7sid

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Human ATM Dimer Bound to Nbs1

Structural highlights

7sid is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 2.53Å
Ligands:ANP, MG
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

ATM_HUMAN Mantle cell lymphoma;B-cell chronic lymphocytic leukemia;Combined cervical dystonia;Ataxia-telangiectasia;Ataxia-telangiectasia variant. The disease is caused by mutations affecting the gene represented in this entry. Defects in ATM contribute to T-cell acute lymphoblastic leukemia (TALL) and T-prolymphocytic leukemia (TPLL). TPLL is characterized by a high white blood cell count, with a predominance of prolymphocytes, marked splenomegaly, lymphadenopathy, skin lesions and serous effusion. The clinical course is highly aggressive, with poor response to chemotherapy and short survival time. TPLL occurs both in adults as a sporadic disease and in younger AT patients.[1] [2] [3] [4] [5] Defects in ATM contribute to B-cell non-Hodgkin lymphomas (BNHL), including mantle cell lymphoma (MCL).[6] [7] [8] Defects in ATM contribute to B-cell chronic lymphocytic leukemia (BCLL). BCLL is the commonest form of leukemia in the elderly. It is characterized by the accumulation of mature CD5+ B-lymphocytes, lymphadenopathy, immunodeficiency and bone marrow failure.[9] [10] [11]

Function

ATM_HUMAN Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. After the introduction of DNA breaks by the RAG complex on one immunoglobulin allele, acts by mediating a repositioning of the second allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. Also involved in signal transduction and cell cycle control. May function as a tumor suppressor. Necessary for activation of ABL1 and SAPK. Phosphorylates DYRK2, CHEK2, p53/TP53, FANCD2, NFKBIA, BRCA1, CTIP, nibrin (NBN), TERF1, RAD9 and DCLRE1C. May play a role in vesicle and/or protein transport. Could play a role in T-cell development, gonad and neurological function. Plays a role in replication-dependent histone mRNA degradation. Binds DNA ends. Phosphorylation of DYRK2 in nucleus in response to genotoxic stress prevents its MDM2-mediated ubiquitination and subsequent proteasome degradation. Phosphorylates ATF2 which stimulates its function in DNA damage response.[12] [13] [14] [15] [16] [17] [18] [19]

Publication Abstract from PubMed

DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, which belongs to the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family. In response to DSBs, ATM is activated by the MRN (Mre11-Rad50-Nbs1) protein complex through a poorly-understood process that also requires double-stranded DNA. Previous studies indicate that the FxF/Y motif of Nbs1 directly binds to ATM, and is required to retain active ATM at sites of DNA damage. Here we report the 2.5 A resolution cryo-EM structures of human ATM and its complex with the Nbs1 FxF/Y motif. In keeping with previous structures of ATM and its yeast homolog Tel1, the dimeric human ATM kinase adopts a symmetric, butterfly-shaped structure. The conformation of the ATM kinase domain is most similar to the inactive states of other PIKKs, suggesting that activation may involve an analogous realigning the N and C lobes along with relieving the blockage of the substrate-binding site. We also show that the Nbs1 FxF/Y motif binds to a conserved hydrophobic cleft within the Spiral domain of ATM, suggesting an allosteric mechanism of activation. We evaluate the importance of these structural findings with mutagenesis and biochemical assays.

Structure of the human ATM kinase and mechanism of Nbs1 binding.,Warren C, Pavletich NP Elife. 2022 Jan 25;11. pii: 74218. doi: 10.7554/eLife.74218. PMID:35076389[20]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
6 reviews cite this structure
Lethal and Non-Lethal Functions of Caspases in the DNA Damage Response.
Lopez et al. (2022)
5 more
6 other articles
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References

