Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex

• Published in: Molecular cell Vol. 76; no. 3; pp. 382 - 394.e6
• Main Authors: Käshammer, Lisa, Saathoff, Jan-Hinnerk, Lammens, Katja, Gut, Fabian, Bartho, Joseph, Alt, Aaron, Kessler, Brigitte, Hopfner, Karl-Peter
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 07-11-2019
• Subjects: ABC ATPase; Acid Anhydride Hydrolases - genetics; Acid Anhydride Hydrolases - metabolism; Acid Anhydride Hydrolases - ultrastructure; coiled-coil; Cryoelectron Microscopy; Deoxyribonucleases - genetics; Deoxyribonucleases - metabolism; Deoxyribonucleases - ultrastructure; DNA Breaks, Double-Stranded; DNA double-strand breaks; DNA repair; DNA Replication; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA, Bacterial - ultrastructure; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli - ultrastructure; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Escherichia coli Proteins - ultrastructure; Exonucleases - genetics; Exonucleases - metabolism; Exonucleases - ultrastructure; homologous recombination; MRE11 Homologue Protein - genetics; MRE11 Homologue Protein - metabolism; MRE11 Homologue Protein - ultrastructure; Mre11-Rad50 complex; nuclease; Nucleic Acid Conformation; SbcC-SbcD complex; SMC-like proteins; Structure-Activity Relationship; SbcC-SbcD complex; coiled-coil; cryoelectron microscopy; homologous recombination; ABC ATPase; nuclease; Mre11-Rad50 complex; SMC-like proteins; DNA double-strand breaks; DNA repair
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2019.07.035

DNA double-strand breaks (DSBs) threaten genome stability throughout life and are linked to tumorigenesis in humans. To initiate DSB repair by end joining or homologous recombination, the Mre11-nuclease Rad50-ATPase complex detects and processes diverse and obstructed DNA ends, but a structural mechanism is still lacking. Here we report cryo-EM structures of the E. coli Mre11-Rad50 homolog SbcCD in resting and DNA-bound cutting states. In the resting state, Mre11’s nuclease is blocked by ATP-Rad50, and the Rad50 coiled coils appear flexible. Upon DNA binding, the two coiled coils zip up into a rod and, together with the Rad50 nucleotide-binding domains, form a clamp around dsDNA. Mre11 moves to the side of Rad50, binds the DNA end, and assembles a DNA cutting channel for the nuclease reactions. The structures reveal how Mre11-Rad50 can detect and process diverse DNA ends and uncover a clamping and gating function for the coiled coils.
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•cryo-EM structure of EcMre11-Rad50 bound to a DNA break•Mre11 dimer binds the DNA end at the side of Rad50•Mre11 and Rad50 assemble a transient DNA cutting channel•The coiled coils form a rod-shaped DNA gate and clamp
Käshammer et al. use cryoelectron microscopy and biochemical studies to reveal, at near-atomic resolution, how the ATP-dependent nuclease Mre11-Rad50 can sense and process a wide range of DNA termini to enable repair and recombination of breaks and hairpins in chromosomal DNA.