar 

  • Liu, S. Z., Shiotani, B., Lahiri, M., Marechal, A., Tse, A., Leung, C. C. Y., Glover, J. N. M., Yang, X. H. H., & Zou, L. (2011). ATR autophosphorylation as a molecular switch for checkpoint activation. Molecular Cell, 43, 192–202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Llorca, O., Rivera-Calzada, A., Grantham, J., & Willison, K. R. (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.

    Article  CAS  PubMed  Google Scholar 

  • Lovejoy, C. A., & Cortez, D. (2009). Common mechanisms of PIKK regulation. DNA Repair (amst), 8, 1004–1008.

    Article  CAS  Google Scholar 

  • Lustig, A. J., & Petes, T. D. (1986). Identification of yeast mutants with altered telomere structure. Proceedings of National Academy Science of United States of America, 83, 1398–1402.

    Article  CAS  Google Scholar 

  • MacDougall, C. A., Byun, T. S., Van, C., Yee, M. C., & Cimprich, K. A. (2007). The structural determinants of checkpoint activation. Genes & Development, 21, 898–903.

    Article  CAS  Google Scholar 

  • Marechal, A., & Zou, L. (2013). DNA damage sensing by the ATM and ATR kinases. Cold Spring Harb Perspect Biol, 5.

  • McKinnon, P. J. (2012). ATM and the molecular pathogenesis of ataxia telangiectasia. Annual Review of Pathology: Mechanisms of Disease, 7, 303–321.

    Article  CAS  Google Scholar 

  • Meek, K., Dang, V., & Lees-Miller, S. P. (2008). DNA-PK: the means to justify the ends? Advances in Immunology, 99, 33–58.

    Article  CAS  PubMed  Google Scholar 

  • Mordes, D. A., Glick, G. G., Zhao, R., & Cortez, D. (2008a). TopBP1 activates ATR through ATRIP and a PIKK regulatory domain. Genes & Development, 22, 1478–1489.

    Article  CAS  Google Scholar 

  • Mordes, D. A., Nam, E. A., & Cortez, D. (2008b). Dpb11 activates the Mec1-Ddc2 complex. Proceedings of National Academy Science of United States of America, 105, 18730–18734.

    Article  CAS  Google Scholar 

  • Murr, R., Vaissiere, T., Sawan, C., Shukla, V., & Herceg, Z. (2007). Orchestration of chromatin-based processes: mind the TRRAP. Oncogene, 26, 5358–5372.

    Article  CAS  PubMed  Google Scholar 

  • Nagasawa, H., Little, J. B., Lin, Y. F., So, S., Kurimasa, A., Peng, Y., Brogan, J. R., Chen, D. J., Bedford, J. S., & Chen, B. P. (2011). Differential role of DNA-PKcs phosphorylations and kinase activity in radiosensitivity and chromosomal instability. Radiation Research, 175, 83–89.

    Article  CAS  PubMed  Google Scholar 

  • Nam, E. A., Zhao, R. X., Glick, G. G., Bansbach, C. E., Friedman, D. B., & Cortez, D. (2011). Thr-1989 phosphorylation is a marker of active ataxia telangiectasia-mutated and Rad3-related (ATR) kinase. Journal of Biological Chemistry, 286, 28707–28714.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Namiki, Y., & Zou, L. (2006). ATRIP associates with replication protein A-coated ssDNA through multiple interactions. Proceedings of National Academy Science of United States of America, 103, 580–585.

    Article  CAS  Google Scholar 

  • Navadgi-Patil, V. M., & Burgers, P. M. (2008). Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. Journal of Biological Chemistry, 283, 35853–35859.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Navadgi-Patil, V. M., & Burgers, P. M. (2009). The unstructured C-terminal tail of the 9-1-1 clamp subunit Ddc1 activates Mec1/ATR via two distinct mechanisms. Molecular Cell, 36, 743–753.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ochi, T., Wu, Q., & Blundell, T. L. (2014). The spatial organization of non-homologous end joining: from bridging to end joining. DNA Repair (amst), 17, 98–109.

    Article  CAS  Google Scholar 

  • Paull, T. T. (2015). Mechanisms of ATM activation. Annual Review of Biochemistry, 84, 711–738.

    Article  CAS  PubMed  Google Scholar 

  • Rao, Q., Liu, M., Tian, Y., Wu, Z., Hao, Y., Song, L., Qin, Z., Ding, C., Wang, H. W., Wang, J., et al. (2018). Cryo-EM structure of human ATR-ATRIP complex. Cell Research, 28, 143–156.

