A novel endonuclease mechanism directly visualized for I-PpoI

Nat Struct Biol. 1999 Dec;6(12):1096-9. doi: 10.1038/70027.

Abstract

A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the previously visualized product complex. This enzyme employs a unique single metal mechanism. A magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule is activated by a histidine residue for an in-line attack on the scissile phosphate. A strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the reaction.

MeSH terms

  • Amino Acid Substitution / genetics
  • Animals
  • Binding Sites
  • Catalysis
  • Cations / metabolism
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • Electrons
  • Endodeoxyribonucleases / chemistry*
  • Endodeoxyribonucleases / genetics
  • Endodeoxyribonucleases / metabolism*
  • Fourier Analysis
  • Magnesium / metabolism
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Oxygen / metabolism
  • Phosphates / metabolism
  • Physarum polycephalum / enzymology*
  • Protein Conformation
  • Sodium / metabolism
  • Solvents
  • Structure-Activity Relationship
  • Water / chemistry
  • Water / metabolism

Substances

  • Cations
  • Phosphates
  • Solvents
  • Water
  • DNA
  • Sodium
  • Endodeoxyribonucleases
  • I-Ppo endonuclease
  • Magnesium
  • Oxygen

Associated data

  • PDB/1A73
  • PDB/1CYQ
  • PDB/1CZ0