Recognition of damaged DNA by Escherichia coli Fpg protein: insights from structural and kinetic data.
Formamidopyrimidine-DNA glycosylase (Fpg) excises oxidized purines from damaged DNA. The recent determination of the three-dimensional structure of the covalent complex of DNA with Escherichia coli Fpg, obtained by reducing the Schiff base intermediate formed during the reaction [Gilboa et al., J. Biol. Chem. 277 (2002) 19811] has revealed a number of potential specific and non-specific interactions between Fpg and DNA. We analyze the structural data for Fpg in the light of the kinetic and thermodynamic data obtained by the method of stepwise increase in ligand complexity to estimate relative contributions of individual nucleotide units of lesion-containing DNA to its total affinity for this enzyme [Ishchenko et al., Biochemistry 41 (2002) 7540]. Stopped-flow kinetic analysis that has allowed the dissection of Fpg catalysis in time [Fedorova et al., Biochemistry 41 (2002) 1520] is also correlated with the structural data.
Zharkov
Dmitry O
DO
Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences (SB RAS), Lavrentieva Avenue 8, Novosibirsk 630090, Russia.
Ishchenko
Alexander A
AA
Douglas
Kenneth T
KT
Nevinsky
Georgy A
GA
D002384:Catalysis; D004247:DNA / Q000737:chemistry; D004249:DNA Damage; D004260:DNA Repair; D043382:DNA-Formamidopyrimidine Glycosylase / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D013816:Thermodynamics
D029968:Escherichia coli Proteins; D004247:DNA; D043382:DNA-Formamidopyrimidine Glycosylase; C468610:DNA-formamidopyrimidine glycosylase, E coli