Functional flexibility of Bacillus stearothermophilus formamidopyrimidine DNA-glycosylase

The formamidopyrimidine-DNA glycosylase (Fpg) recognizes and eliminates efficiently 8-oxoguanine, an abundant mutagenic DNA lesion. The X-ray structure of the inactive E3Q mutant of Fpg from Bacillus stearothermophilus, complexed to an 8-oxoG-containing DNA, revealed a small peptide (called the alphaF-beta10 loop) involved in the recognition of the lesion via an interaction with the protonated N(7) atom. This region, which is disordered in the X-ray models where an abasic site-containing DNA is bound to Fpg, interacts tightly with the 8-oxoG which appears to be confined within the enzyme. Molecular dynamics simulations were performed on this mutant and the wild type derived model at 298 and 323K, to determine if this tight assembly around the 8-oxoG was due to the mutation and/or to an inappropriate experimental temperature. Differences in the relative orientation of the protein structural domains and in the architecture around the damaged base were observed, depending on the presence of the mutation and/or on the temperature. This data allowed us to show that the recognition of the damaged base by the wild type enzyme close to its optimal temperature might require significant movements of the enzyme, leading to conformational changes that could not be detected within the only X-ray structure. In addition, a dynamics performed with a normal guanine suggests that the alphaF-beta10 loop dynamics could be needed by the active Fpgs to distinguish a damaged guanine from a normal nucleotide.