Structure of the human ATM kinase and mechanism of Nbs1 binding

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Abstract

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 Å 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.

Data availability

Cryo-EM maps have been deposited in the EMDB under accession codes EMD_25140 and EMD_25141. Coordinates have been deposited in the PDB under accession codes 7SIC and 7SID.

The following data sets were generated

1. Warren C
2. Pavletich NP
(2022) Structure of the human ATM kinase and mechanism of Nbs1 binding
RCSB Protein Data Bank, 7SIC.

https://www.rcsb.org/structure/7SIC
1. Warren C
2. Pavletich NP
(2022) Structure of the human ATM kinase and mechanism of Nbs1 binding
RCSB Protein Data Bank, 7SID.

https://www.rcsb.org/structure/7SID
1. Warren C
2. Pavletich NP
(2022) Structure of the human ATM kinase and mechanism of Nbs1 binding
Electron Microscopy Data Bank, EMD-25140.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-25140
1. Warren C
2. Pavletich NP
(2022) Structure of the human ATM kinase and mechanism of Nbs1 binding
Electron Microscopy Data Bank, EMD-25141.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-25141

Article and author information

Author details

Christopher Warren

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

Competing interests
The authors declare that no competing interests exist.
Nikola P Pavletich

Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute, New York, United States

For correspondence
pavletin@mskcc.org

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6039-3956

Funding

National Cancer Institute (5F32CA247320)

Christopher Warren

National Cancer Institute (CA008748)

Nikola P Pavletich

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.