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ATM

Tuesday 28 October 2003

Definition: Ataxia telangiectasia mutated (ATM) is a serine/threonine protein kinase (EC 2.7.11.1) that is recruited and activated by DNA double-strand breaks.

It phosphorylates several key proteins that initiate activation of the DNA damage checkpoint, leading to cell cycle arrest, DNA repair or apoptosis. Several of these targets, including p53, CHK2 and H2AX are tumor suppressors.

The protein is named for the disorder Ataxia telangiectasia caused by mutations of ATM.

Structure

The ATM gene codes for a 350 kDa protein consisting of 3056 amino acids.

ATM belongs to the superfamily of Phosphatidylinositol 3-kinase-related kinases (PIKKs). The PIKK superfamily comprises six Ser/Thr-protein kinases that show a sequence similarity to phosphatidylinositol 3-kinases (PI3Ks).

This protein kinase family includes amongst others ATR (ATM- and RAD3-related), DNA-PKcs (DNA-dependent protein kinase catalytic subunit) and mTOR (mammalian target of rapamycin).

Characteristic for ATM are five domains. These are from N-Terminus to C-Terminus the HEAT repeat domain, the FRAP-ATM-TRRAP (FAT) domain, the kinase domain (KD), the PIKK-regulatory domain (PRD) and the FAT-C-terminal (FATC) domain.
- The HEAT repeats directly bind to the C-terminus of NBS1.
- The FAT domain interacts with ATM’s kinase domain to stabilize the C-terminus region of ATM itself.
- The KD domain resumes kinase activity, while the PRD and the FATC domain regulate it.

Although no structure for ATM has been solved, the overall shape of ATM is very similar to DNA-PKcs and is composed of a head and a long arm that is thought to wrap around double-stranded DNA after a conformational change.

The entire N-terminal domain together with the FAT domain are predicted to adobt an α-helical structure, which was found by sequence analysis.

This α-helical structure is believed to form a tertiary structure, which has a curved, tubular shape present for example in the Huntingtin protein, which also contains HEAT repeats.

FATC is the C-terminal domain with a length of about 30 amino acids. It is highly conserved and consists of an α-helix followed by a sharp turn, which is stabilized by a disulfide bond

Functions

- ATM is activated by mechanisms that sense double stranded DNA breaks.
- ATM transmits signals to arrest the cell cycle after DNA damage. It acts through p53 in the G1/S checkpoint.
- At the G2/M checkpoint, ATM acts both through p53-dependent mechanisms and through the inactivation of CDC25 phosphatase, which disrupts the cyclin B-CDK1 complex.
- ATM is a component of a network of genes that include BRCA1 and BRCA2, which link DNA damage with cell-cycle arrest and apoptosis (the BASC complex).

A trimeric complex of the three proteins MRE11, RAD50 and NBS1 (XRS in yeast), called the MRN complex in humans, recruits ATM to double strand breaks (DSBs) and holds the two ends together.

ATM directly interacts with the NBS1 subunit and phosphorylates the histone variant H2AX on Ser139. This phosphorylation generates binding sites for adaptor proteins with a BRCT domain. These adaptor proteins then recruit different factors including the effector protein kinase CHK2 and the tumor suppressor p53.

The ATM-mediated DNA damage response consists of a rapid and a delayed response. The effector kinase CHK2 is phopsphorylated and thereby activated by ATM.

Activated CHK2 phophorylates phosphatase CDC25A which is degraded thereupon and can no longer dephosphororylate CDK2-Cyclin resulting in cell-cycle arrest. If the DSB can not be repaired during this rapid response, ATM additionally phophorylates MDM2 and p53 at Ser15.

p53 is also phosphorylated by the effector kinase CHK2.

These phosphorylation events lead to stabilization and activation of p53 and subsequent transcription of numerous p53 target genes including Cdk inhibitor p21 which lead to long-term cell-cycle arrest or even apoptosis.

