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

Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA
EMBO J 17 5214-26 (1998)
Related entries: 1akz, 1ssp, 4skn

Cited: 251 times
EuropePMC logo PMID: 9724657

Abstract

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.

Reviews - 2ssp mentioned but not cited (2)

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  6. Crystal structure of mimivirus uracil-DNA glycosylase. Kwon E, Pathak D, Chang HW, Kim DY. PLoS One 12 e0182382 (2017)


Reviews citing this publication (54)

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  1. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature 384 87-92 (1996)

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