Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil‐DNA glycosylase with DNA

Three high‐resolution crystal structures of DNA complexes with wild‐type and mutant human uracil‐DNA glycosylase (UDG), coupled kinetic characterizations and comparisons with the refined unbound UDG structure help resolve fundamental issues in the initiation of DNA base excision repair (BER): damage detection, nucleotide flipping versus extrahelical nucleotide capture, avoidance of apurinic/apyrimidinic (AP) site toxicity and coupling of damage‐specific and damage‐general BER steps. Structural and kinetic results suggest that UDG binds, kinks and compresses the DNA backbone with a ‘Ser–Pro pinch’ and scans the minor groove for damage. Concerted shifts in UDG simultaneously form the catalytically competent active site and induce further compression and kinking of the double‐stranded DNA backbone only at uracil and AP sites, where these nucleotides can flip at the phosphate–sugar junction into a complementary specificity pocket. Unexpectedly, UDG binds to AP sites more tightly and more rapidly than to uracil‐containing DNA, and thus may protect cells sterically from AP site toxicity. Furthermore, AP‐endonuclease, which catalyzes the first damage‐general step of BER, enhances UDG activity, most likely by inducing UDG release via shared minor groove contacts and flipped AP site binding. Thus, AP site binding may couple damage‐specific and damage‐general steps of BER without requiring direct protein–protein interactions.