5GKE

Structure of EndoMS-dsDNA1 complex

Summary for 5GKE

• Entry DOI: 10.2210/pdb5gke/pdb
• Related: 5GKF 5GKG 5GKH 5GKI 5GKJ
• Descriptor: Endonuclease EndoMS, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3'), ... (6 entities in total)
• Functional Keywords: endonucleases, dna-binding, hydrolase-dna complex, hydrolase/dna
• Biological source: Thermococcus kodakarensis KOD1; More
• Total number of polymer chains: 4
• Total formula weight: 67031.64

Authors

Nakae, S.,Hijikata, A.,Tsuji, T.,Yonezawa, K.,Kouyama, K.,Mayanagi, K.,Ishino, S.,Ishino, Y.,Shirai, T. (deposition date: 2016-07-04, release date: 2016-11-02, Last modification date: 2023-11-08)

Primary citation

Nakae, S.,Hijikata, A.,Tsuji, T.,Yonezawa, K.,Kouyama, K.I.,Mayanagi, K.,Ishino, S.,Ishino, Y.,Shirai, T.
Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24:1960-1971, 2016

PubMed 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.

PubMed: 27773688
DOI: 10.1016/j.str.2016.09.005

Experimental method

X-RAY DIFFRACTION (2.4 Å)