The essential, conserved Tel2 protein plays a role in the response to DNA damage and replication stress in a wide range of eukaryotes. Tel2 interacts physically with multiple members of the PI3-kinase related protein kinase (PIKK) family in mammalian cells and fission yeast. In mammalian cells, loss of Tel2 leads to destabilization of PIKKs. Our previous work in the yeast Saccharomyces cerevisiae showed that Tel2 interacts with the PIKK Tel1 (yeast ATM kinase), and that this interaction is abrogated by the only known non-lethal TEL2 mutation in S. cerevisiae, tel2-1. We showed that this mutation specifically disrupts the function of Tel1 and not the function of the closely related protein Mec1 (yeast ATR kinase) in DNA damage responses. Here we show that Tel2 and Mec1 interact in S. cerevisiae, and that surprisingly, this physical interaction is also disrupted by the tel2-1 mutation. Although the tel2-1 mutation leads to moderately lower Mec1 levels, the ability of Mec1 to localize to a site of DNA damage and to function in DNA damage signaling remains intact. These results suggest that the model of Tel2 as solely a global regulator of PIKK stability is insufficient. Rather, Tel2 can specifically and differentially regulate the function of individual PIKKs.