  1. ↑ Vorechovsky I, Luo L, Dyer MJ, Catovsky D, Amlot PL, Yaxley JC, Foroni L, Hammarstrom L, Webster AD, Yuille MA. Clustering of missense mutations in the ataxia-telangiectasia gene in a sporadic T-cell leukaemia. Nat Genet. 1997 Sep;17(1):96-9. PMID:9288106 doi:http://dx.doi.org/10.1038/ng0997-96
  2. ↑ Stilgenbauer S, Schaffner C, Litterst A, Liebisch P, Gilad S, Bar-Shira A, James MR, Lichter P, Dohner H. Biallelic mutations in the ATM gene in T-prolymphocytic leukemia. Nat Med. 1997 Oct;3(10):1155-9. PMID:9334731
  3. ↑ Stankovic T, Kidd AM, Sutcliffe A, McGuire GM, Robinson P, Weber P, Bedenham T, Bradwell AR, Easton DF, Lennox GG, Haites N, Byrd PJ, Taylor AM. ATM mutations and phenotypes in ataxia-telangiectasia families in the British Isles: expression of mutant ATM and the risk of leukemia, lymphoma, and breast cancer. Am J Hum Genet. 1998 Feb;62(2):334-45. PMID:9463314 doi:http://dx.doi.org/10.1086/301706
  4. ↑ Yuille MA, Coignet LJ, Abraham SM, Yaqub F, Luo L, Matutes E, Brito-Babapulle V, Vorechovsky I, Dyer MJ, Catovsky D. ATM is usually rearranged in T-cell prolymphocytic leukaemia. Oncogene. 1998 Feb 12;16(6):789-96. PMID:9488043 doi:http://dx.doi.org/10.1038/sj.onc.1201603
  5. ↑ Stoppa-Lyonnet D, Soulier J, Lauge A, Dastot H, Garand R, Sigaux F, Stern MH. Inactivation of the ATM gene in T-cell prolymphocytic leukemias. Blood. 1998 May 15;91(10):3920-6. PMID:9573030
  6. ↑ Schaffner C, Stilgenbauer S, Rappold GA, Dohner H, Lichter P. Somatic ATM mutations indicate a pathogenic role of ATM in B-cell chronic lymphocytic leukemia. Blood. 1999 Jul 15;94(2):748-53. PMID:10397742
  7. ↑ Schaffner C, Idler I, Stilgenbauer S, Dohner H, Lichter P. Mantle cell lymphoma is characterized by inactivation of the ATM gene. Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2773-8. PMID:10706620 doi:http://dx.doi.org/10.1073/pnas.050400997
  8. ↑ Vorechovsky I, Luo L, Dyer MJ, Catovsky D, Amlot PL, Yaxley JC, Foroni L, Hammarstrom L, Webster AD, Yuille MA. Clustering of missense mutations in the ataxia-telangiectasia gene in a sporadic T-cell leukaemia. Nat Genet. 1997 Sep;17(1):96-9. PMID:9288106 doi:http://dx.doi.org/10.1038/ng0997-96
  9. ↑ Stankovic T, Weber P, Stewart G, Bedenham T, Murray J, Byrd PJ, Moss PA, Taylor AM. Inactivation of ataxia telangiectasia mutated gene in B-cell chronic lymphocytic leukaemia. Lancet. 1999 Jan 2;353(9146):26-9. PMID:10023947 doi:http://dx.doi.org/S0140-6736(98)10117-4
  10. ↑ Schaffner C, Stilgenbauer S, Rappold GA, Dohner H, Lichter P. Somatic ATM mutations indicate a pathogenic role of ATM in B-cell chronic lymphocytic leukemia. Blood. 1999 Jul 15;94(2):748-53. PMID:10397742
  11. ↑ Bullrich F, Rasio D, Kitada S, Starostik P, Kipps T, Keating M, Albitar M, Reed JC, Croce CM. ATM mutations in B-cell chronic lymphocytic leukemia. Cancer Res. 1999 Jan 1;59(1):24-7. PMID:9892178
  12. ↑ Matsuoka S, Rotman G, Ogawa A, Shiloh Y, Tamai K, Elledge SJ. Ataxia telangiectasia-mutated phosphorylates Chk2 in vivo and in vitro. Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10389-94. PMID:10973490 doi:http://dx.doi.org/10.1073/pnas.190030497
  13. ↑ Bakkenist CJ, Kastan MB. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature. 2003 Jan 30;421(6922):499-506. PMID:12556884 doi:http://dx.doi.org/10.1038/nature01368
  14. ↑ Ali A, Zhang J, Bao S, Liu I, Otterness D, Dean NM, Abraham RT, Wang XF. Requirement of protein phosphatase 5 in DNA-damage-induced ATM activation. Genes Dev. 2004 Feb 1;18(3):249-54. PMID:14871926 doi:http://dx.doi.org/10.1101/gad.1176004
  15. ↑ Bhoumik A, Takahashi S, Breitweiser W, Shiloh Y, Jones N, Ronai Z. ATM-dependent phosphorylation of ATF2 is required for the DNA damage response. Mol Cell. 2005 May 27;18(5):577-87. PMID:15916964 doi:http://dx.doi.org/10.1016/j.molcel.2005.04.015
  16. ↑ Kaygun H, Marzluff WF. Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. Nat Struct Mol Biol. 2005 Sep;12(9):794-800. Epub 2005 Aug 7. PMID:16086026 doi:http://dx.doi.org/10.1038/nsmb972
  17. ↑ Kozlov SV, Graham ME, Peng C, Chen P, Robinson PJ, Lavin MF. Involvement of novel autophosphorylation sites in ATM activation. EMBO J. 2006 Aug 9;25(15):3504-14. Epub 2006 Jul 13. PMID:16858402 doi:http://dx.doi.org/7601231
  18. ↑ Sun Y, Xu Y, Roy K, Price BD. DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity. Mol Cell Biol. 2007 Dec;27(24):8502-9. Epub 2007 Oct 8. PMID:17923702 doi:http://dx.doi.org/10.1128/MCB.01382-07
  19. ↑ Taira N, Yamamoto H, Yamaguchi T, Miki Y, Yoshida K. ATM augments nuclear stabilization of DYRK2 by inhibiting MDM2 in the apoptotic response to DNA damage. J Biol Chem. 2010 Feb 12;285(7):4909-19. doi: 10.1074/jbc.M109.042341. Epub 2009 , Dec 4. PMID:19965871 doi:10.1074/jbc.M109.042341
  20. ↑ Warren C, Pavletich NP. Structure of the human ATM kinase and mechanism of Nbs1 binding. Elife. 2022 Jan 25;11:e74218. PMID:35076389 doi:10.7554/eLife.74218

Contents


PDB ID 7sid

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