Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease

Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway. [Display omitted] •EndoMS (NucS) is a restriction enzyme that is active on mismatched dsDNA•EndoMS (NucS) undergoes a large conformational change in binding to dsDNA•EndoMS (NucS)-PCNA-dsDNA complex structure was elucidated•EndoMS (NucS) might be involved in a DNA mismatch repair pathway Nakae et al. present structures of the EndoMS (NucS)-dsDNA complex, revealing a class of restriction enzymes that is primarily active on DNA containing mismatched bases in various background sequences, and mounted on the DNA clamp (PCNA). EndoMS might be involved in a unique DNA mismatch repair pathway in Archaea.