PDBsum entry: 1ihf

Transcription/DNA

PDB id: 1ihf

Contents

Protein chains

96 a.a. *

94 a.a. *

DNA/RNA

Metals

_CD ×15

Waters ×385

* Residue conservation analysis

PDB id:

1ihf

Name:

Transcription/DNA

Title:

Integration host factor/DNA complex

Structure:

DNA (35-mer). Chain: c. Engineered: yes. DNA (5'- d( Gp Gp Cp Cp Ap Ap Ap Ap Ap Ap Gp Cp Ap Tp T)-3'). Chain: d. Engineered: yes. DNA (5'- d( Gp Cp Tp Tp Ap Tp Cp Ap Ap Tp Tp Tp Gp Tp Tp Gp C

Source:

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

Biol. unit:

Pentamer (from PQS)

Resolution:

2.20Å R-factor: 0.192 R-free: 0.255

Authors:

P.A.Rice,S.-W.Yang,K.Mizuuchi,H.A.Nash

Key ref:

P.A.Rice et al. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell, 87, 1295-1306. PubMed id: 8980235 DOI: 10.1016/S0092-8674(00)81824-3

Date:

21-Aug-96 Release date: 12-Feb-97

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.

 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/S0092-8674(00)81824-3

Cell 87:1295-1306 (1996)

PubMed id: 8980235

Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.

P.A.Rice, S.Yang, K.Mizuuchi, H.A.Nash.

ABSTRACT

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 proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.

Selected figure(s)

Figure 3.
Figure 3. Proline 65 Intercalates Between Base PairsStereo close-up view of the tip of the α subunit arm. The protein Cαs and the side chain of P65 are shown. Consensus sequence bases are green; others, blue.

Figure 8.
Figure 8. Model for IHF-Induced Juxtaposition of Binding Sites in a Nucleoprotein ArrayThe model shows a portion of attL, one of the partners involved in the excision of λ prophage. This segment of DNA binds one protomer of IHF and one protomer of the 40 kDa λ integrase (Int; shown in green). The Int protomer recognizes two segments of attL (C′ and Pl′; shown in lavender) with its large and small domains, respectively ([20]). To estimate the positions of these Int binding sites in the complex, B-form DNA extensions were modeled onto the ends of the duplex in the IHF-DNA structure. This shows that bending due to IHF can expedite Int binding by bringing the phosphate backbones of the C′ and Pl′ binding sites to within 25 Å of each other.

The above figures are reprinted by permission from Cell Press: Cell (1996, 87, 1295-1306) copyright 1996.

Figures were selected by the author.