DNA glycosylase/AP lyases

The bacterial formamidopyrimidine-DNA glycosylase (alias Fpg or MutM) is a bifunctional base-repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines from oxidatively damaged DNA. The crystal structures of the Fpg (MutM) enzymes from Thermus thermophilus, Lactococcus lactis Escherichia coli Bacillus stearothermophilus and the sequence similar endonuclease VIII (Nei) from E. all share the same... 

Figure 11.2 BER pathway. BER is initiated by DNA glycosylases that recognize lesions and hydrolyze the glycosidic bond linking the base to the sugar phosphate backbone. Monofunctional DNA glycosylases (top left) generate abasic site products that are cleaved at the 5 -phosphodiester bond by APE1. Bifunctional DNA glycosylases/AP lyases (top right) remove the abasic site and leave a...

Girard, P. M., Guibourt, N., and Boiteux, S. (1997). The Oggl protein of Saccharomyces cerevisiae A 7,8-dihydro-8-oxoguanine DNA glycosylase/AP lyase whose lysine 241 is a critical residue for catalytic activity. Nucleic Adds Res. 25, 3204-3211. 

The concluding steps of BER involve DNA synthesis to replace the damaged nucleotide and ligation. If the glycosylase has an associated AP lyase activity, it can generate a 3 -a, [) unsaturated aldehyde (Figure 23.7). This residue must be pro-... 

Figure 5. Reaction mechanism catalised by ofthe Fpg protein-DNA glycosylase and AP lyase process. The...

Figure 13.11 Reaction sequence of the base excision repair pathway. The base excision repair (BER) pathway is exemplified for the uracil excision-repair reactions. Only the lesioned (e.g. uracil) part of one strand nucleotide structure of the dsDNA is shown. The excision of uracil by uracil DNA glycosylase without associated AP-lyase generally follows AP-endonuclease and 5 -deoxyribophosphodiesterase which cleave the nucleotide chain. The repair with N-glycosylase is associated with AP-lyase (P-elimination reaction catalyzed by AP-lyase converts the deoxyribose residue to aldehyde form) and 3 -phosphodiesterase. The single nucleotide gap is filled by DNA polymerase (dCTP is required to replace uracil) and DNA ligase...

After the action of AP endonuclease on an abasic site, DNA repair polymerase (polymerase /3 in eukaryotes or polymerase I in bacteria) can remove the dRP group (so-called dRPase activity ) (Allinson etal, 2001). This reaction is catalyzed by the N-terminal domain of polymerase /3 via an imine intermediate, analogous to the AP lyase activity of bifunctional glycosylases (Piersen et al, 1996 Prasad et al, 1998). If this step... 

Vidal, A. E., Hickson, I. D., Boiteux, S., and RadiceUa, J. P. (2001b). Mechanism of stimulation of the DNA glycosylase activity of hOGGl by the major human AP endonuclease Bypass of the AP lyase activity step. Nucleic Acids Res. 29, 1285-1292. 

Base excision is used to correct defects involving a single base. Figure 65.2 shows how the erroneous base uracil (derived from cytosine) is cleaved from the V C of deoxyribose by DNA glycosylase to leave an AP site (for structure of DNA, see Fig. 60.2). An AP site is a site without either a purine or a pyrimidine - described as apurinic or apyrimidinic . Alternatively, it is known as an abasic site . Then AP endonuclease cleaves the 5 C bond. This is followed by deoxyribose phosphate lyase that removes deoxyribose phosphate by cleaving the 3 C bond. Finally, the gap is filled by DNA polymerase and the nick is sealed by DNA ligase. 

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