A structural gap in Dpo4 supports mutagenic bypass of a major benzo[ a ]pyrene dG adduct in DNA through template misalignment
- 18 September 2007
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 104 (38), 14905-14910
- https://doi.org/10.1073/pnas.0700717104
Abstract
Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-N 2-deoxyguanosine (BP–dG), was placed at a template–primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a −1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5′ to the adduct to serve as the template, resulting in a −1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and −1 frameshift mutations.This publication has 43 references indexed in Scilit:
- Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base DisplacementJournal of Molecular Biology, 2005
- Two-step error-prone bypass of the (+)- and (−)-trans-anti-BPDE-N2-dG adducts by human DNA polymerases η and κMutation research. Reviews in mutation research, 2002
- Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancersOncogene, 2002
- Preferential Misincorporation of Purine Nucleotides by Human DNA Polymerase η Opposite Benzo[a]pyrene 7,8-Diol 9,10-Epoxide Deoxyguanosine AdductsOnline Journal of Public Health Informatics, 2002
- Use of TLS parameters to model anisotropic displacements in macromolecular refinementActa crystallographica. Section D, Structural biology, 2001
- Stereochemical Origin of Opposite Orientations in DNA Adducts Derived from Enantiomeric anti-Benzo[a]pyrene Diol Epoxides with Different Tumorigenic PotentialsBiochemistry, 1999
- The major, N2-dG adduct of (+)-anti-B[a]PDE induces G->A mutations in a 5'-AGA-3' sequence contextCarcinogenesis: Integrative Cancer Research, 1999
- [20] Processing of X-ray diffraction data collected in oscillation modeMethods in Enzymology, 1997
- Are base substitution and frameshift mutagenesis pathways interrelated? An analysis based upon studies of the frequencies and specificities of mutations induced by the (+)-anti diol epoxide of benzo[a]pyreneMutation research. Reviews in mutation research, 1995
- Mutagenesis by (+)-anti-B[α]P-N2-Gua, the major adduct of activated benzo[α]pyrene, when studied in an Escherichia coli plasmid using site-directed methodsCarcinogenesis: Integrative Cancer Research, 1992