Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance

• Published in: DNA repair 2022-08, Vol.116, p.103353-103353, Article 103353
• Main Authors: Rechkunova, Nadejda I., Zhdanova, Polina V., Lebedeva, Natalia A., Maltseva, Ekaterina A., Koval, Vladimir V., Lavrik, Olga I.
• Format: Article
• Language: English
• Subjects: Base excision repair; Benzo[a]pyrene; DNA polymerase; Lesion bypass; Molecular dynamics
• ISSN: 1568-7864; 1568-7856
• DOI: 10.1016/j.dnarep.2022.103353

DNA polymerases β (Pol β) and λ (Pol λ) belong to one structural family (X family) and possess the same enzymatic activities. Nonetheless, these enzymes have differences in their catalytic efficiency and specificity. We have previously reported that these enzymes can bypass bulky benzo[a]pyrene–DNA adducts via translesion synthesis during gap-filling reactions, although efficiency and specificity are dependent on the reaction conditions and adduct conformation. In the present study, we analyzed structural features of Pols β and λ complexed with a gapped DNA duplex containing either cis- or trans-benzo[a]pyrene-diol epoxide-N2-dG (BP-dG) using molecular dynamics simulations. It was found that the most pronounced structural difference lies in the positioning of the trans-BP-dG residue relative to secondary structures of the protein; this dissimilarity may explain the differences between Pols β and λ in gap-filling/translesion synthesis. In the case of Pol β, trans-BP-dG turned out to be positioned parallel to the α-helix and β-sheet. In the Pol λ complex, trans-BP-dG is perpendicular to the α-helix. This difference persisted throughout the molecular dynamics trajectory. Selectivity for the BP-dG isomers remained after a deletion of noncatalytic domains of Pol λ. Modeling of Pol λ or β complexes with cis-BP-dG–containing DNA in the presence of Mn2+ either at both metal-binding sites or at the catalytic site only revealed that for both enzymes, the model of the complex containing both Mg2+ and Mn2+ is stabler than that containing two Mn2+ ions. This observation may reflect a shared property of these enzymes: the preference for Mn2+ in terms of catalysis and for Mg2+ regarding triphosphate coordination during the translesion reaction. •The positioning of trans-BP-dG differs in the DNA complexes with Pol λ and Pol β.•Pol λ N-terminal domains have no effect on the selectivity towards BP-dG conformers.•A model of the Pol λ complex with Mg2+ and Mn2+ is more stable than that with Mn2+.•In the course of simulation, one Mn2+ ion leaves Pol β complex with the cis-BP-dG-DNA.