5GKG: Structure Of Endoms-dsdna1'' Complex

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.
PDB ID: 5GKGDownload
MMDB ID: 144508
PDB Deposition Date: 2016/7/4
Updated in MMDB: 2016/11
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Thermococcus kodakarensis KOD1
Similar Structures:
Biological Unit for 5GKG: tetrameric; determined by author and by software (PISA)
Molecular Components in 5GKG
Label Count Molecule
Proteins (2 molecules)
Endonuclease Endoms
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*gp*cp*tp*ap*cp*ap*gp*gp*tp*cp*gp*tp*cp*c)- 3')
Molecule annotation
DNA (5'-d(*gp*gp*ap*cp*gp*ap*cp*gp*tp*gp*tp*ap*gp*cp*g)- 3')
Molecule annotation
Chemicals (7 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB