Mlh1–Pms1 couples ATP-driven DNA compaction with nick-dependent endonuclease activation

In eukaryotes, mismatch repair begins with MutS homolog (MSH) complexes detecting mismatches and recruiting the proliferating cell nuclear antigen (PCNA)-stimulated endonuclease Mlh1–Pms1/PMS2 (yeast/human), which nicks the DNA to allow downstream proteins to remove the mismatch. Although Mlh1–Pms1 is an ATPase and this activity is essential in vivo, ATP is not required for nicking in vitro, leaving its function unresolved. Using yeast proteins, we show that Mlh1–Pms1 uses ATP to compact continuous DNA, a behavior which may act as a search mechanism for strand-discrimination signals. When a pre-existing nick is encountered, compaction is suppressed and Mlh1–Pms1 instead stabilizes the site, protecting it from replication factor C (RFC)/PCNA-induced melting. Phased nicking assays further reveal that the timing of Mlh1–Pms1 encountering a pre-existing nick relative to RFC/PCNA determines whether the complex remains suppressed or becomes activated. Together, these results support a model of Mlh1–Pms1 using ATP-driven global compaction to toggle between a search mode and a PCNA-licensed repair mode.