The nuclease activity of the yeast Dna2 protein, which is related to the RecB-like nucleases, is essential in vivo

Saccharomyces cerevisiae Dna2 protein is required for DNA replication and r epair and is associated with multiple biochemical activities: DNA-dependent ATPase, DNA helicase, and DNA nuclease. To investigate which of these acti vities is important for the cellular functions of Dna2, we have identified separation of function mutations that selectively inactivate the helicase o r nuclease. me describe the effect of six such mutations on ATPase, helicas e, and nuclease after purification of the mutant proteins from yeast or bac ulovirus-infected insect cells. A mutation in the Walker A box in the C-ter minal third of the protein affects helicase and ATPase but not nuclease; a mutation in the N-terminal domain (amino acid 504) affects ATPase, helicase , and nuclease. Two mutations in the N-terminal domain abolish nuclease but do not reduce helicase activity (amino acids 657 and 675) and identify the putative nuclease active site. Two mutations immediately adjacent to the p roposed nuclease active site (amino acids 640 and 693) impair nuclease acti vity in the absence of ATP but completely abolish nuclease activity in the presence of ATP. These results suggest that, although the Dna2 helicase and nuclease activities can be independently affected by some mutations, the t wo activities appear to interact, and the nuclease activity is regulated in a complex manner by ATP. Physiological analysis shows that both ATPase and nuclease are important for the essential function of DNA2 in DNA replicati on and for its role in double-strand break repair. Four of the nuclease mut ants are not only loss of function mutations but also exhibit a dominant ne gative phenotype.