In eukaryotic cells, DNA mismatch repair is initiated by a conserved family of MutS (Msh) and MutL (Mlh) homolog proteins. Mlh1 is unique among Mlh proteins because it is required in mismatch repair and for wild-type levels of crossing over during meiosis. In this study, 60 new alleles of MLH1 were examined for defects in vegetative and meiotic mismatch repair as well as in meiotic crossing over. Four alleles predicted to disrupt the Mlh1p ATPase activity conferred defects in all functions assayed. Three mutations, mlh1-2, -29, and -31, caused defects in mismatch repair during vegetative growth but allowed nearly wild-type levels of meiotic crossing over and spore viability. Surprisingly, these mutants did not accumulate high levels of postmeiotic segregation at the ARG4 recombination hotspot. In biochemical assays, Pms1p failed to copurify with mlh1-2, and two-hybrid studies indicated that this allele did not interact with Pms1p and Mlh3p but maintained wild-type interactions with Exo1p and Sgs1p. mlh1-29 and mlh1-31 did not alter the ability of Mlh1p-Pms1p to form a ternary complex with a mismatch substrate and Msh2p-Msh6p, suggesting that the region mutated in these alleles could be responsible for signaling events that take place after ternary complex formation. These results indicate that mismatches formed during genetic recombination are processed differently than during replication and that, compared to mismatch repair functions, the meiotic crossing-over role of MLH1 appears to be more resistant to mutagenesis, perhaps indicating a structural role for Mlh1p during crossing over.In eukaryotes, mismatch repair plays a critical role in mutation avoidance and is carried out by the MutSLH family of proteins (for reviews, see references 13, 36, and 40). During vegetative growth, these proteins recognize and bind DNA mispairs that result primarily from replication errors or DNA damage. In Escherichia coli, MutS binding to DNA mispairs results in the recruitment of MutL, a matchmaker protein that functions in postreplicative mismatch repair by interacting with both the MutH endonuclease and UvrD helicase (22, 23). These interactions coordinate mispair recognition with DNA strand-specific signals so that mispairs are removed via excision and resynthesis steps that occur on the newly replicated strand.Eukaryotes contain multiple MutS (Msh) and MutL (Mlh) homologs, with six Msh and four Mlh homologs present in Saccharomyces cerevisiae (36). Genetic and biochemical studies have shown that the eukaryotic homologs display specialized functions with respect to the types of DNA substrates on which they act (10, 36, 40). In S. cerevisiae, the Mlh proteins form heterodimers (Mlh1p-Pms1p, Mlh1p-Mlh3p, and Mlh1p-Mlh2p) that display unique functions. Mlh1p is considered a central member of this group because heterodimers have not been identified among the other members (45, 70). The Mlh1p-Pms1p complex plays a major role in postreplicative mismatch repair, while the other two Mlh complexes appear to be redundant with Mlh1p-P...