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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.

Pereira de Jésus K, Serre L, Zelwer C, Castaing B
Nucleic Acids Res 33 5936-44 (2005)
Related entries: 1nnj, 1pji, 1pjj

Cited: 25 times
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Abstract

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 betadelta-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.

Reviews - 1pm5 mentioned but not cited (2)

  1. Recent advances in the structural mechanisms of DNA glycosylases. Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Biochim Biophys Acta 1834 247-271 (2013)
  2. The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage. Prakash A, Doublié S, Wallace SS. Prog Mol Biol Transl Sci 110 71-91 (2012)

Articles - 1pm5 mentioned but not cited (5)

  1. Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA. Imamura K, Wallace SS, Doublié S. J Biol Chem 284 26174-26183 (2009)
  2. 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. Pereira de Jésus K, Serre L, Zelwer C, Castaing B. Nucleic Acids Res 33 5936-5944 (2005)
  3. Diversity of Cultivable Microbes From Soil of the Fildes Peninsula, Antarctica, and Their Potential Application. Cong B, Yin X, Deng A, Shen J, Tian Y, Wang S, Yang H. Front Microbiol 11 570836 (2020)
  4. Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Cieśla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B. Nucleic Acids Res 42 10748-10761 (2014)
  5. Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights. Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guérin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B. Int J Mol Sci 21 E2058 (2020)


Reviews citing this publication (3)

  1. DNA base repair--recognition and initiation of catalysis. Dalhus B, Laerdahl JK, Backe PH, Bjørås M. FEMS Microbiol Rev 33 1044-1078 (2009)
  2. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Boiteux S, Coste F, Castaing B. Free Radic Biol Med 107 179-201 (2017)
  3. DNA glycosylases search for and remove oxidized DNA bases. Wallace SS. Environ Mol Mutagen 54 691-704 (2013)

Articles citing this publication (15)

  1. Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence--stopped-flow pre-steady-state kinetics. Kuznetsov NA, Vorobjev YN, Krasnoperov LN, Fedorova OS. Nucleic Acids Res 40 7384-7392 (2012)
  2. Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C. Proc Natl Acad Sci U S A 113 7792-7797 (2016)
  3. Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine. Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace SS, Doublié S. DNA Repair (Amst) 11 714-725 (2012)
  4. Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode. Coste F, Ober M, Le Bihan YV, Izquierdo MA, Hervouet N, Mueller H, Carell T, Castaing B. Chem Biol 15 706-717 (2008)
  5. Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies. Jia L, Shafirovich V, Geacintov NE, Broyde S. Biochemistry 46 5305-5314 (2007)
  6. Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling. Sicoli G, Mathis G, Aci-Sèche S, Saint-Pierre C, Boulard Y, Gasparutto D, Gambarelli S. Nucleic Acids Res 37 3165-3176 (2009)
  7. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases. Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B. Nucleic Acids Res 39 6277-6290 (2011)
  8. Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM. Sung RJ, Zhang M, Qi Y, Verdine GL. J Biol Chem 287 18044-18054 (2012)
  9. Recognition and excision properties of 8-halogenated-7-deaza-2'-deoxyguanosine as 8-oxo-2'-deoxyguanosine analogues and Fpg and hOGG1 inhibitors. Yin Y, Sasaki S, Taniguchi Y. Chembiochem 16 1190-1198 (2015)
  10. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF. DNA Repair (Amst) 12 196-204 (2013)
  11. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD. J Am Chem Soc 144 8054-8065 (2022)
  12. Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing. Franck C, Stéphane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C. Nucleic Acids Res 50 11072-11092 (2022)
  13. Synthesis of a stabilized version of the imidazolone DNA lesion. Mueller H, Hopfinger M, Carell T. Chembiochem 9 1617-1622 (2008)
  14. Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes. Barrantes-Reynolds R, Wallace SS, Bond JP. PLoS One 6 e25246 (2011)
  15. Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. Popov AV, Endutkin AV, Vorobjev YN, Zharkov DO. BMC Struct Biol 17 5 (2017)


Related citations provided by authors (1)

  1. Crystal structure of the Lactococcus lactis Formamidopyrimidine DNA glycosylase bound to an abasic site analogue-containing DNA. Serre L, Pereira de Jesus K, Boiteux S, Zelwer C, Castaing B EMBO J. 21 2854-2865 (2002)

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