Differing Conformational Pathways Before and After Chemistry for Insertion of dATP versus dCTP Opposite 8-OxoG in DNA Polymerase β

Abstract

To elucidate how human DNA polymerase beta (pol beta) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol beta. Analyses reveal that the thumb closing of pol beta before chemistry is hampered when the incorrect nucleotide dATP is bound opposite 8-oxoG; the unfavorable interaction between active-site residue Tyr(271) and dATP that causes an anti to syn change in the 8-oxoG (syn):dATP complex explains this slow motion, in contrast to the 8-oxoG (anti):dCTP system. Such differences in conformational pathways before chemistry for mismatched versus matched complexes help explain the preference for correct insertion across 8-oxoG by pol beta. Together with reference studies with a nonlesioned G template, we propose that 8-oxoG leads to lower efficiency in pol beta's incorporation of dCTP compared with G by affecting the requisite active-site geometry for the chemical reaction before chemistry. Furthermore, because the active site is far from ready for the chemical reaction after partial closing or even full thumb closing, we suggest that pol beta is tightly controlled not only by the chemical step but also by a closely related requirement for subtle active-site rearrangements after thumb movement but before chemistry.

DNA polymerase Family X: Function, structure, and cellular roles

“…However, translesion synthesis by Pol β occurred with relatively high fidelity, as Pol β had the highest efficiency inserting the correct nucleotide dCTP opposite the lesion [95]. Use of dynamics simulations suggests that the motion of the fingers subdomain and destabilization of the closed form of the polymerase in the presence of the mismatched lesion are key determinants for the fidelity of translesion synthesis opposite 8oxoG [96, 97]. …”

Untitled

“…Molecular dynamics simulations of pol β/DNA substrate complexes with 8-oxo G [20] have shown that the closing conformational pathway of pol β is slowed by d A TP insertion opposite 8-oxo G (the thumb subdomain cannot attain a fully closed conformation after 18 ns simulation) but that the closing process is unaffected by d C TP opposite 8-oxo G . Specifically, unfavorable interactions between the nascent base pair and Tyr271 on the thumb subdomain cause the adenine base on d A TP to flip to a syn conformation when 8-oxo G :d A TP is bound to the pol β/DNA substrate complex.…”

“…We only consider the 8-oxo G ( anti ):d C TP ( anti ) (abbreviated as 8-oxo G :d C TP) and 8-oxo G ( syn ):d A TP ( anti ) (8-oxo G :d A TP) conformations here because these two are usually found in a DNA duplex. Earlier dynamics simulations also indicate that the anti : anti conformation is less favorable than the syn : anti conformation for the 8-oxo G :d A TP mispair in pol β [20]. …”

“…With the bulkier Tyr271 replaced by alanine, the thumb subdomain of pol β is expected to close faster onto the nascent base pair than in the wild-type simulation [20]. …”

Reprint of “Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair”

“…These enzymes either fail to bypass the lesion when it persists in the template DNA or perform mutagenic repair by inserting a wrong, pro-mutagenic, nucleotide opposite the lesion [23-25]. In addition, during periods of oxidative stress, pol β can perform mutation-prone repair by inserting the oxidized dNTP pool nucleotide 8-oxodGTP ( syn ) opposite to template adenine base [26]. …”