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

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


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

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Publisher: Public Library of Science
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    1. (2005). A closed conformation for the Pol lambda catalytic cycle.
    2. (2004). Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.
    3. Aggarwal AK (2004) Replication by human DNA polymerase-iota occurs by Hoogsteen basepairing.
    4. (1994). AMoRe: An Automated Package for Molecular Replacement.
    5. (1997). Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exoand human immunodeficiency virus-1 reverse transcriptase using steadystate and pre-steady-state kinetics.
    6. (2004). Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gammadelta Tcell ligand T10.
    7. (1993). Conformational coupling in DNA polymerase fidelity.
    8. (2004). Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.
    9. (2001). Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus.
    10. (2001). Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain.
    11. (2001). Crystal structure of a Yfamily DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication.
    12. (2004). Crystal structure of the catalytic core of human DNA polymerase kappa.
    13. (2004). Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
    14. (1997). Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism.
    15. (2003). Damage repair DNA polymerases Y.
    16. (2005). DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4. Analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.
    17. (2004). Dpo4 is hindered in extending a GT mismatch by a reverse wobble.
    18. (2000). Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta.
    19. (2004). Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase.
    20. (2005). Eukaryotic translesion synthesis DNA polymerases: Specificity of structure and function.
    21. (2005). Fidelity of Dpo4: Effect of metal ions, nucleotide selection and pyrophosphorolysis.
    22. (2001). Fidelity of nucleotide insertion at 8-oxo7,8-dihydroguanine by mammalian DNA polymerase delta. Steady-state and pre-steady-state kinetic analysis.
    23. (2004). Functions of DNA polymerases.
    24. (1995). Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies.
    25. (2002). In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase I (Klenow fragment).
    26. (1991). Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG.
    27. (2004). Lesion (in)tolerance reveals insights into DNA replication fidelity.
    28. (2004). Mechanism of DNA polymerization catalyzed by Sulfolobus solfataricus P2 DNA polymerase IV.
    29. (2004). Nucleotide insertion opposite a cis–syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
    30. (2003). Oxidative damage to DNA: Formation, measurement and biochemical features.
    31. (2003). Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
    32. (1997). Refinement of macromolecular structures by the maximum-likelihood method.
    33. (2003). Replication of a cis–syn thymine dimer at atomic resolution.
    34. (2000). Review article: Chronic inflammation and reactive oxygen and nitrogen metabolism—Implications in DNA damage and mutagenesis.
    35. (2004). Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
    36. (1998). Steady-state and presteady-state kinetic analysis of 8-oxo-7,8-dihydroguanosine triphosphate incorporation and extension by replicative and repair DNA polymerases.
    37. (2004). Structural basis for the dual coding potential of 8-oxoguanosine by a highfidelity DNA polymerase.
    38. (2003). Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential.
    39. (2001). Structure of the catalytic core of S. cerevisiae DNA polymerase eta: Implications for translesion DNA synthesis.
    40. (2004). Structures of mismatch replication errors observed in a DNA polymerase.
    41. (2001). Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol eta.
    42. (2004). Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases.
    43. (1998). Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme.
    44. (2005). Trading places: How do DNA polymerases switch during translesion DNA synthesis?
    45. (2001). Yeast DNA polymerase eta utilizes an induced-fit mechanism of nucleotide incorporation.

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