Processing of oxidative dna damage

Oxidative DNA base damages are removed from DNA by DNA glycosylases that appear to have either pyrimidine or purine specificity. In E. coli, pyrimidine lesions are recognized and removed by the DNA glycosylases, endonucleases III and VIII, while purine lesions are removed by FAPY DNA glycosylase. The pyrimidine-specific glycosylases recognize a broad range of substrates including pyrimidine ring saturation and fragmentation products as well as unsaturated products where the pyrimidine ring remains structurally intact. FAPY DNA glycosylase recognizes and removes formamidopyrimidines and 8-oxoguanine from DNA and, to a lesser extent, a number of pyrimidine products. All three enzymes have a DNA lyase activity which cleaves the DNA backbone 3′ to the lesion. Endo III leaves an α, β unsaturated aldehyde attached to the 3′ end of the nick while endo VIII and FAPY catalyze an additional δ-elimination reaction leaving a 3′ phosphate. Because these glycosylases leave a blocked 3′ terminus, the block must be removed by a 5′ AP endonuclease to create a substrate for polymerization. In all cases, the intermediate prior to polymerization and ligation is a single base gap. Endo III has been crystallized and its structure, together with mutational analysis, suggest that the enzyme may act by a base flipping mechanism with the substrate pyrimidine flipping out from the DNA molecule into the enzyme's active site prior to chemistry. Endo VIII and FAPY share sequence homology with one another; both contain four cysteines at the carboxyl terminus which coordinate a single zinc molecule. In FAPY, the zinc finger has been implicated in DNA binding while the N-terminus is required for enzyme catalysis. The biological function of FAPY is to remove 8-oxoG residues, potent premutagenic lesions, from 8-oxoG-C pairs of E. coli cells lacking this activity are spontaneous mutators. The biological roles of endonucleases III and VIII have yet to be elucidated but are under investigation.