Long-range allosteric restraint by the Spiral-Pincer scaffold gates oxidative activation of the ATM kinase

Abstract

ATM is a master regulator of the DNA-damage response, activated either by DNA double-strand breaks through the MRN complex or, independently, by oxidative stress, which drives disulfide bond formation between Cys2991 residues on the two halves of the ATM dimer. Although both pathways involve release of the PIKK regulatory domain (PRD) from the kinase active site, how the distant Spiral--Pincer scaffold regulates access to this state remains unclear, partly because the PRD--FAT-TRD3 interface is unresolved in available experimental structures. Here, we combine an AlphaFold3-completed full-length ATM dimer model with well-tempered metadynamics to map its conformational landscape. We find that an oxidation-competent conformation already exists in the resting dimer, although it is rarely populated, supporting conformational selection rather than induction of a new state. Removing Spiral--Pincer eliminates this restriction: the conformation becomes dominant, and the landscape narrows to a few well-separated states. The dimer's two halves respond unequally, one loop of the PRD rearranging substantially while the other remains unchanged, via specific domain contacts rather than a direct route to the reactive cysteines. This identifies Spiral--Pincer as a release-controlled brake on ATM activation, a mechanism that may extend across the wider PIKK kinase family.