Integration host factor: putting a twist on protein-DNA recognition |
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Authors: | Lynch Thomas W Read Erik K Mattis Aras N Gardner Jeffrey F Rice Phoebe A |
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Affiliation: | Department of Biochemistry and Molecular Biology, The University of Chicago, 920 E 58th Street CLSC 221, Chicago, IL 60637, USA. |
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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. |
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Keywords: | indirect readout X-ray crystallography gel-shift assay mutants protein-DNA interactions |
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