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Nucleic Acids Research 2005 33(18):5936-5944; doi:10.1093/nar/gki879
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Published online 20 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA

Karine Pereira de Jésus, Laurence Serre1, Charles Zelwer and Bertrand Castaing*

Centre de Biophysique Moléculaire, CNRS rue Charles Sadron, 45071 Orléans cedex 02, France 1Institut de Biologie Structurale, CEA-CNRS-UJF 41 rue Jules Horowitz, 38027 Grenoble cedex 01, France

*To whom correspondence should be addressed. Tel: +33 2 38 25 78 43; Fax: +33 2 38 63 15 17; Email: castaing{at}cnrs-orleans.fr

Received June 29, 2005. Revised September 16, 2005. Accepted September 16, 2005.

Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by ß{delta}-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'–C4'–C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.

Present address: Karine Pereira de Jésus, Oncology and Molecular Endocrinology Research Center, Laval University Medical Center and Laval University, Quebec, Canada


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