4XPU

The crystal structure of EndoV from E.coli

Summary for 4XPU

• Entry DOI: 10.2210/pdb4xpu/pdb
• Descriptor: Endonuclease V (2 entities in total)
• Functional Keywords: endonuclease v, inosine, dna repair, rna cleavage, hydrolase
• Biological source: Escherichia coli O45:K1 (strain S88 / ExPEC)
• Cellular location: Cytoplasm : B7MIY4
• Total number of polymer chains: 2
• Total formula weight: 47835.39

Authors

Xie, W.,Zhang, Z. (deposition date: 2015-01-18, release date: 2015-08-19, Last modification date: 2023-11-08)

Primary citation

Zhang, Z.,Jia, Q.,Zhou, C.,Xie, W.
Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair
Sci Rep, 5:12754-12754, 2015

PubMed Abstract: Endonuclease V (EndoV) is a ubiquitous protein present in all three kingdoms of life, responsible for the specific cleavages at the second phosphodiester bond 3' to inosine. E. coli EndoV (EcEndoV) is the first member discovered in the EndoV family. It is a small protein with a compact gene organization, yet with a wide spectrum of substrate specificities. However, the structural basis of its substrate recognition is not well understood. In this study, we determined the 2.4 Å crystal structure of EcEndoV. The enzyme preserves the general 'RNase H-like motif' structure. Two subunits are almost fully resolved in the asymmetric unit, but they are not related by any 2-fold axes. Rather, they establish "head-to-shoulder" contacts with loose interactions between each other. Mutational studies show that mutations that disrupt the association mode of the two subunits also decrease the cleavage efficiencies of the enzyme. Further biochemical studies suggest that EcEndoV is able to bind to single-stranded, undamaged DNA substrates without sequence specificity, and forms two types of complexes in a metal-independent manner, which may explain the wide spectrum of substrate specificities of EcEndoV.

PubMed: 26244280
DOI: 10.1038/srep12754

Experimental method

X-RAY DIFFRACTION (2.4 Å)