Initiation of Base Excision Repair: Glycosylase Mechanisms and Structures

Abstract

The base excision repair pathway is an organism's primary defense against mutations induced by oxidative, alkylating, and other DNA-damaging agents. This pathway is initiated by DNA glycosylases that excise the damaged base by cleavage of the glycosidic bond between the base and the DNA sugar-phosphate backbone. A subset of glycosylases has an associated apurinic/apyrimidinic (AP) lyase activity that further processes the AP site to generate cleavage of the DNA phosphate backbone. Chemical mechanisms that are supported by biochemical and structural data have been proposed for several glycosylases and glycosylase/AP lyases. This review focuses on the chemical mechanisms of catalysis in the context of recent structural information, with emphasis on the catalytic residues and the active site conformations of several cocrystal structures of glycosylases with their substrate DNAs. Common structural motifs for DNA binding and damage specificity as well as conservation of acidic residues and amino groups for catalysis are discussed.

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

“…Bifunctional DNA glycosylases further process the AP site via b or bd elimination reaction. A mechanistic distinction between these two types of enzymes is that monofunctional DNA glycosylases typically use an activated water molecule as a nucleophile in attacking sugar C1′ of the target nucleotide, where bifunctional glycosylases/AP lyases often use e-NH 2 of a lysine or the N-terminal proline as the active site nucleophile [37]. An intermediate step is the formation of a transient Schiff base between the amino group and the C1′ of deoxyribose for both base excision and DNA strand cleavage.…”

“…They are categorized into two families based on tertiary structure, active site characteristics and AP lyase reaction, and are named after the prototype Nth [endonuclease III] and Fpg (formamidopyrimidine-DNA glycosylase) [37]. The Nth family utilizes an internal Lys residue as the active site for β elimination reaction, generating a 3′ phospho a,β-unsaturated aldehyde (3′ PUA), also named 3′ phosphor 4-hydroxylpentenal, at the strand break.…”

Role of active site tyrosines in dynamic aspects of DNA binding by AP endonuclease☆

“…NaBH 4 reduces and stabilizes the AP-site so that no βelimination product forms (43). NaBH 4 does not interfere with the glycosylase because UNG has no lyase activity (7,30,31). Furthermore, the β-elimination product of an AP-site inhibits enzymatic activity (43).…”

Base excision repair synthesis of DNA containing 8-oxoguanine in Escherichia coli

“…While Fpg did not excise 8-oxo-G efficiently when paired with a Nei excised 8-oxo-G in 8-oxo-G:A and in 8-oxo-G:C pair to a similar degree. Thus, Nei can backup Fpg by repairing 8-oxo-G:C in addition to 8-oxo-G:A. Nei shares the N-terminal amino acids of Fpg, especially, the N-terminal Pro, which is considered as an active site of Fpg in terms of 8-oxo-G glycosylase/AP lyase activity (McCullough et al, 1999). Recently, MutH, one member of methyldirected mismatch repair system of E. coli was reported to be involved in repair of 8-oxo-G in DNA, even though it was not demonstrated whether it remove directly 8-oxo-G, adenine misincorporated opposite 8-oxo-G or both (Wyrzykowski and Volkert, 2003).…”