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Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases. Nucleic Acids Res 2011; 39:6277-90. [PMID: 21486746 PMCID: PMC3152353 DOI: 10.1093/nar/gkr215] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/28/2011] [Accepted: 03/20/2011] [Indexed: 11/13/2022] Open
Abstract
DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base damages guiding the damaged DNA through repair synthesis. We report here biochemical and structural evidence for the irreversible entrapment of DNA glycosylases by 5-hydroxy-5-methylhydantoin, an oxidized thymine lesion. The first crystal structure of a suicide complex between DNA glycosylase and unrepaired DNA has been solved. In this structure, the formamidopyrimidine-(Fapy) DNA glycosylase from Lactococcus lactis (LlFpg/LlMutM) is covalently bound to the hydantoin carbanucleoside-containing DNA. Coupling a structural approach by solving also the crystal structure of the non-covalent complex with site directed mutagenesis, this atypical suicide reaction mechanism was elucidated. It results from the nucleophilic attack of the catalytic N-terminal proline of LlFpg on the C5-carbon of the base moiety of the hydantoin lesion. The biological significance of this finding is discussed.
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Affiliation(s)
- Yann-Vaï Le Bihan
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Maria Angeles Izquierdo
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Pierre Aller
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Françoise Culard
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Tim H. Gehrke
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Kadija Essalhi
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Thomas Carell
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France, Department of Chemistry and Biochemistry, Center for Integrated Protein Science CIPS, Ludwig-Maximilians University Munich, Butenandt strasse 5-13 (Haus F), D-81377 Munich, Germany and Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
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Gelin A, Redrejo-Rodríguez M, Laval J, Fedorova OS, Saparbaev M, Ishchenko AA. Genetic and biochemical characterization of human AP endonuclease 1 mutants deficient in nucleotide incision repair activity. PLoS One 2010; 5:e12241. [PMID: 20808930 PMCID: PMC2923195 DOI: 10.1371/journal.pone.0012241] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/25/2010] [Indexed: 11/19/2022] Open
Abstract
Background Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair enzyme involved in both base excision repair (BER) and nucleotide incision repair (NIR) pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 5′ to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells. Methodology/Principal Finding We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 3′→5′ exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites. Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase β and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells. Conclusion/Significance Taken together, these data further substantiate the role of NIR as a distinct and separable function of APE1 that is essential for processing of potentially lethal oxidative DNA lesions.
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Affiliation(s)
- Aurore Gelin
- CNRS UMR8126, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Modesto Redrejo-Rodríguez
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Jacques Laval
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Murat Saparbaev
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Alexander A. Ishchenko
- CNRS UMR8200 Groupe «Réparation de l′ADN», Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
- * E-mail:
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