The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization*

The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signaling, and repair. Here, we present the first structural insight for dimers of Mec1·Ddc2 and Tel1 using single-particle electron microscopy. Both kinases reveal a head to head dimer with one major dimeric interface through the N-terminal HEAT (named after Huntingtin, elongation factor 3, protein phosphatase 2A, and yeast kinase TOR1) repeat. Their dimeric interface is significantly distinct from the interface of mTOR complex 1 dimer, which oligomerizes through two spatially separate interfaces. We also observe different structural organizations of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1·Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated, providing potential access of substrates to this kinase, even in its dimeric form.

• Publication year

  2016

• Venue

  Journal of Biological Chemistry

• Publication date

  2016-04-28

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1074/jbc.M115.708263PMID 27129217PMCID 4919432
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Structure of the human dimeric ATM kinase

  2016cited by this paper
• Architecture of human mTOR complex 1

  2016influential reference
• SUPPLEMENTAL INFORMATION TO : Lagging strand maturation factor Dna 2 is a component of the replication checkpoint initiation machinery

  2015cited by this paper
• A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation

  2015cited by this paper
• Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy

  2015cited by this paper
• Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2.

  2015cited by this paper
• Structures of SMG1-UPFs complexes: SMG1 contributes to regulate UPF2-dependent activation of UPF1 in NMD.

  2014influential reference
• Mec 1 p is essential for phosphorylation of the yeast DNA damage checkpoint protein Ddc 1 p , which physically interacts with Mec 3 p

  2013cited by this paper
• mTOR kinase structure, mechanism and regulation by the rapamycin-binding domain

  2013cited by this paper
• RELION: Implementation of a Bayesian approach to cryo-EM structure determination

  2012influential reference
• Prevention of overfitting in cryo-EM structure determination

  2012cited by this paper
• A Bayesian View on Cryo-EM Structure Determination

  2012cited by this paper
• Regulation of Rad51 function by phosphorylation

  2011cited by this paper
• Tel1ATM and Rad3ATR kinases promote Ccq1-Est1 interaction to maintain telomeres in fission yeast

  2011cited by this paper
• ATR autophosphorylation as a molecular switch for checkpoint activation.

  2011influential reference
• The Unstructured C-terminal Tail of Yeast Dpb11 (Human TopBP1) Protein Is Dispensable for DNA Replication and the S Phase Checkpoint but Required for the G2/M Checkpoint*

  2011cited by this paper
• Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment

  2011cited by this paper
• The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8.

  2011cited by this paper
• Structure of the human mTOR complex I and its implications for rapamycin inhibition.

  2010cited by this paper
• ATM Activation by Oxidative Stress

  2010cited by this paper
• mTOR Ser-2481 Autophosphorylation Monitors mTORC-specific Catalytic Activity and Clarifies Rapamycin Mechanism of Action*

  2009cited by this paper
• Crystal Structure of DNA-PKcs Reveals a Large Open-Ring Cradle Comprised of HEAT Repeats

  2009influential reference
• A tale of two tails: activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1.

  2009cited by this paper
• Emerging common themes in regulation of PIKKs and PI3Ks

  2009influential reference
• A Novel Tel1/ATM N-Terminal Motif, TAN, Is Essential for Telomere Length Maintenance and a DNA Damage Response

  2008cited by this paper
• SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs

  2008influential reference
• TopBP1 activates ATR through ATRIP and a PIKK regulatory domain.

  2008influential reference
• Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding.

  2008cited by this paper
• Dpb11 activates the Mec1–Ddc2 complex

  2008cited by this paper
• Yeast DNA Replication Protein Dpb11 Activates the Mec1/ATR Checkpoint Kinase*

  2008cited by this paper
• Function of a Conserved Checkpoint Recruitment Domain in ATRIP Proteins

  2007cited by this paper
• EMAN2: an extensible image processing suite for electron microscopy.

  2007cited by this paper
• DNA Damage-Induced Acetylation of Lysine 3016 of ATM Activates ATM Kinase Activity

  2007cited by this paper
• Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair.

  2006cited by this paper
• The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint.

  2006influential reference
• Dimerization of the ATRIP protein through the coiled-coil motif and its implication to the maintenance of stalled replication forks.

  2005influential reference
• ATRIP binding to replication protein A-single-stranded DNA promotes ATR-ATRIP localization but is dispensable for Chk1 phosphorylation.

  2005cited by this paper
• Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs).

  2005cited by this paper
• ATRIP Oligomerization Is Required for ATR-dependent Checkpoint Signaling*

  2005cited by this paper
• Role of the C terminus of Mec1 checkpoint kinase in its localization to sites of DNA damage.

  2005cited by this paper
• Direct Activation of the ATM Protein Kinase by the Mre11/Rad50/Nbs1 Complex

  2004cited by this paper
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004cited by this paper
• PI 3-kinase related kinases: 'big' players in stress-induced signaling pathways.

  2004influential reference
• Electron microscopy and 3D reconstructions reveal that human ATM kinase uses an arm-like domain to clamp around double-stranded DNA

  2003cited by this paper
• Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes

  2003cited by this paper
• Accurate determination of local defocus and specimen tilt in electron microscopy.

  2003cited by this paper
• Visualization of DNA‐induced conformational changes in the DNA repair kinase DNA‐PKcs

  2003cited by this paper
• DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation

  2003influential reference
• Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks.

