title: Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase.
abstract: 8-Oxoguanine (8OG) is the most prevalent form of oxidative DNA damage. In bacteria, 8OG is excised by formamidopyrimidine glycosylase (Fpg) as the initial step in base excision repair. To efficiently excise this lesion, Fpg must discriminate between 8OG and an excess of guanine in duplex DNA. In this study, we explore the structural basis underlying this high degree of selectivity. Two structures have been reported in which Fpg is bound to DNA, differing with respect to the position of the lesion in the active site, one structure showing 8OG bound in the syn conformation and the other in the anti conformation. Remarkably, the results of our all-atom simulations are consistent with both structures. The syn conformation observed in the crystallographic structure of Fpg obtained from Bacillus stearothermophilus is stabilized through interaction with E77, a nonconserved residue. Replacement of E77 with Ser, creating the Fpg sequence found in Escherichia coli and other bacteria, results in preferred binding of 8OG in the anti conformation. Our calculations provide novel insights into the roles of active site residues in binding and recognition of 8OG by Fpg.
authors.affiliation: Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Song
authors.forename: Viktor
authors.initials: V
authors.lastname: Hornak
authors.forename: Carlos
authors.initials: C
authors.lastname: de Los Santos
authors.forename: Arthur P
authors.initials: AP
authors.lastname: Grollman
authors.forename: Carlos
authors.initials: C
authors.lastname: Simmerling
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D017124:Conserved Sequence; D004260:DNA Repair / Q000502:physiology; D043382:DNA-Formamidopyrimidine Glycosylase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001411:Geobacillus stearothermophilus / Q000201:enzymology*; D006147:Guanine / Q000031:analogs & derivatives* / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation
chemical_list: C024829:8-hydroxyguanine; D006147:Guanine; D043382:DNA-Formamidopyrimidine Glycosylase