    Article  CAS  PubMed  Google Scholar 

  • Reddy, Y. V., Ding, Q., Lees-Miller, S. P., Meek, K., & Ramsden, D. A. (2004). Non-homologous end joining requires that the DNA-PK complex undergo an autophosphorylation-dependent rearrangement at DNA ends. Journal of Biological Chemistry, 279, 39408–39413.

    Article  CAS  PubMed  Google Scholar 

  • Rivera-Calzada, A., López-Perrote, A., Melero, R., Boskovic, J., Muñoz-Hernández, H., Martino, F., & Llorca, O. (2015). Structure and assembly of the PI3K-like protein kinases (PIKKs) revealed by electron microscopy. AIMS Biophysics, 2, 36–57.

    Article  CAS  Google Scholar 

  • Rivera-Calzada, A., Maman, J. D., Spagnolo, L., Pearl, L. H., & Llorca, O. (2005). Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Structure, 13, 243–255.

    Article  CAS  PubMed  Google Scholar 

  • Rubinson, E. H., Gowda, A. S., Spratt, T. E., Gold, B., & Eichman, B. F. (2010). An unprecedented nucleic acid capture mechanism for excision of DNA damage. Nature, 468, 406–411.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saldivar, J. C., Cortez, D., & Cimprich, K. A. (2017). The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nature Reviews Molecular Cell Biology, 18, 622–636.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Savitsky, K., Bar-Shira, A., Gilad, S., Rotman, G., Ziv, Y., Vanagaite, L., Tagle, D. A., Smith, S., Uziel, T., Sfez, S., et al. (1995). A single ataxia telangiectasia gene with a product similar to PI-3 kinase. Science, 268, 1749–1753.

    Article  CAS  PubMed  Google Scholar 

  • Schatz, D. G., & Swanson, P. C. (2011). V(D)J recombination: mechanisms of initiation. Annual Review of Genetics, 45, 167–202.

    Article  CAS  PubMed  Google Scholar 

  • Scully, R., Panday, A., Elango, R., & Willis, N. A. (2019). DNA double-strand break repair-pathway choice in somatic mammalian cells. Nature Reviews Molecular Cell Biology, 20, 698–714.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharif, H., Li, Y., Dong, Y., Dong, L., Wang, W. L., Mao, Y., & Wu, H. (2017). Cryo-EM structure of the DNA-PK holoenzyme. Proceedings of National Academy Science of United States of America, 114, 7367–7372.

    Article  CAS  Google Scholar 

  • Shiotani, B., & Zou, L. (2009). Single-Stranded DNA Orchestrates an ATM-to-ATR Switch at DNA Breaks. Molecular Cell, 33, 547–558.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sibanda, B. L., Chirgadze, D. Y., Ascher, D. B., & Blundell, T. L. (2017). DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science, 355, 520–524.

    Article  CAS  PubMed  Google Scholar 

  • Sibanda, B. L., Chirgadze, D. Y., & Blundell, T. L. (2010). Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats. Nature, 463, 118–121.

    Article  CAS  PubMed  Google Scholar 

  • So, S., Davis, A. J., & Chen, D. J. (2009). Autophosphorylation at serine 1981 stabilizes ATM at DNA damage sites. Journal of Cell Biology, 187, 977–990.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spagnolo, L., Rivera-Calzada, A., Pearl, L. H., & Llorca, O. (2006). Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. Molecular Cell, 22, 511–519.

    Article  CAS  PubMed  Google Scholar 

  • Sun, Y., Jiang, X., Chen, S., Fernandes, N., & Price, B. D. (2005). A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proceedings of National Academy Science of United States of America, 102, 13182–13187.

    Article  CAS  Google Scholar 

  • Sun, Y., Xu, Y., Roy, K., & Price, B. D. (2007). DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity. Molecular and Cellular Biology, 27, 8502–8509.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suwa, A., Hirakata, M., Takeda, Y., Jesch, S. A., Mimori, T., & Hardin, J. A. (1994). DNA-dependent protein kinase (Ku protein-p350 complex) assembles on double-stranded DNA. Proceedings of National Academy Science of United States of America, 91, 6904–6908.

    Article  CAS  Google Scholar 

  • Takai, H., Wang, R. C., Takai, K. K., Yang, H., & de Lange, T. (2007). Tel2 regulates the stability of PI3K-related protein kinases. Cell, 131, 1248–1259.

