title: Insertion of oxidized nucleotide triggers rapid DNA polymerase opening.
abstract: A novel mechanism is unveiled to explain why a pro-mutagenic nucleotide lesion (oxidized guanine, 8-oxoG) causes the mammalian DNA repair polymerase-β (pol-β) to rapidly transition to an inactive open conformation. The mechanism involves unexpected features revealed recently in time-lapse crystallography. Specifically, a delicate water network associated with a lesion-stabilizing auxilliary product ion Mg(p) triggers a cascade of events that leads to poor active site geometry and the rupture of crucial molecular interactions between key residues in both the anti(8-oxoG:C) and syn(8-oxoG:A) systems. Once the base pairs in these lesioned systems are broken, dislocation of both Asp192 (a metal coordinating ligand) and the oxoG phosphate group (PO4) interfere with the hydrogen bonding between Asp192 and Arg258, whose rotation toward Asp192 is crucial to the closed-to-open enzyme transition. Energetically, the lesioned open states are similar in energy to those of the corresponding closed complexes after chemistry, in marked contrast to the unlesioned pol-β anti(G:C) system, whose open state is energetically higher than the closed state. The delicate surveillance system offers a fundamental protective mechanism in the cell that triggers DNA repair events which help deter insertion of oxidized lesions.
authors.affiliation: Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA.
authors.forename: Taejin
authors.initials: T
authors.lastname: Kim
authors.affiliation: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
authors.forename: Bret D
authors.initials: BD
authors.lastname: Freudenthal
authors.affiliation: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
authors.forename: William A
authors.initials: WA
authors.lastname: Beard
authors.affiliation: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Wilson
authors.affiliation: Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA Schlick@nyu.edu.
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D020029:Base Pairing; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D019951:DNA Polymerase beta / Q000737:chemistry*; D004260:DNA Repair; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical
chemical_list: D004247:DNA; D019951:DNA Polymerase beta