DNA damages

Throughout the cell cycle, the DNA is monitored for damage. Damages result from errors during replication, by-products of metabolism, general toxic drugs or ionizing radiation.

The cell cycle has different DNA damage checkpoints, which inhibit or maintain the next cell cycle step.

There are two main checkpoints, the G1/S and the G2/M, during the cell cycle, which preserve correct progression.

ATM plays a role in cell cycle delay after DNA damage, especially after double-strand breaks (DSBs). ATM together with NBS1 act as primary DSB sensor proteins.

Different mediators, such as MRE11 and MDC1, acquire post-translational modifications which are generated by the sensor proteins.

These modified mediator proteins then amplify the DNA damage signal, and transduce the signals to downstream effectors such as CHK2 and p53.

ATM mediates two-step response to DNA double strand breaks. In the rapid response activated ATM phosphorylates effector kinase CHK2 which phophphorylates CDC25A, targeting it for ubiquitination and degradation.

Therefore phosphorylated CDK2-Cyclin accumulates and progression through the cell cycle is blocked. In the delayed response ATM phophorylates the inhibitor of p53, MDM2, and p53 which is also phosphorylated by Chk2.

The resulting activation and stabilization of p53 leads to an increased expression of Cdk inhibitor p21, which further helps to keep Cdk activity low and to maintain long-term cell cycle arrest.

Regulation

A functional MRN complex is required for ATM activation after double strand breaks (DSBs). The complex functions upstream of ATM in mammalian cells and induces conformational changes that facilitate an increase in the affinity of ATM towards its substrates, such as CHK2 and p53.

Inactive ATM is present in the cells without DSBs as dimers or multimers. Upon DNA damage, ATM autophosphorylates on residue Ser1981. This phosphorylation provokes dissociation of ATM dimers, which is followed by the release of active ATM monomers.

Further autophosphorylation (of residues Ser367 and Ser1893) is required for normal activity of the ATM kinase.

Activation of ATM by the MRN complex is preceded by at least two steps, i.e. recruitment of ATM to DSB ends by the mediator of DNA damage checkpoint protein 1 (MDC1) which binds to MRE11, and the subsequent stimulation of kinase activity with the NBS1 C-terminus. The three domains FAT, PRD and FATC are all involved in regulating the activity of the KD kinase domain.

The FAT domain interacts with ATM’s KD domain to stabilize the C-terminus region of ATM itself.

The FATC domain is critical for kinase activity and highly sensitive to mutagenesis. It mediates protein-protein interaction for example with the histone acetyltransferase TIP60 (HIV-1 Tat interacting protein 60 kDa), which acetylates ATM on residue Lys3016.

The acetylation occurs in the C-terminal half of the PRD domain and is required for ATM kinase activation and for its conversion into monomers. While deletion of the entire PRD domain abolishes the kinase activity of ATM, specific small deletions show no effect.

Pathology

- germline mutations in

  • ataxia-telangiectasia
  • breast cancer predisposition (#17001623#, #16832357#)

- mutation/deletion in rhabdomyosarcoma (#12673126#)

Ataxia telangiectasia (AT) is a rare human disease characterized by extreme cellular sensitivity to radiation and a predisposition to cancer. All AT patients contain mutations in the AT-mutated gene (ATM). Most other AT-like disorders are defective in genes encoding the MRN protein complex.

One feature of the ATM protein is its rapid increase in kinase activity immediately following double-strand break formation. The phenotypic manifestation of AT is due to the broad range of substrates for the ATM kinase, involving DNA repair, apoptosis, G1/S, intra-S checkpoint and G2/M checkpoints, gene regulation, translation initiation, and telomere maintenance.

Therefore a defect in ATM has severe consequences, leading up to tumor formation. For example, the increased risk for breast cancer in AT patients has been implicated by the involvement of ATM in the interaction and phosphorylation of BRCA1 and its associated proteins following DNA damage.

