Sae2 integrates CDK and checkpoint phosphorylation to coordinate MRX cleavage with checkpoint attenuation.

Yeast Sae2 plays a dual role in the DNA damage response by suppressing Rad53 activation and stimulating DNA end clipping via the MRX complex. Using AlphaFold3-based modeling and mutational analysis, here we show that Mec1/Tel1-dependent phosphorylation of Sae2 at T90 or T279 is sufficient to restrain Rad9-Rad53 interaction and Rad53 kinase activation. Cells expressing a non-phosphorylatable Sae2 double mutant (T90A T279A) display persistent Rad53 activation, whereas phosphomimetic Sae2 variants (T90E or T279E) restore normal checkpoint inactivation. Structural modeling and charge-reversal genetics indicate that electrostatic interactions between phosphorylated T90/T279 of Sae2 and Rad53 residue R70 are critical for this regulation. In addition, T279 phosphorylation, but not T90, cooperates with cyclin-dependent kinase (CDK)-dependent phosphorylation of Sae2 S267 to promote MRX-dependent resolution of hairpin DNA structures and processing of meiotic double-strand breaks (DSBs). A Sae2 T279E phosphomimetic partially rescues both hairpin cleavage defects and DNA damage sensitivity of tel1Δ cells, indicating that Tel1 promotes MRX activity primarily through Sae2 T279 phosphorylation.