title: Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase.
abstract: We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10-13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately -6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately -3.3 kcal/mol) together with other specific interactions (ΔG° approximately -0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k(cat) term instead; the rate increases by 6-7 orders of magnitude for cognate DNA as compared with non-cognate one. The k(cat) values for substrates of different sequences correlate with the DNA twist, while the K(M) values correlate with ΔG° of the DNA fragments surrounding the lesion (position from -6 to +6). The functions for predicting the K(M) and k(cat) values for different sequences containing oxoG were found.
authors.affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Department of Molecular Biology, Novosibirsk State University, 2 Pirogova Street and SB RAS Institute of Cytology and Genetics, 10 Lavrentieva Avenue, Novosibirsk 630090, Russia.
authors.forename: Oleg O
authors.initials: OO
authors.lastname: Kirpota
authors.forename: Anton V
authors.initials: AV
authors.lastname: Endutkin
authors.forename: Michail P
authors.initials: MP
authors.lastname: Ponomarenko
authors.forename: Petr M
authors.initials: PM
authors.lastname: Ponomarenko
authors.forename: Dmitry O
authors.initials: DO
authors.lastname: Zharkov
authors.forename: Georgy A
authors.initials: GA
authors.lastname: Nevinsky
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D045647:DNA Glycosylases / Q000737:chemistry* / Q000378:metabolism; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry; D006801:Humans; D007700:Kinetics; D008024:Ligands; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D008024:Ligands; D009838:Oligodeoxyribonucleotides; C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA; D045647:DNA Glycosylases; C479058:oxoguanine glycosylase 1, human