5ZB8

Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus

Summary for 5ZB8

• Entry DOI: 10.2210/pdb5zb8/pdb
• Descriptor: PfuEndoQ, ZINC ION, SAMARIUM (III) ION, ... (4 entities in total)
• Functional Keywords: endonuclease, dna repair, dna binding protein
• Biological source: Pyrococcus furiosus
• Total number of polymer chains: 5
• Total formula weight: 226898.01

Authors

Miyazono, K.,Ito, T.,Tanokura, M. (deposition date: 2018-02-10, release date: 2018-04-04, Last modification date: 2024-03-27)

Primary citation

Miyazono, K.I.,Ishino, S.,Makita, N.,Ito, T.,Ishino, Y.,Tanokura, M.
Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus.
Nucleic Acids Res., 46:4807-4818, 2018

PubMed Abstract: Because base deaminations, which are promoted by high temperature, ionizing radiation, aerobic respiration and nitrosative stress, produce mutations during replication, deaminated bases must be repaired quickly to maintain genome integrity. Recently, we identified a novel lesion-specific endonuclease, PfuEndoQ, from Pyrococcus furiosus, and PfuEndoQ may be involved in the DNA repair pathway in Thermococcales of Archaea. PfuEndoQ recognizes a deaminated base and cleaves the phosphodiester bond 5' of the lesion site. To elucidate the structural basis of the substrate recognition and DNA cleavage mechanisms of PfuEndoQ, we determined the structure of PfuEndoQ using X-ray crystallography. The PfuEndoQ structure and the accompanying biochemical data suggest that PfuEndoQ recognizes a deaminated base using a highly conserved pocket adjacent to a Zn2+-binding site and hydrolyses a phosphodiester bond using two Zn2+ ions. The PfuEndoQ-DNA complex is stabilized by a Zn-binding domain and a C-terminal helical domain, and the complex may recruit downstream proteins in the DNA repair pathway.

PubMed: 29660024
DOI: 10.1093/nar/gky261

Experimental method

X-RAY DIFFRACTION (2.5 Å)