Insertion of oxidized nucleotide triggers rapid DNA polymerase opening

Taejin Kim, Bret D. Freudenthal, William A. Beard, Samuel H. Wilson, Tamar Schlick

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)4409-4424
Number of pages16
JournalNucleic Acids Research
Volume44
Issue number9
DOIs
StatePublished - May 19 2016

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DNA-Directed DNA Polymerase
DNA Repair
Nucleotides
Crystallography
Guanine
Hydrogen Bonding
Base Pairing
Rupture
Catalytic Domain
Metals
Phosphates
Ions
Ligands
Water
Enzymes

ASJC Scopus subject areas

  • Genetics

Cite this

Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. / Kim, Taejin; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.; Schlick, Tamar.

In: Nucleic Acids Research, Vol. 44, No. 9, 19.05.2016, p. 4409-4424.

Research output: Contribution to journalArticle

Kim, Taejin ; Freudenthal, Bret D. ; Beard, William A. ; Wilson, Samuel H. ; Schlick, Tamar. / Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. In: Nucleic Acids Research. 2016 ; Vol. 44, No. 9. pp. 4409-4424.
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