2HT0

IHF bound to doubly nicked DNA

Summary for 2HT0

• Entry DOI: 10.2210/pdb2ht0/pdb
• Related: 1B8Z 1IHF 1OUZ 1OWF 1OWG 1P51 1P71 1P78
• Descriptor: 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3', 5'-D(*TP*GP*AP*TP*AP*AP*GP*CP*AP*AP*TP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3', ... (8 entities in total)
• Functional Keywords: dna bending, kink, nick, protein-dna complex, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 6
• Total formula weight: 43600.53

Authors

Swinger, K.K.,Rice, P.A. (deposition date: 2006-07-24, release date: 2006-11-28, Last modification date: 2024-02-14)

Primary citation

Swinger, K.K.,Rice, P.A.
Structure-based Analysis of HU-DNA Binding.
J.Mol.Biol., 365:1005-1016, 2007

PubMed Abstract: HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show 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. This is similar to sequence preferences shown by the eukaryotic nucleosome.

PubMed: 17097674
DOI: 10.1016/j.jmb.2006.10.024

Experimental method

X-RAY DIFFRACTION (2 Å)