title: Integration host factor: putting a twist on protein-DNA recognition.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, 920 E 58th Street CLSC 221, Chicago, IL 60637, USA.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Lynch
authors.forename: Erik K
authors.initials: EK
authors.lastname: Read
authors.forename: Aras N
authors.initials: AN
authors.lastname: Mattis
authors.forename: Jeffrey F
authors.initials: JF
authors.lastname: Gardner
authors.forename: Phoebe A
authors.initials: PA
authors.lastname: Rice
mesh_terms: D019943:Amino Acid Substitution; D020029:Base Pairing / Q000502:physiology; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D034982:Integration Host Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D016296:Mutagenesis; D011487:Protein Conformation
chemical_list: D004269:DNA, Bacterial; D034982:Integration Host Factors