1q3b › Citations

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.

Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G
Nucleic Acids Res 33 5006-16 (2005)
Related entries: 1q39, 1q3c

Cited: 23 times
EuropePMC logo PMID: 16145054

Abstract

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme.

Reviews - 1q3b 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 - 1q3b 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. Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Golan G, Zharkov DO, Feinberg H, Fernandes AS, Zaika EI, Kycia JH, Grollman AP, Shoham G. Nucleic Acids Res 33 5006-5016 (2005)
  3. Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments. Eckenroth BE, Cao VB, Averill AM, Dragon JA, Doublié S. Structure 29 29-42.e4 (2021)
  4. Local conformational changes in the DNA interfaces of proteins. Sunami T, Kono H. PLoS One 8 e56080 (2013)
  5. Breaking the Rules: Protein Sculpting in NEIL2 Regulation. Tsutakawa SE, Sarker AH. Structure 29 1-2 (2021)


Reviews citing this publication (4)

  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)
  4. Eukaryotic ribosomal protein S3: A constituent of translational machinery and an extraribosomal player in various cellular processes. Graifer D, Malygin A, Zharkov DO, Karpova G. Biochimie 99 8-18 (2014)

Articles citing this publication (12)

  1. Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA. Liu M, Imamura K, Averill AM, Wallace SS, Doublié S. Structure 21 247-256 (2013)
  2. 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)
  3. Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger. Kropachev KY, Zharkov DO, Grollman AP. Biochemistry 45 12039-12049 (2006)
  4. Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. Ghoneim M, Spies M. Nano Lett 14 5920-5931 (2014)
  5. New environment-sensitive multichannel DNA fluorescent label for investigation of the protein-DNA interactions. Kuznetsova AA, Kuznetsov NA, Vorobjev YN, Barthes NP, Michel BY, Burger A, Fedorova OS. PLoS One 9 e100007 (2014)
  6. Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII. Kladova OA, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Genes (Basel) 8 E140 (2017)
  7. Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis. Carroll BL, Zahn KE, Hanley JP, Wallace SS, Dragon JA, Doublié S. Nucleic Acids Res 49 13165-13178 (2021)
  8. A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase. Kakhkharova ZI, Zharkov DO, Grin IR. Int J Mol Sci 23 2212 (2022)
  9. Thermodynamics of the DNA Repair Process by Endonuclease VIII. Kladova OA, Kuznetsov NA, Fedorova OS. Acta Naturae 11 29-37 (2019)
  10. 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)
  11. Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases. Diatlova EA, Mechetin GV, Zharkov DO. Cells 11 3192 (2022)
  12. 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)


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