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Sci Rep. 2015 Aug 5;5:12754. doi: 10.1038/srep12754.

Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair.

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1] State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China [2] Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou 510006, People's Republic of China.
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 430 E. 67th Street, New York, NY 10065, USA.


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.

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