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

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.

[1]  H. Nash,et al.  Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target. , 1995, The EMBO journal.

[2]  W. McClure,et al.  Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). , 1990, Nucleic acids research.

[3]  R. Sauer,et al.  Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. , 1995, Biochemistry.

[4]  D C Rees,et al.  A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA. , 1998, Science.

[5]  G. Koudelka.  Recognition of DNA structure by 434 repressor. , 1998, Nucleic acids research.

[6]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[7]  R. Gumport,et al.  The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA. , 1995, Biochemistry.

[8]  S. Diekmann,et al.  Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer. , 1999, Nucleic acids research.

[9]  Peter B. Dervan,et al.  Recognition of the four Watson–Crick base pairs in the DNA minor groove by synthetic ligands , 1998, Nature.

[10]  S. Phillips,et al.  Direct and indirect readout in mutant Met repressor-operator complexes. , 2000, Structure.

[11]  Richard H. Lathrop,et al.  DNA sequence and structure: direct and indirect recognition in protein-DNA binding , 2002, ISMB.

[12]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Dickerson,et al.  Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. , 2001, Journal of molecular biology.

[14]  R. Gumport,et al.  The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA‐binding specificities. , 1992, The EMBO journal.

[15]  Mike Carson,et al.  RIBBONS 2.0 , 1991 .

[16]  A. Sirko,et al.  The role of integration host factor In gene expression in Escherichia coli , 1992, Molecular microbiology.

[17]  W. Olson,et al.  A-form conformational motifs in ligand-bound DNA structures. , 2000, Journal of molecular biology.

[18]  M. Suzuki,et al.  Stereochemical basis of DNA bending by transcription factors. , 1995, Nucleic acids research.

[19]  Struther Arnott,et al.  The structure of B-DNA in oriented fibers. , 1996, Journal of biomolecular structure & dynamics.

[20]  R. Gumport,et al.  Genetic analysis of Escherichia coli integration host factor interactions with its bacteriophage lambda H' recognition site , 1991, Journal of bacteriology.

[21]  Steven Hahn,et al.  Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.

[22]  J. Carey.  [8] Gel retardation , 1991 .

[23]  M. Fried.  Measurement of protein‐DNA interaction parameters by electrophoresis mobility shift assay , 1989, Electrophoresis.

[24]  R. Gumport,et al.  Mutants of Escherichia coli integration host factor: DNA-binding and recombination properties. , 1994, Biochimie.

[25]  S. Sligar,et al.  Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Phoebe A Rice,et al.  Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn , 1996, Cell.

[27]  N. Craig,et al.  E. coli integration host factor binds to specific sites in DNA , 1984, Cell.

[28]  J. Perona,et al.  Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation , 2002, Nature Structural Biology.

[29]  A. Oppenheim,et al.  Genetic and biochemical analysis of the integration host factor of Escherichia coli. , 1993, Journal of molecular biology.

[30]  H. Nash,et al.  Purification and properties of the Escherichia coli protein factor required for lambda integrative recombination. , 1981, The Journal of biological chemistry.

[31]  D. Friedman,et al.  Integration host factor: A protein for all reasons , 1988, Cell.

[32]  G. Shulman,et al.  Disruption of IRS-2 causes type 2 diabetes in mice , 1998, Nature.

[33]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[34]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[35]  T. Kunkel,et al.  Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking. , 2001, Journal of molecular biology.

[36]  H. Nash,et al.  The interaction of E. coli IHF protein with its specific binding sites , 1989, Cell.

[37]  J. Widom,et al.  Role of DNA sequence in nucleosome stability and dynamics , 2001, Quarterly Reviews of Biophysics.

[38]  R. Sauer,et al.  Assembly of the Arc repressor-operator complex: cooperative interactions between DNA-bound dimers. , 1993, Biochemistry.

[39]  H. Nash,et al.  Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its target DNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[40]  E. Read,et al.  Specific Recognition of DNA by Integration Host Factor , 2000, The Journal of Biological Chemistry.