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

Thomas W. Lynch, Erik K. Read, Aras N. Mattis, Jeffrey F. Gardner, Phoebe A. Rice

Research output: Contribution to journalArticle


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 βGlu44 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-βGlu44Ala 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.

Original languageEnglish (US)
Pages (from-to)493-502
Number of pages10
JournalJournal of Molecular Biology
Issue number3
StatePublished - Jul 11 2003


  • Gel-shift assay
  • Indirect readout
  • Mutants
  • Protein-DNA interactions
  • X-ray crystallography

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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