Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion

Olga Rechkoblit, Lucy Malinina, Yuan Cheng, Vitaly Kuryavyi, Suse Broyde, Nicholas E. Geacintov, Dinshaw J. Patel

Research output: Contribution to journalArticle

Abstract

7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG•C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases.

Original languageEnglish (US)
Article numbere11
Pages (from-to)25-42
Number of pages18
JournalPLoS Biology
Volume4
Issue number1
DOIs
StatePublished - Jan 2006

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Phosphates
phosphates
Nucleotides
nucleotides
Thumb
Fingers
DNA
DNA Primers
nucleosides
DNA primers
crystal structure
Mechanics
Nucleosides
mechanics
Base Pairing
DNA damage
DNA Damage
reactive oxygen species
Reactive Oxygen Species
Crystal structure

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. / Rechkoblit, Olga; Malinina, Lucy; Cheng, Yuan; Kuryavyi, Vitaly; Broyde, Suse; Geacintov, Nicholas E.; Patel, Dinshaw J.

In: PLoS Biology, Vol. 4, No. 1, e11, 01.2006, p. 25-42.

Research output: Contribution to journalArticle

Rechkoblit, Olga ; Malinina, Lucy ; Cheng, Yuan ; Kuryavyi, Vitaly ; Broyde, Suse ; Geacintov, Nicholas E. ; Patel, Dinshaw J. / Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. In: PLoS Biology. 2006 ; Vol. 4, No. 1. pp. 25-42.
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