Integration host factor: putting a twist on protein-DNA recognition

J Mol Biol. 2003 Jul 11;330(3):493-502. doi: 10.1016/s0022-2836(03)00529-1.


Integration host factor (IHF) is a DNA-bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant.

Publication types

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

MeSH terms

  • Amino Acid Substitution
  • Base Pairing / physiology
  • Binding Sites
  • Crystallography, X-Ray
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / metabolism*
  • Integration Host Factors / chemistry*
  • Integration Host Factors / genetics
  • Integration Host Factors / metabolism*
  • Models, Molecular
  • Mutagenesis
  • Protein Conformation


  • DNA, Bacterial
  • Integration Host Factors

Associated data

  • PDB/1OUZ
  • PDB/1OWF
  • PDB/1OWG