Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.
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.
Wang
Yanli
Y
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York, USA.
Reddy
Sujatha
S
Beard
William A
WA
Wilson
Samuel H
SH
Schlick
Tamar
T
D020029:Base Pairing; D001665:Binding Sites; D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000648:ultrastructure*; D003838:Deoxyadenine Nucleotides / Q000737:chemistry*; D003845:Deoxycytosine Nucleotides / Q000737:chemistry*; D004789:Enzyme Activation; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation
D003838:Deoxyadenine Nucleotides; D003845:Deoxycytosine Nucleotides; C024107:2'-deoxycytidine 5'-triphosphate; D006147:Guanine; C064582:8-oxyguanine; D019951:DNA Polymerase beta; C026600:2'-deoxyadenosine triphosphate