Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Abstract

Background: Considerable interest surrounds how 8-oxoguanine DNA glycosylase (hOGG1) distinguishes rare oxoG lesions from undamaged G residues. Results: Even when G is forcibly inserted into the lesion-recognition pocket on the enzyme, it is not cleaved. Conclusion:The hOGG1 active site can discriminate G from oxoG at the stage of catalysis. Significance: HOGG1 has a catalytic checkpoint that prevents accidental cleavage of undamaged DNA.

A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi

“…2b and Supplementary Table 1. Sharp bending of the DNA duplex and base flipping are also observed in the structures of DNA glycosylases and AP site-specific endonucleases [17][18][19][20][21][22] . In addition, some type II restriction endonucleases also flip a base out of the DNA helix to optimize protein-DNA interactions [23][24][25] .…”

DNA Damage Processing by Human 8-Oxoguanine-DNA Glycosylase Mutants with the Occluded Active Site

“…Outside of the base-binding pocket but still in the active site, Lys-249 is poised for the nucleophilic attack at C1Ј, and Asp-268 forms a hydrogen bond with O4Ј of the target nucleotide, assisting the deoxyribose ring opening and stabilizing the positive charge that develops on the ring when the base leaves. The only bond specific for 8-oxo-G versus G is formed by N7, which, in the pyrrolic type as in 8-oxo-G, donates a hydrogen bond to the main chain O of Gly-42 but cannot do so in the pyridinic type as in G. Interestingly, if G is forcibly presented to the active site in nearly the same conformation as 8-oxo-G, it is still not excised (19). As the N-glycosidic bond in oxo-dG is chemically more stable than in dG (37), this can only be explained by small but multiple perturbations in the active site structure when the base in the pocket is normal.…”

“…In particular, four sequential conformations of the nucleotide eversion are known as follows: the early structure where the target base is disengaged from its Watson-Crick interactions, unstacked, and slightly pushed toward the major groove (15); the intermediate structure where the target base falls in a so-called "exo-site" at the entrance to the active site (14); the advanced structure where the target base is almost at its final position but has not yet formed all specific bonds with the base-binding pocket of OGG1 (16,17,19); and the precatalytic structure with the damaged base poised for removal (8,11,16). Steered molecular dynamics with umbrella sampling indicates that all intermediate conformations are energetically similar with 2-4 kcal/mol barriers between them, whereas the final fully everted conformation is 10 -12 kcal/mol lower than the intermediates.…”

Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III

“…Such disturbance of DNA conformation in both specific and nonspecific complexes may result from the attempts of the enzyme to flip out the sampled base independently of whether it is damaged or not. Active eversion of undamaged bases from DNA in the process of lesion search was also shown for hOGG1 (23,24). Also, in all available structures of DNA glycosylases with undamaged DNA (23,(55)(56)(57)(58)(59)(60) the wedging residue of the enzyme is already inserted in DNA, so Leu 81 of Endo III might be expected to behave in the same way as it was recently shown by single-molecules studies in Refs.…”

“…3B) forms a hydrogen bond between the amide carbonyl of its side chain and the amino group of the opposite cytosine. Interestingly, hOGG1 can also guide the undamaged G base through the exosite into the active site, albeit less efficiently, but cannot cleave its N-glycosidic bond indicating strong discrimination selectivity between damaged and undamaged DNA (23,24). A stepwise thermodynamic analysis (21) reveals that the discrimination of nonspecific G base versus specific oxoG base mostly occurs at the second step of the DNA binding.…”