Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site

Reactive oxygen species are byproducts of normal aerobic respiration and ionizing radiation, and they readily react with DNA to form a number of base lesions, including the mutagenic 8-oxo-7,8-dihydroguanine (8-oxoG), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG), 4,6-diamino-5-formamidopyrimidine (FapyA), and 8-oxo-7,8-dihydroadenine (8-oxoA). Such oxidative lesions are removed by the base excision repair pathway, which is initiated by DNA glycosylases such as the formamidopyrimidine-DNA glycosylase (Fpg) in Escherichia coli. The 8-oxoG, FapyG, and FapyA lesions are bound and excised by Fpg, while structurally similar 8-oxoA is excised by Fpg very poorly. We carried out molecular modeling and molecular dynamics simulations to interpret substrate discrimination within the active site of E. coli Fpg. Lys-217 and Met-73 were identified as residues playing important roles in the recognition of the oxidized imidazole ring in the substrate bases, and the Watson-Crick edge of the damaged base plays a role in optimally positioning the base within the active site. The recognition and excision of FapyA likely result from the opened imidazole ring, while 8-oxoA's lack of flexibility and closed imidazole ring may contribute to Fpg's inability to excise this base. Different interactions between each base and the enzyme specificity pocket account for differential treatment of the various lesions by this enzyme, and thus elucidate the structure-function relationship involved in an initial step of base excision repair.