Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Publication Type:Journal Article
Source:Structure, Volume 17, Issue 5, p.725-36 (2009)
Keywords:Base Pairing, Base Sequence, Binding Sites, Crystallography, X-Ray, DNA, DNA Damage, DNA Polymerase beta, DNA Repair, Guanine, Molecular Sequence Data, Nucleic Acid Conformation, Protein Conformation
<p>7,8-Dihydro-8-oxoguanine (oxoG), the predominant oxidative DNA damage lesion, is processed differently by high-fidelity and Y-family lesion bypass polymerases. Although high-fidelity polymerases extend predominantly from an A base opposite an oxoG, the Y-family polymerases Dpo4 and human Pol eta preferentially extend from the oxoG*C base pair. We have determined crystal structures of extension Dpo4 ternary complexes with oxoG opposite C, A, G, or T and the next nascent base pair. We demonstrate that neither template backbone nor the architecture of the active site is perturbed by the oxoG(anti)*C and oxoG*A pairs. However, the latter manifest conformational heterogeneity, adopting both oxoG(syn)*A(anti) and oxoG(anti)*A(syn) alignment. Hence, the observed reduced primer extension from the dynamically flexible 3'-terminal primer base A is explained. Because of homology between Dpo4 and Pol eta, such a dynamic screening mechanism might be utilized by Dpo4 and Pol eta to regulate error-free versus error-prone bypass of oxoG and other lesions.</p>