PDBsum entry: 2iif

Recombination/DNA

PDB id: 2iif

Contents

Protein chain

204 a.a. *

DNA/RNA

Metals

_MN ×8

Waters ×163

* Residue conservation analysis

PDB id:

2iif

Name:

Recombination/DNA

Title:

Single chain integration host factor mutant protein (scihf2- k45ae) in complex with DNA

Structure:

Phage p h' site. Chain: c. Engineered: yes. DNA (5'- d( Dgp Dgp Dcp Dcp Dap Dap Dap Dap Dap Dap Dgp Dcp Dap Dtp Dt)-3'). Chain: d. Engineered: yes. DNA (5'-

Source:

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

Resolution:

2.72Å R-factor: 0.237 R-free: 0.274

Authors:

Q.Bao,P.Droege,C.A.Davey

Key ref:

Q.Bao et al. (2007). A divalent metal-mediated switch controlling protein-induced DNA bending. J Mol Biol, 367, 731-740. PubMed id: 17276457 DOI: 10.1016/j.jmb.2006.09.082

Date:

28-Sep-06 Release date: 20-Feb-07

Protein chain

Q14F23  (Q14F23_ECOLX) -  Integration host factor subunit alpha

Seq: 99 a.a.

Struc: 204 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription (5 terms)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1016/j.jmb.2006.09.082

J Mol Biol 367:731-740 (2007)

PubMed id: 17276457

A divalent metal-mediated switch controlling protein-induced DNA bending.

Q.Bao, H.Chen, Y.Liu, J.Yan, P.Dröge, C.A.Davey.

ABSTRACT

Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found to adopt two stable conformational states in complex with a specific DNA target. In the so-called open state, the degree of protein-induced DNA bending is reduced significantly compared with the closed state. The conformational switch between these states is controlled by divalent metal binding in two electronegative zones arising from the lysine-to-glutamate substitution in the protein body proximal to the phosphate backbone of one DNA arm. We show that this switch can be employed to control the efficiency of site-specific recombination catalyzed by lambda integrase. Introduction of acidic residues at the protein-DNA interface holds potential for the design of metal-mediated switches for the investigation of functional relationships.

Selected figure(s)

Figure 1.
Figure 1. Sequence of scIHF2-K45αE and EMSA. (a) Numbering of residues follows that of the heteromeric IHF. The two short linkers are shaded. The αK45E substitution and corresponding residue in the β-subunit are underlined. (b) EMSA analysis of complexes formed between the 34 bp long, radio-labeled H′ and either scIHF2 or scIHF2-K45αE. Figure 1. Sequence of scIHF2-K45αE and EMSA. (a) Numbering of residues follows that of the heteromeric IHF. The two short linkers are shaded. The αK45E substitution and corresponding residue in the β-subunit are underlined. (b) EMSA analysis of complexes formed between the 34 bp long, radio-labeled H′ and either scIHF2 or scIHF2-K45αE.

Figure 5.
Figure 5. Protein–DNA interactions in the crystal structures of the scIHF2-DNA and scIHF2-K45αE–DNA complexes. (a) The scIHF2–DNA complex, with protein regions corresponding to the α and β-subunits of wild-type IHF colored green and blue, respectively. Regions differing in primary sequence with respect to IHF are colored red, including the linker amino acids (thick tubes) used to fuse the α and β-subunits. The boxed area associated with the left DNA arm corresponds to the section viewed in (c), (d) and (e). (b) Superposition of the scIHF2–DNA (yellow) and IHF–DNA (α-subunit, magenta; β-subunit, cyan; DNA, blue) models. (c) and (d) Simulated annealing, F[o] − F[c] omit maps (blue), contoured at 4σ and 3σ, superimposed on the (c) scIHF2–DNA and (d) scIHF2-K45αE-DNA models, respectively. Residues αQ43 and αK45 of scIHF2–DNA and αQ43 and αE45 of scIHF2-K45αE–DNA were omitted. An anomalous difference map (brown), contoured at 3σ, denotes the positions of manganese ions (cyan spheres) in (d). Water molecules are shown as red spheres, and hydrogen and coordinate bonds are indicated by broken lines. (e) Structural comparison of the scIHF2-DNA (yellow) and scIHF2-K45αE-DNA (green) complexes in stereo view. Mn^2+ associated with the αK45E mutant are shown as cyan spheres. Figure 5. Protein–DNA interactions in the crystal structures of the scIHF2-DNA and scIHF2-K45αE–DNA complexes. (a) The scIHF2–DNA complex, with protein regions corresponding to the α and β-subunits of wild-type IHF colored green and blue, respectively. Regions differing in primary sequence with respect to IHF are colored red, including the linker amino acids (thick tubes) used to fuse the α and β-subunits. The boxed area associated with the left DNA arm corresponds to the section viewed in (c), (d) and (e). (b) Superposition of the scIHF2–DNA (yellow) and IHF–DNA (α-subunit, magenta; β-subunit, cyan; DNA, blue) models. (c) and (d) Simulated annealing, F[o] − F[c] omit maps (blue), contoured at 4σ and 3σ, superimposed on the (c) scIHF2–DNA and (d) scIHF2-K45αE-DNA models, respectively. Residues αQ43 and αK45 of scIHF2–DNA and αQ43 and αE45 of scIHF2-K45αE–DNA were omitted. An anomalous difference map (brown), contoured at 3σ, denotes the positions of manganese ions (cyan spheres) in (d). Water molecules are shown as red spheres, and hydrogen and coordinate bonds are indicated by broken lines. (e) Structural comparison of the scIHF2-DNA (yellow) and scIHF2-K45αE-DNA (green) complexes in stereo view. Mn^2+ associated with the αK45E mutant are shown as cyan spheres.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 731-740) copyright 2007.

Figures were selected by the author.