  2002cited by this paper
• DNA-dependent Protein Kinase Catalytic Subunit

  2002cited by this paper
• Pie1, a Protein Interacting with Mec1, Controls Cell Growth and Checkpoint Responses in Saccharomyces cerevisiae

  2001cited by this paper
• Characterization of mec1Kinase-Deficient Mutants and of New Hypomorphic mec1Alleles Impairing Subsets of the DNA Damage Response Pathway

  2001cited by this paper
• The checkpoint protein Ddc2, functionally related to S. pombe Rad26, interacts with Mec1 and is regulated by Mec1-dependent phosphorylation in budding yeast.

  2000cited by this paper
• LCD1: an essential gene involved in checkpoint control and regulation of the MEC1 signalling pathway in Saccharomyces cerevisiae

  2000cited by this paper
• EMAN: semiautomated software for high-resolution single-particle reconstructions.

  1999cited by this paper
• MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks.

  1999cited by this paper
• Control of the DNA damage checkpoint by chk1 and rad53 protein kinases through distinct mechanisms.

  1999cited by this paper
• A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication

  1998cited by this paper
• Mec1p is essential for phosphorylation of the yeast DNA damage checkpoint protein Ddc1p, which physically interacts with Mec3p

  1998cited by this paper
• A meiotic recombination checkpoint controlled by mitotic checkpoint genes

  1996cited by this paper
• The ATM homologue MEC1 is required for phosphorylation of replication protein A in yeast.

  1996cited by this paper
• A new generation of the IMAGIC image processing system.

  1996cited by this paper
• Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways.

  1996cited by this paper
• Regulation of RAD53 by the ATM-Like Kinases MEC1 and TEL1 in Yeast Cell Cycle Checkpoint Pathways

  1996cited by this paper
• TEL1, an S. cerevisiae homolog of the human gene mutated in ataxia telangiectasia, is functionally related to the yeast checkpoint gene MEC1.

  1995cited by this paper
• A Three-dimensional

  year unknowncited by this paper

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  2026cites this paper
• Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA

  2025cites this paper
• Infectious bacteria, but not the microbiota, induce a NOX-ATM-cytokine pathway that controls epithelial turnover.

  2025cites this paper
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  2025cites this paper
• Targeting the ATM pathway in cancer: Opportunities, challenges and personalized therapeutic strategies.

  2024cites this paper
• Oxidative stress and the multifaceted roles of ATM in maintaining cellular redox homeostasis

  2024cites this paper
• Structural insights into the activation of ataxia-telangiectasia mutated by oxidative stress

  2023cites this paper
• Structure and function of the apical PIKKs in double-strand break repair.

  2023cites this paper
• A DNA damage–induced phosphorylation circuit enhances Mec1ATR Ddc2ATRIP recruitment to Replication Protein A

  2022cites this paper
• Targeting the ATM Kinase to Enhance the Efficacy of Radiotherapy and Outcomes for Cancer Patients.

  2022cites this paper
• ATR activation is regulated by dimerization of ATR activating proteins

  2021cites this paper
• Molecular basis of human ATM kinase inhibition

  2021cites this paper
• Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)

  2021cites this paper
• Structures and regulations of ATM and ATR, master kinases in genome integrity.

  2020cites this paper
• Mechanism of Auto-inhibition and Activation of Mec1ATR Checkpoint Kinase

  2020influential citation
• Structural basis of homologous recombination

  2019cites this paper
• NMR– and MD simulation–based structural characterization of the membrane-associating FATC domain of ataxia telangiectasia mutated

  2019cites this paper
• Activation of Tel1ATM kinase requires Rad50 ATPase and long nucleosome-free DNA but no DNA ends

  2019cites this paper
• Discovery of a Pathogenic Variant rs139379666 (p. P2974L) in ATM for Breast Cancer Risk in Chinese Populations

  2019cites this paper
• Structural insights into the critical DNA damage sensors DNA-PKcs, ATM and ATR.

  2019cites this paper
• Structure of nucleotide-bound Tel1ATM reveals the molecular basis of inhibition and structural rationale for disease mutations

  2019cites this paper
• Mec1ATR Autophosphorylation and Ddc2ATRIP Phosphorylation Regulates DNA Damage Checkpoint Signaling.

  2019cites this paper
• Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations

  2019cites this paper
• Near-Complete Structure and Model of Tel1ATM from Chaetomium thermophilum Reveals a Robust Autoinhibited ATP State.

  2019cites this paper
• Neurodegeneration in ataxia‐telangiectasia: Multiple roles of ATM kinase in cellular homeostasis

  2018cites this paper
• Phosphorylation of Wat1, human Lst8 homolog is critical for the regulation of TORC2 -Gad8 dependent pathway in fission yeast Schizosacchromyces pombe.

  2018cites this paper
• Establishment of the early cilia preassembly protein complex during motile ciliogenesis

  2018cites this paper
• Architecture and activation of phosphatidylinositol 3-kinase related kinases.

  2018influential citation
• Breaking up with ATM

  2018cites this paper
• The essential kinase ATR: ensuring faithful duplication of a challenging genome

  2017cites this paper
• Single-Particle Electron Microscopy Analysis of DNA Repair Complexes.

  2017cites this paper
• Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.

  2017influential citation
• Structures of closed and open conformations of dimeric human ATM

  2017cites this paper
• Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution

  2017cites this paper
• 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP

  2017cites this paper
• Assembly and activation of DNA damage sensing kinase Mec1-Ddc2

  2017influential citation
• The Human Mitochondrial Chaperonin: It Takes Two Single-Rings to Tango

  2017cites this paper
• Insights into Rad3 kinase recruitment from the crystal structure of the DNA damage checkpoint protein Rad26

  2017cites this paper
• Cryo-EM structure of human ATR-ATRIP complex

  2017cites this paper
• ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response.

  2017cites this paper
• Mec1/ATR, the Program Manager of Nucleic Acids Inc.

  2016cites this paper