DNA apurinic-apyrimidinic site binding and excision by endonuclease IV

Nat Struct Mol Biol. 2008 May;15(5):515-22. doi: 10.1038/nsmb.1414. Epub 2008 Apr 13.

Abstract

Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • DNA / metabolism
  • Deoxyribonuclease IV (Phage T4-Induced) / chemistry
  • Deoxyribonuclease IV (Phage T4-Induced) / genetics
  • Deoxyribonuclease IV (Phage T4-Induced) / metabolism*
  • Escherichia coli / enzymology*
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Models, Molecular
  • Protein Structure, Secondary

Substances

  • DNA
  • Deoxyribonuclease IV (Phage T4-Induced)

Associated data

  • PDB/2NQ9
  • PDB/2NQH
  • PDB/2NQJ