References

- Schoch C, Kohlmann A, Dugas M, Kern W, Schnittger S, Haferlach T. Impact of trisomy 8 on expression of genes located on chromosome 8 in different AML subgroups. Genes Chromosomes Cancer. 2006 Dec;45(12):1164-8. PMID: #17001623#

- Renwick A, Thompson D, Seal S, Kelly P, Chagtai T, Ahmed M, North B, Jayatilake H, Barfoot R, Spanova K, McGuffog L, Evans DG, Eccles D; Breast Cancer Susceptibility Collaboration (UK); Easton DF, Stratton MR, Rahman N. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet. 2006 Aug;38(8):873-5. PMID: #16832357#

- Yang J, Xu ZP, Huang Y, Hamrick HE, Duerksen-Hughes PJ, Yu YN. ATM and ATR: sensing DNA damage. World J Gastroenterol. 2004 Jan 15;10(2):155-60. PMID: #14716813#

- Huber A, Bai P, de Murcia JM, de Murcia G. PARP-1, PARP-2 and ATM in the DNA damage response: functional synergy in mouse development. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):1103-8. PMID: #15279798#

- Shiloh Y, Andegeko Y, Tsarfaty I. In search of drug treatment for genetic defects in the DNA damage response: the example of ataxia-telangiectasia. Semin Cancer Biol. 2004 Aug;14(4):295-305. PMID: #15219622#

- Lavin MF, Birrell G, Chen P, Kozlov S, Scott S, Gueven N. ATM signaling and genomic stability in response to DNA damage. Mutat Res. 2005 Jan 6;569(1-2):123-32. PMID: #15603757#

- Lavin MF, Scott S, Gueven N, Kozlov S, Peng C, Chen P. Functional consequences of sequence alterations in the ATM gene. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):1197-205. PMID: #15279808#

- Chun HH, Gatti RA. Ataxia-telangiectasia, an evolving phenotype. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):1187-96. PMID: #15279807#

- Hammond EM, Giaccia AJ. The role of ATM and ATR in the cellular response to hypoxia and re-oxygenation. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):1117-22. PMID: #15279800#

- Huber A, Bai P, de Murcia JM, de Murcia G. PARP-1, PARP-2 and ATM in the DNA damage response: functional synergy in mouse development. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):1103-8. PMID: #15279798#

- Koundrioukoff S, Polo S, Almouzni G. Interplay between chromatin and cell cycle checkpoints in the context of ATR/ATM-dependent checkpoints. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):969-78. PMID: #15279783#

- Abraham RT. The ATM-related kinase, hSMG-1, bridges genome and RNA surveillance pathways. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):919-25. PMID: #15279777#

- Kurz EU, Lees-Miller SP. DNA damage-induced activation of ATM and ATM-dependent signaling pathways. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):889-900. PMID: #15279774#

- McKinnon PJ. ATM and ataxia telangiectasia. EMBO Rep. 2004 Aug;5(8):772-6. PMID: #15289825#

- Gumy-Pause F, Wacker P, Sappino AP. ATM gene and lymphoid malignancies. Leukemia. 2004 Feb;18(2):238-42. PMID: #14628072#

- Shiloh Y. ATM and related protein kinases: safeguarding genome integrity. Nat Rev Cancer. 2003 Mar;3(3):155-68. PMID: #12612651#

- Pandita TK. ATM function and telomere stability. Oncogene. 2002 Jan 21;21(4):611-8. PMID: #11850786#

- Kastan MB, Lim DS. The many substrates and functions of ATM. Nat Rev Mol Cell Biol. 2000 Dec;1(3):179-86. PMID: #11252893#

- Jeggo PA, Carr AM, Lehmann AR. Splitting the ATM: distinct repair and checkpoint defects in ataxia-telangiectasia. Trends Genet. 1998 Aug;14(8):312-6. PMID: #9724963#

- Rotman G, Shiloh Y. ATM: from gene to function. Hum Mol Genet. 1998;7(10):1555-63. PMID: #9735376#

Portfolio

  • ATM and the BASC complex
  • ATM molecular pathway.