Substrate Discrimination by Formamidopyrimidine-DNA Glycosylase: Distinguishing Interactions within the Active Site

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• 作者：Rebecca A. Perlow-Poehnelt ; Dmitry O. Zharkov ; Arthur P. Grollman ; and Suse Broyde
• 刊名：Biochemistry
• 出版年：2004
• 出版时间：December 28, 2004
• 年：2004
• 卷：43
• 期：51
• 页码：16092 - 16105
• 全文大小：1295K
• 年卷期：v.43,no.51(December 28, 2004)
• ISSN：1520-4995

文摘

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 removedby 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 boundand excised by Fpg, while structurally similar 8-oxoA is excised by Fpg very poorly. We carried outmolecular modeling and molecular dynamics simulations to interpret substrate discrimination within theactive site of E. coli Fpg. Lys-217 and Met-73 were identified as residues playing important roles in therecognition of the oxidized imidazole ring in the substrate bases, and the Watson-Crick edge of thedamaged base plays a role in optimally positioning the base within the active site. The recognition andexcision of FapyA likely result from the opened imidazole ring, while 8-oxoA's lack of flexibility andclosed imidazole ring may contribute to Fpg's inability to excise this base. Different interactions betweeneach base and the enzyme specificity pocket account for differential treatment of the various lesions bythis enzyme, and thus elucidate the structure-function relationship involved in an initial step of baseexcision repair.