Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease

Abstract

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.

A Tangled Web: Origins of Reproductive Parasitism

“…( B ) Sequence and predicted structures of pLbAR_38 PD-(D/E)XK nuclease domains. Structure at top depicts modeling of the conserved nuclease domain to Pyrococcus abyssi endoMS (PDBID: 5GKE) ( Nakae et al. 2016 ), and the cryptic nuclease domain to P .…”

“…The specific coordinates assigned for predicted ovarian tumor (OTU) cysteine protease (Pfam OTU, PF02338) ( Makarova et al. 2000 ), endoMS-like ( Nakae et al. 2016 ) and NucS-like ( Ren et al.…”

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

“…( b ) Close-up views of the TgMcrC dimer interfaces formed by the two nuclease domains (upper right panel) and the two N-terminal domains (lower right panel). ( c ) Superposition of the monomeric structures of TgMcrC and EndoMS (PDB: 5GKF; Nakae et al, 2016). The conserved residues involved in the cleavage activity are labeled and shown as spheres.…”

“…The DNA-bound structures of other PD-(D/E)xK nucleases provide a template for modeling McrC’s cleavage activity. Of the many structural homologs identified by the DALI server (Holm and Rosenstrom, 2010), the coordinates of the Thermococcus kodakarensis EndoMS endonuclease (PDB: 5GKF; Z-score 7.9; Nakae et al, 2016) provided the best framework for these purposes. EndoMS binds DNA as a dimer, with each active site attacking a single strand of the DNA duplex to induce a double-strand break.…”

“…EndoMS binds DNA as a dimer, with each active site attacking a single strand of the DNA duplex to induce a double-strand break. As with other PD-(D/E)xK enzymes, Asp165 EndoMS , Glu179 EndoMS and Lys181 EndoMS coordinate a divalent metal cofactor that is required for catalytic function (Knizewski et al, 2007; Nakae et al, 2016). Structural superposition confirms TgMcrC’s C terminus shares the same fold and identifies Asp340 TgMcrC , Asp354 TgMcrC and Lys356 TgMcrC as putative catalytic side chains based on their spatial alignment with the EndoMS metal-binding residues (Figure 6c).…”