    Article  CAS  PubMed  Google Scholar 

  • Tannous, E. A., Yates, L. A., Zhang, X., & Burgers, P. M. (2021). Mechanism of auto-inhibition and activation of Mec1(ATR) checkpoint kinase. Nature Structural & Molecular Biology, 28, 50–61.

    Article  CAS  Google Scholar 

  • Walker, A. I., Hunt, T., Jackson, R. J., & Anderson, C. W. (1985). Double-stranded DNA induces the phosphorylation of several proteins including the 90 000 mol. wt. heat-shock protein in animal cell extracts. EMBO Journal, 4, 139–145.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, X., Chu, H., Lv, M., Zhang, Z., Qiu, S., Liu, H., Shen, X., Wang, W., & Cai, G. (2016). Structure of the intact ATM/Tel1 kinase. Nature Communications, 7, 11655.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, X., Ran, T., Zhang, X., Xin, J., Zhang, Z., Wu, T., Wang, W., & Cai, G. (2017). 3.9 A structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Science, 358, 1206–1209.

    Article  CAS  PubMed  Google Scholar 

  • Xiao, J., Liu, M., Qi, Y., Chaban, Y., Gao, C., Pan, B., Tian, Y., Yu, Z., Li, J., Zhang, P., et al. (2019). Structural insights into the activation of ATM kinase. Cell Research, 29, 683–685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xin, J., Xu, Z., Wang, X., Tian, Y., Zhang, Z., & Cai, G. (2019). Structural basis of allosteric regulation of Tel1/ATM kinase. Cell Research, 29, 655–665.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yaneva, M., Kowalewski, T., & Lieber, M. R. (1997). Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies. EMBO Journal, 16, 5098–5112.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang, H., Jiang, X., Li, B., Yang, H. J., Miller, M., Yang, A., Dhar, A., & Pavletich, N. P. (2017). Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Nature, 552, 368–373.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yates, L.A., Williams, R.M., Hailemariam, S., Ayala, R., Burgers, P., and Zhang, X. (2020). Cryo-EM Structure of Nucleotide-Bound Tel1(ATM) Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations. Structure, 28, 96–104. e103

    Google Scholar 

  • Yin, X., Liu, M., Tian, Y., Wang, J., & Xu, Y. (2017). Cryo-EM structure of human DNA-PK holoenzyme. Cell Research, 27, 1341–1350.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • You, Z., Chahwan, C., Bailis, J., Hunter, T., & Russell, P. (2005). ATM activation and its recruitment to damaged DNA require binding to the C terminus of Nbs1. Molecular and Cellular Biology, 25, 5363–5379.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeman, M. K., & Cimprich, K. A. (2014). Causes and consequences of replication stress. Nature Cell Biology, 16, 2–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, S., Yajima, H., Huynh, H., Zheng, J., Callen, E., Chen, H. T., Wong, N., Bunting, S., Lin, Y. F., Li, M., et al. (2011). Congenital bone marrow failure in DNA-PKcs mutant mice associated with deficiencies in DNA repair. Journal of Cell Biology, 193, 295–305.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou, Z.W., Liu, C., Li, T.L., Bruhn, C., Krueger, A., Min, W., Wang, Z.Q., & Carr, A.M. (2013). An essential function for the ATR-activation-domain (AAD) of TopBP1 in mouse development and cellular senescence. PLoS Genet, 9, e1003702.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu, L., Li, L., Qi, Y., Yu, Z., & Xu, Y. (2019). Cryo-EM structure of SMG1-SMG8-SMG9 complex. Cell Research, 29, 1027–1034.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zou, L., Cortez, D., & Elledge, S. J. (2002). Regulation of ATR substrate selection by Rad17-dependent loading of Rad9 complexes onto chromatin. Genes & Development, 16, 198–208.

    Article  CAS  Google Scholar 

  • Zou, L., & Elledge, S. J. (2003). Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science, 300, 1542–1548.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31830107 and 31821002). We thank Dr Jessica Tamanini at Shenzhen University Health Science Center for editing the manuscript prior to submission. We would like to acknowledge the vast number of other highly valuable papers that could not be cited in this review due to space limitations.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Jianxiong Xiao or Qinhui Rao.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xiao, J., Rao, Q. & Xu, Y. The activation mechanisms of master kinases in the DNA damage response. GENOME INSTAB. DIS. 2, 211–224 (2021). https://doi.org/10.1007/s42764-021-00045-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42764-021-00045-y

Keywords

Navigation