Sequence specificity and biochemical characterization of the RusA Holliday junction resolvase of Escherichia coli

J Biol Chem. 1997 Jun 6;272(23):14873-82. doi: 10.1074/jbc.272.23.14873.


The RusA protein of Escherichia coli is an endonuclease that resolves Holliday intermediates in recombination and DNA repair. Analysis of its subunit structure revealed that the native protein is a dimer. Its resolution activity was investigated using synthetic X-junctions with homologous cores. Resolution occurs by dual strand incision predominantly 5' of CC dinucleotides located symmetrically. A junction lacking homology is not resolved. The efficiency of resolution is related inversely to the number of base pairs in the homologous core, which suggests that branch migration is rate-limiting. Inhibition of resolution at high ratios of protein to DNA suggests that binding of RusA may immobilize the junction point at non-cleavable sites. Resolution is stimulated by alkaline pH and by Mn2+. The protein is unstable in the absence of substrate DNA and loses approximately 80% of its activity within 1 min under standard reaction conditions. DNA binding stabilizes the activity. Junction resolution is inhibited in the presence of RuvA. This observation probably explains why RusA is unable to promote efficient recombination and DNA repair in ruvA+ strains unless it is expressed at a high level.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Base Sequence
  • Chromatography, Affinity
  • Chromatography, Gel
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Nucleotidyltransferases / biosynthesis
  • DNA Nucleotidyltransferases / isolation & purification
  • DNA Nucleotidyltransferases / metabolism*
  • DNA-Binding Proteins / metabolism
  • Escherichia coli / enzymology*
  • Hydrogen-Ion Concentration
  • Kinetics
  • Magnesium Chloride / pharmacology
  • Manganese / pharmacology
  • Oligodeoxyribonucleotides / chemistry
  • Oligodeoxyribonucleotides / metabolism
  • Recombinant Proteins / biosynthesis
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • Substrate Specificity
  • Transposases


  • DNA-Binding Proteins
  • Oligodeoxyribonucleotides
  • Recombinant Proteins
  • Magnesium Chloride
  • Manganese
  • DNA
  • DNA Nucleotidyltransferases
  • Transposases