Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn

@article{Rice1996CrystalSO,
  title={Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn},
  author={Phoebe A. Rice and Shu-wei Yang and Kiyoshi Mizuuchi and Howard A. Nash},
  journal={Cell},
  year={1996},
  volume={87},
  pages={1295-1306}
}
Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a… 
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The results provide direct experimental evidence for concerted DNA bending by HU, and the abrogation of this effect at HU to DNA ratios above about one HU dimer per 10-12 bp suggests a unique role for HU in the dynamic modulation of bacterial nucleoid structure.
Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
TLDR
It is shown that IHF-DNA structural multimodality is more elaborate than previously thought, and insights into how this drives mechanical switching towards strongly bent DNA are provided.
Integration host factor: putting a twist on protein-DNA recognition.
TLDR
Comparison of crystal structures and relative binding affinities 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.
Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
TLDR
It is shown that IHF–DNA structural multimodality is more elaborate than previously thought, and insights into how this drives mechanical switching towards strongly bent DNA are provided.
Recognition of a TG Mismatch The Crystal Structure of Very Short Patch Repair Endonuclease in Complex with a DNA Duplex
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The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution and provides detailed insights into the catalytic mechanism for end onuclease activity.
The solution structure of an HMG-I(Y)–DNA complex defines a new architectural minor groove binding motif
The solution structure of a complex between a truncated form of HMG-I(Y), consisting of the second and third DNA binding domains (residues 51–90), and a DNA dodecamer containing the PRDII site of the…
A good turn for DNA: the structure of integration host factor bound to DNA.
The crystal structure of integration host factor (IHF) complexed with DNA shows how a small heterodimeric protein can induce a big bend in DNA. IHF exerts leverage in the minor groove and wraps DNA…
Structure-based analysis of HU-DNA binding.
TLDR
It is shown that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove, similar to sequence preferences shown by the eukaryotic nucleosome.
Extreme DNA Bending: Molecular Basis of the Regulatory Breadth of IHF
TLDR
The sequence of the IHF protein of the soil bacterium Pseudomonas putida is used as a starting point to examine in detail the basis of the recognition of DNA sequences by this nucleoid-associated protein, in particular the correlation between sequence conservation and DNA interaction for each ofThe Integration host factor chains.
Concerted binding and bending of DNA by Escherichia coli integration host factor.
TLDR
These results are the first analysis by synchrotron footprinting of the fast kinetics of a protein-DNA interaction and suggest that IHF binds its specific site through a multiple-step mechanism in which the first step is facilitated diffusion along the length of the duplex followed by subsequent binding and bending of the DNA in a concerted manner.
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TLDR
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