ArticleBiochemistry2006
Catalytic mechanism of Escherichia coli endonuclease VIII: roles of the intercalation loop and the zinc finger.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- Deep-branching Chloroflexota lineages illuminate the eco-evolutionary foundation of cross-ecosystem colonization.Nature communications · 2026Article
- Functional roles and cancer variants of the bifunctional glycosylase NEIL2.Environmental and molecular mutagenesis · 2024Review
- The H2TH-like motif of the Escherichia coli multifunctional protein KsgA is required for DNA binding involved in DNA repair and the suppression of mutation frequencies.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2023Article
- Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.International journal of molecular sciences · 2022Article
- Cytotoxic Effect of Graphene Oxide Nanoribbons onNanomaterials (Basel, Switzerland) · 2021Article
- Inhibitors of DNA Glycosylases as Prospective Drugs.International journal of molecular sciences · 2020Review
- Zinc binding proteome of a phytopathogenRoyal Society open science · 2019Article
- Excision of the doubly methylated basePhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII.Genes · 2017Article
- Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition.Nucleic acids research · 2015Article
- New environment-sensitive multichannel DNA fluorescent label for investigation of the protein-DNA interactions.PloS one · 2014Article
- Article
- DNA glycosylases search for and remove oxidized DNA bases.Environmental and molecular mutagenesis · 2013Review
- Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA.Structure (London, England : 1993) · 2013Article
- Competition for zinc binding in the host-pathogen interaction.Frontiers in cellular and infection microbiology · 2013Review
- Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA.The Journal of biological chemistry · 2012Article
- The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage.Progress in molecular biology and translational science · 2012Review
- Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes.PloS one · 2011Article
- Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.The Journal of biological chemistry · 2009Article
- Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases.DNA repair · 2009Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Endonuclease VIII (Nei) excises oxidatively damaged pyrimidines from DNA and shares structural and functional homology with formamidopyrimidine-DNA glycosylase. Although the structure of Escherichia coli Nei is solved [Zharkov et al. (2002) EMBO J. 21, 789-800], the functions of many of its amino acid residues involved in catalysis and substrate specificity are not known. We constructed a series of Nei mutants that interfere with eversion of the damaged base from the helix (QLY69-71AAA, DeltaQLY69-71) or perturb the conserved zinc finger (R171A, Q261A). Steady-state kinetics were measured with these mutant enzymes using substrates containing 5,6-dihydrouracil, two enantiomers of thymine glycol, 8-oxo-7,8-dihydroguanine, and an abasic site positioned opposite each of the four canonical DNA bases. To some extent, all Nei mutants were deficient in processing damaged DNA, with mutations in the zinc finger generally having a more profound effect. Wild-type Nei showed prominent opposite-base specificity (G > C approximately = T > A) when the lesion was 5,6-dihydrouracil or cis-(5S,6R)-thymine glycol but not for other lesions tested. Mutations in the Q69-Y71 loop eliminated this effect. Only wild-type Nei and Nei-Q261A mutants could be reductively cross-linked to damaged base-containing DNA. Experiments involving trapping with NaBH4 and the kinetics of DNA cleavage catalyzed by Nei-Q261A suggested that this mutant was deficient in regenerating free enzyme from the Nei-DNA covalent complex formed during the reaction. We conclude that the opposite-base specificity of Nei is primarily governed by residues in the Q69-Y71 loop and that both this loop and the zinc finger contribute significantly to the substrate specificity of Nei.
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