PDBsum entry: 1ouz

Transcription/DNA

PDB-id: 1ouz

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Protein chains

96 a.a. *

94 a.a. *

DNA/RNA

Waters ×162

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1ouz

Name:

Transcription/DNA

Title:

Crystal structure of a mutant ihf (betae44a) complexed with a variant h' site (t44a)

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 Ap Gp Cp Ap Cp

Source:

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

Biological unit:

Pentamer (from PQS)

UniProt:

Chain A: P0A6X7 (IHFA_ECOLI)

Seq:	99 a.a.
Struc:	96 a.a.

Chain B: P0A6Y1 (IHFB_ECOLI)

Seq:

94 a.a.

Struc:

94 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Resolution:

2.41Å

R-factor:

0.241

R-free:

0.271

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:

25-Mar-03

Release date:

15-Jul-03

Related entries:

1ihf
crystal structure of an ihf-DNA complex: a protein-induced
DNA u-turn

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Key reference

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.