Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis

Cell. 1999 Aug 6;98(3):397-408. doi: 10.1016/s0092-8674(00)81968-6.


Endonuclease IV is the archetype for a conserved apurinic/apyrimidinic (AP) endonuclease family that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites. The crystal structures of Endonuclease IV and its AP-DNA complex at 1.02 and 1.55 A resolution reveal how an alpha8beta8 TIM barrel fold can bind dsDNA. Enzyme loops intercalate side chains at the abasic site, compress the DNA backbone, bend the DNA approximately 90 degrees, and promote double-nucleotide flipping to sequester the extrahelical AP site in an enzyme pocket that excludes undamaged nucleotides. These structures suggest three Zn2+ ions directly participate in phosphodiester bond cleavage and prompt hypotheses that double-nucleotide flipping and sharp bending by AP endonucleases provide exquisite damage specificity while aiding subsequent base excision repair pathway progression.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Caenorhabditis elegans / enzymology
  • Carbon-Oxygen Lyases / chemistry*
  • Carbon-Oxygen Lyases / metabolism*
  • Computer Graphics
  • Conserved Sequence
  • Crystallography, X-Ray
  • DNA / chemistry*
  • DNA / metabolism*
  • DNA Damage
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Deoxyribonuclease IV (Phage T4-Induced)
  • Escherichia coli / enzymology
  • Escherichia coli Proteins*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Saccharomyces cerevisiae / enzymology
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Zinc / metabolism


  • Escherichia coli Proteins
  • DNA
  • Deoxyribonuclease IV (Phage T4-Induced)
  • endonuclease IV, E coli
  • Carbon-Oxygen Lyases
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Zinc

Associated data

  • PDB/1QTM
  • PDB/1QUM