PDBsum entry: 1owf

Transcription/DNA

PDB id: 1owf

Contents

Protein chains

96 a.a. *

94 a.a. *

DNA/RNA

Waters ×153

* Residue conservation analysis

PDB id:

1owf

Name:

Transcription/DNA

Title:

Crystal structure of a mutant ihf (betae44a) complexed with the native h' site

Structure:

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

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Pentamer (from PQS)

Resolution:

1.95Å R-factor: 0.232 R-free: 0.273

Authors:

T.W.Lynch,E.K.Read,A.N.Mattis,J.F.Gardner,P.A.Rice

Key ref:

T.W.Lynch et al. (2003). Integration host factor: putting a twist on protein-DNA recognition. J Mol Biol, 330, 493-502. PubMed id: 12842466 DOI: 10.1016/S0022-2836(03)00529-1

Date:

28-Mar-03 Release date: 15-Jul-03

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: 94 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 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/S0022-2836(03)00529-1

J Mol Biol 330:493-502 (2003)

PubMed id: 12842466

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

T.W.Lynch, E.K.Read, A.N.Mattis, J.F.Gardner, P.A.Rice.

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.

Selected figure(s)

Figure 1.
Figure 1. Structure of the IHF-H' DNA complex. (a) Ribbon view of the overall X-ray structure with the a subunit in grey, the b subunit in pink, the consensus sequence DNA bases in green and the less conserved bases in blue. (b) Stereo view of the contacts between IHF and the TTR element of the H' site. (c) The duplex DNAs used for crystal growth and binding analysis. The numbering corresponds to bases 19-47 of bacteriophage l, and the position of the nick needed for crystallization is marked by the arrow.

Figure 2.
Figure 2. Simulated-annealing omit maps of the WT and three variant IHF/H' complexes. Simulated-annealing omit maps are superimposed on the final model for each structure. Residues bArg42, bGlu44/bAla44, bArg46, and base-pair 44 were omitted. (a) WT-IHF/H',[9.] contoured at 3.5s. (b) IHF-bGlu44Ala/H', contoured at 3.5s. (c) WT-IHF/H'44A, contoured at 3.5s. (d) IHF-bGlu44Ala/H'44A, contoured at 2.2s.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 493-502) copyright 2003.

Figures were selected by the author.