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.

doi:10.1371/journal.pbio.0040011

Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion

Journal Article · Tue Jan 03 00:00:00 EST 2006 · PLoS Biology (Online)

DOI:https://doi.org/10.1371/journal.pbio.0040011· OSTI ID:1627144

Rechkoblit, Olga ^[1]; Malinina, Lucy ^[2]; Cheng, Yuan ^[2]; Kuryavyi, Vitaly ^[2]; Broyde, Suse ^[3]; Geacintov, Nicholas E. ^[4]; Patel, Dinshaw J. ^[2]

Memorial Sloan-Kettering Cancer Center, New York, NY (United States); DOE/OSTI
Memorial Sloan-Kettering Cancer Center, New York, NY (United States)
New York University (NYU), NY (United States)
New York University (NYU), NY (United States). Chemistry Dept.

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 oxoGC 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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1627144

Journal Information:: PLoS Biology (Online), Journal Name: PLoS Biology (Online) Journal Issue: 1 Vol. 4; ISSN 1545-7885

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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