PDBsum entry: 2zhh

Transcription

PDB id: 2zhh

Contents

Protein chain

120 a.a. *

Ligands

FES

DTT

* Residue conservation analysis

PDB id:

2zhh

Name:

Transcription

Title:

Crystal structure of soxr

Structure:

Redox-sensitive transcriptional activator soxr. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: soxr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.20Å R-factor: 0.244 R-free: 0.276

Authors:

S.Watanabe,A.Kita,K.Kobayashi,K.Miki

Key ref:

S.Watanabe et al. (2008). Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA. Proc Natl Acad Sci U S A, 105, 4121-4126. PubMed id: 18334645 DOI: 10.1073/pnas.0709188105

Date:

05-Feb-08 Release date: 25-Mar-08

Protein chain

P0ACS2  (SOXR_ECOLI) -  Redox-sensitive transcriptional activator soxR

Seq: 154 a.a.

Struc: 120 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to oxidative stress (3 terms)
• Biochemical function: nucleotide binding (7 terms)

DOI no: 10.1073/pnas.0709188105

Proc Natl Acad Sci U S A 105:4121-4126 (2008)

PubMed id: 18334645

Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA.

S.Watanabe, A.Kita, K.Kobayashi, K.Miki.

ABSTRACT

The [2Fe-2S] transcription factor SoxR, a member of the MerR family, functions as a bacterial sensor of oxidative stress such as superoxide and nitric oxide. SoxR is activated by reversible one-electron oxidation of the [2Fe-2S] cluster and then enhances the production of various antioxidant proteins through the soxRS regulon. In the active state, SoxR and other MerR family proteins activate transcription from unique promoters, which have a long 19- or 20-bp spacer between the -35 and -10 operator elements, by untwisting the promoter DNA. Here, we show the crystal structures of SoxR and its complex with the target promoter in the oxidized (active) state. The structures reveal that the [2Fe-2S] cluster of SoxR is completely solvent-exposed and surrounded by an asymmetric environment stabilized by interaction with the other subunit. The asymmetrically charged environment of the [2Fe-2S] cluster probably causes redox-dependent conformational changes of SoxR and the target promoter. Compared with the promoter structures with the 19-bp spacer previously studied, the DNA structure is more sharply bent, by approximately 1 bp, with the two central base pairs holding Watson-Crick base pairs. Comparison of the target promoter sequences of the MerR family indicates that the present DNA structure represents the activated conformation of the target promoter with a 20-bp spacer in the MerR family.

Selected figure(s)

Figure 2.
Asymmetric environment of the [2Fe-2S] cluster of SoxR. (A) Stereoview of the [2Fe-2S] cluster environment in stick representation. Iron and sulfur atoms are indicated by brown and green spheres, respectively. The electron density of a F [o]−F [c] omit map calculated by omitting the two sulfur atoms of the [2Fe-2S] cluster is shown at 6σ (red). NH-S hydrogen bonds are represented in orange broken lines. (B) Surface representation of the Fe-S cluster-binding domain. Iron and sulfur atoms of the [2Fe-2S] cluster and cysteine residues are colored in brown and green, respectively. (C) Stereoview of the interactions between the Fe-S cluster-binding domain and the DNA-binding domain of the other subunit. The other subunit is shown in white.

Figure 3.
Activated conformation of target promoter of SoxR. (A) Side and top views of the overall structure of the soxS promoter with the global DNA helical axis (cyan line) (46). (B) Comparison of the 20-bp promoter structures of SoxR (blue) and MtaN (red). Two promoter structures are superimposed on each half-site of DNA. (C) The electron density of simulated annealing omit map (20- to 2.8-Å resolution) around the middle of the promoter is shown at 1.5σ. Thy1′ and Ade1 are indicated.

Figures were selected by an automated process.