PDBsum entry: 2ht0

Transcription/DNA

PDB id: 2ht0

Contents

Protein chains

96 a.a. *

93 a.a. *

DNA/RNA

Metals

_CD

Waters ×260

* Residue conservation analysis

PDB id:

2ht0

Name:

Transcription/DNA

Title:

Ihf bound to doubly nicked DNA

Structure:

5'-d( Cp Gp Gp Tp Gp Cp Ap Ap Cp Ap Ap Ap T)-3'. Chain: c. Engineered: yes. 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'. Chain: d. Engineered: yes. 5'-

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Organism_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

2.00Å R-factor: 0.235 R-free: 0.278

Authors:

K.K.Swinger,P.A.Rice

Key ref:

K.K.Swinger and P.A.Rice (2007). Structure-based Analysis of HU-DNA Binding. J Mol Biol, 365, 1005-1016. PubMed id: 17097674 DOI: 10.1016/j.jmb.2006.10.024

Date:

24-Jul-06 Release date: 28-Nov-06

Protein chain

P0A6X7  (IHFA_ECOLI) -  Integration host factor subunit alpha

Seq: 99 a.a.

Struc: 96 a.a.

Protein chain

P0A6Y1  (IHFB_ECOLI) -  Integration host factor subunit beta

Seq: 94 a.a.

Struc: 93 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: conjugation (5 terms)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1016/j.jmb.2006.10.024

J Mol Biol 365:1005-1016 (2007)

PubMed id: 17097674

Structure-based Analysis of HU-DNA Binding.

K.K.Swinger, P.A.Rice.

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.

Selected figure(s)

Figure 1.
Figure 1. IHF–DNA and AHU–DNA cocrystal structures. (a) Stereoview of a superposition of the IHF–DNA and AHU–DNA complexes. IHF protein is shown in grey and white, IHF DNA is pink (1IHF). AHU is gold and the bound DNA is green (1P71). Proline residues at the tips of the arm-like β-ribbon extension are in yellow. (b) The AHU–DNA complex (1P71) is color-coded as in Table 1. The protein subunits are gold and orange, and the intercalating proline residues are in yellow. Canonical DNA is blue, unpaired bases are green (stacked) or grey (flipped), and mismatches are pink (from Figure 3 of Swinger et al.).^10

Figure 4.
Figure 4. Comparisons of IHF-kinked DNA and AHU-kinked DNA. (a) A stereoview of a superposition of kinked DNA from the previously published IHF–DNA structure in pink (1IHF), and the sharper of the kinks in the AHU–DNA structure in green (1P78). The tips of the β-ribbon protein arms are shown in white (IHF) and gold (AHU), with the intercalating proline residues in yellow. Bases at the kink in these two structures superimpose remarkably well considering the differences in sequences and the presence of an extra T in the AHU structure (marked by an asterisk). The sequences for the portions of the structures shown are in green for AHU and in pink for IHF. The asterisk marks the intercalated T. (b) A stereoview of a superposition of kinked DNA from a nicked IHF–DNA structure deposited recently with the RCSB Protein Data Bank in pink (2HT0) and the AHU–DNA structure in green. The nick in the IHF DNA backbone in this structure is directly at the site of kinking. Proteins are color-coded as in (a). The superposition of paired bases in these two structures is even closer than that observed in (a). The arrow by the IHF sequence in pink marks the location of the nick. This view illustrates that a nick and an extra T similarly relieve strain in the kinked DNA backbone.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 1005-1016) copyright 2007.

Figures were selected by the author.