Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

Abstract

Endonuclease V (EndoV) initiates a major base-repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures of Thermotoga maritima EndoV in complex with a hypoxanthine lesion substrate and with product DNA. The PYIP wedge motif acts as a minor groove–damage sensor for helical distortions and base mismatches and separates DNA strands at the lesion. EndoV incises DNA with an unusual offset nick 1 nucleotide 3′ of the lesion, as the deaminated adenine is rotated ∼ 90° into a recognition pocket ∼ 8 Å from the catalytic site. Tight binding by the lesion-recognition pocket in addition to Mg²⁺ and hydrogen-bonding interactions to the DNA ends stabilize the product complex, suggesting an orderly recruitment of downstream proteins in this base-repair pathway.