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

<div class='caption-title'>(A) Time course of 32P 5′-end-labeled 13-mer primer extension on 19-mer G (left panel) or oxoG (right panel) templates in the presence of all four dNTPs by Dpo4. The labeled (−1) position or 13-mer represents the 13-mer primer with the 3′ end positioned one base before the G or oxoG; the 14-mer extended to position (0) opposite G or oxoG; the 19-mer extended to position (+5) corresponds to full extension.</div>
<div class='caption-title'>(A) Schematic of the pairing of the oxoG-containing 19-mer template strand with the 13-mer primer strand ending in a 2′,3′-dideoxynucleotide in the preinsertion binary complex with Dpo4.</div>
<div class='caption-title'>(A) oxoG(anti) paired with dCTP(anti) in the oxoG-modified insertion ternary complex, with a coordinated Ca2+ cation. 2Fo-Fc 1.95 Å electron density map contoured at 1σ level (1.95 Å resolution).</div>
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ
OpenAccess logo PLoS Biol 4 e11 (2006)
Related entries: 2asd, 2asj, 2asl, 2au0

Cited: 92 times
EuropePMC logo PMID: 16379496

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.

Reviews - 2atl mentioned but not cited (2)

  1. An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Yang W. Biochemistry 53 2793-2803 (2014)
  2. Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Broyde S, Wang L, Rechkoblit O, Geacintov NE, Patel DJ. Trends Biochem Sci 33 209-219 (2008)

Articles - 2atl mentioned but not cited (3)

  1. Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ. Nat Struct Mol Biol 17 379-388 (2010)
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  3. Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4. Jung H, Lee S. Biochem J 477 2859-2871 (2020)


Reviews citing this publication (13)

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