TY - JOUR

T1 - Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance

AU - Rechkunova, Nadejda I.

AU - Zhdanova, Polina V.

AU - Lebedeva, Natalia A.

AU - Maltseva, Ekaterina A.

AU - Koval, Vladimir V.

AU - Lavrik, Olga I.

N1 - Funding Information: This study was supported by the Russian Science Foundation (grant No. 21-64-00017 ), by the Russian Foundation for Basic Research (grant No. 19-34-90052 , for the MD simulation of complexes with two metals), and by the Ministry of Higher Education and Science (project No. 121031300041-4 , for DNA duplex preparation and protein purification). Publisher Copyright: © 2022 Elsevier B.V.

PY - 2022/8

Y1 - 2022/8

N2 - 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.

AB - 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.

KW - Base excision repair

KW - Benzo[a]pyrene

KW - DNA polymerase

KW - Lesion bypass

KW - Molecular dynamics

UR - http://www.scopus.com/inward/record.url?scp=85132409417&partnerID=8YFLogxK

U2 - 10.1016/j.dnarep.2022.103353

DO - 10.1016/j.dnarep.2022.103353

M3 - Article

C2 - 35696855

AN - SCOPUS:85132409417

VL - 116

JO - DNA Repair

JF - DNA Repair

SN - 1568-7864

M1 - 103353

ER -