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Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication.

Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese LS
J Biol Chem 280 3764-70 (2005)
Cited: 44 times
EuropePMC logo PMID: 15548515

Abstract

Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.

Reviews - 1xc9 mentioned but not cited (2)

  1. 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)
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Articles - 1xc9 mentioned but not cited (3)

  1. DNA conformations and their sequence preferences. Svozil D, Kalina J, Omelka M, Schneider B. Nucleic Acids Res 36 3690-3706 (2008)
  2. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Nucleic Acids Res 35 4275-4288 (2007)
  3. Study on dietary intake, risk assessment, and molecular toxicity mechanism of benzo[α]pyrene in college students in China Bashu area. Ge Y, Yan H, Shi X, Wu Z, Wang Y, Zhang Z, Luo Q, Liu W, Liang L, Peng L, Hu J. Food Sci Nutr 10 4155-4167 (2022)


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  1. Biological properties of single chemical-DNA adducts: a twenty year perspective. Delaney JC, Essigmann JM. Chem Res Toxicol 21 232-252 (2008)
  2. Polycyclic aromatic hydrocarbons and PAH-related DNA adducts. Ewa B, Danuta MŠ. J Appl Genet 58 321-330 (2017)
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  4. Bst polymerase - a humble relative of Taq polymerase. Oscorbin I, Filipenko M. Comput Struct Biotechnol J 21 4519-4535 (2023)

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  17. Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations. Wang L, Wu M, Yan SF, Patel DJ, Geacintov NE, Broyde S. Chem Res Toxicol 18 441-456 (2005)
  18. Comparative Error-Free and Error-Prone Translesion Synthesis of N(2)-2'-Deoxyguanosine Adducts Formed by Mitomycin C and Its Metabolite, 2,7-Diaminomitosene, in Human Cells. Bose A, Surugihalli C, Pande P, Champeil E, Basu AK. Chem Res Toxicol 29 933-939 (2016)
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Related citations provided by authors (2)

  1. Observing translation synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase. Hsu GW, Kiefer JR, Becherel OJ, Fuchs RPP, Beese LS To be published -
  2. Structures of Mismatch Replication Errors Observed in a DNA Polymerase. Johnson SJ, Beese LS Cell 116 803-816 (2004)

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