PDBsum entry 2zhg

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protein dna_rna ligands links
Transcription/DNA PDB id
Protein chain
121 a.a. *
Waters ×22
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Crystal structure of soxr in complex with DNA
Structure: Redox-sensitive transcriptional activator soxr. Chain: a. Engineered: yes. DNA (5'- d( Dgp Dcp Dcp Dtp Dcp Dap Dap Dgp Dtp Dtp Dap Dap Dcp Dtp P Dgp Dgp Dc)-3'). Chain: b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: soxr. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
2.80Å     R-factor:   0.243     R-free:   0.281
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
05-Feb-08     Release date:   25-Mar-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0ACS2  (SOXR_ECOLI) -  Redox-sensitive transcriptional activator SoxR
154 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to oxidative stress   3 terms 
  Biochemical function     DNA binding     4 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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21292540 A.S.Fleischhacker, and P.J.Kiley (2011).
Iron-containing transcription factors and their roles as sensors.
  Curr Opin Chem Biol, 15, 335-341.  
21226770 M.Gu, and J.A.Imlay (2011).
The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide.
  Mol Microbiol, 79, 1136-1150.  
21153861 S.K.Checa, and F.C.Soncini (2011).
Bacterial gold sensing and resistance.
  Biometals, 24, 419-427.  
20047321 J.C.Genereux, A.K.Boal, and J.K.Barton (2010).
DNA-mediated charge transport in redox sensing and signaling.
  J Am Chem Soc, 132, 891-905.  
20214403 J.C.Genereux, and J.K.Barton (2010).
Mechanisms for DNA charge transport.
  Chem Rev, 110, 1642-1662.  
20807206 M.E.Pérez Audero, B.M.Podoroska, M.M.Ibáñez, A.Cauerhff, S.K.Checa, and F.C.Soncini (2010).
Target transcription binding sites differentiate two groups of MerR-monovalent metal ion sensors.
  Mol Microbiol, 78, 853-865.  
20230832 M.Kumaraswami, K.J.Newberry, and R.G.Brennan (2010).
Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR.
  J Mol Biol, 398, 264-275.
PDB code: 3iao
19822742 A.I.Arunkumar, G.C.Campanello, and D.P.Giedroc (2009).
Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state.
  Proc Natl Acad Sci U S A, 106, 18177-18182.
PDB codes: 2kjb 2kjc
19508286 D.P.Giedroc (2009).
Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator.
  Mol Microbiol, 73, 1-4.  
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
19651620 P.E.Lee, B.Demple, and J.K.Barton (2009).
DNA-mediated redox signaling for transcriptional activation of SoxR.
  Proc Natl Acad Sci U S A, 106, 13164-13168.  
19727950 Y.Dai, J.Liu, C.Zheng, A.Wu, J.Zeng, and G.Qiu (2009).
Cys92, Cys101, Cys197, and Cys203 are crucial residues for coordinating the iron-sulfur cluster of RhdA from Acidithiobacillus ferrooxidans.
  Curr Microbiol, 59, 559-564.  
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
18980370 A.A.Gorodetsky, M.C.Buzzeo, and J.K.Barton (2008).
DNA-mediated electrochemistry.
  Bioconjug Chem, 19, 2285-2296.  
18449575 F.C.Lo, C.L.Chen, C.M.Lee, M.C.Tsai, T.T.Lu, W.F.Liaw, and S.S.Yu (2008).
A study of NO trafficking from dinitrosyl-iron complexes to the recombinant E. coli transcriptional factor SoxR.
  J Biol Inorg Chem, 13, 961-972.  
18658145 K.J.Newberry, J.L.Huffman, M.C.Miller, N.Vazquez-Laslop, A.A.Neyfakh, and R.G.Brennan (2008).
Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.
  J Biol Chem, 283, 26795-26804.
PDB codes: 3d6y 3d6z 3d70 3d71
18485078 R.P.Bonocora, G.Caignan, C.Woodrell, M.H.Werner, and D.M.Hinton (2008).
A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription.
  Mol Microbiol, 69, 331-343.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.