PDBsum entry 2h6c

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protein Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
208 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Crystal structure of reduced cprk in absence of any ligand
Structure: Chlorophenol reduction gene k. Chain: a, b. Synonym: cprk. Engineered: yes
Source: Desulfitobacterium dehalogenans. Organism_taxid: 36854. Gene: cprk. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.90Å     R-factor:   0.235     R-free:   0.307
Authors: C.Levy,D.Leys
Key ref:
M.G.Joyce et al. (2006). CprK crystal structures reveal mechanism for transcriptional control of halorespiration. J Biol Chem, 281, 28318-28325. PubMed id: 16803881 DOI: 10.1074/jbc.M602654200
31-May-06     Release date:   04-Jul-06    
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Protein chains
Pfam   ArchSchema ?
Q9LAS2  (Q9LAS2_9FIRM) -  Putative transcription regulator
232 a.a.
208 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     1 term  


DOI no: 10.1074/jbc.M602654200 J Biol Chem 281:28318-28325 (2006)
PubMed id: 16803881  
CprK crystal structures reveal mechanism for transcriptional control of halorespiration.
M.G.Joyce, C.Levy, K.Gábor, S.M.Pop, B.D.Biehl, T.I.Doukov, J.M.Ryter, H.Mazon, H.Smidt, R.H.van den Heuvel, S.W.Ragsdale, J.van der Oost, D.Leys.
Halorespiration is a bacterial respiratory process in which haloorganic compounds act as terminal electron acceptors. This process is controlled at transcriptional level by CprK, a member of the ubiquitous CRP-FNR family. Here we present the crystal structures of oxidized CprK in presence of the ligand ortho-chlorophenolacetic acid and of reduced CprK in absence of this ligand. These structures reveal that highly specific binding of chlorinated, rather than the corresponding non-chlorinated, phenolic compounds in the NH(2)-terminal beta-barrels causes reorientation of these domains with respect to the central alpha-helix at the dimer interface. Unexpectedly, the COOH-terminal DNA-binding domains dimerize in the non-DNA binding state. We postulate the ligand-induced conformational change allows formation of interdomain contacts that disrupt the DNA domain dimer interface and leads to repositioning of the helix-turn-helix motifs. These structures provide a structural framework for further studies on transcriptional control by CRP-FNR homologs in general and of halorespiration regulation by CprK in particular.
  Selected figure(s)  
Figure 4.
FIGURE 4. Overlay of the NH[2]-terminal domains of both CprK structures. An overlay is shown that was created by superimposition of the B and C -helices of both ligand-free CprK and the CHPA-bound CprK structures with central helices colored blue for both structures, while the NH[2]-terminal -barrel (residues 20-108 for both structures) is colored green for the CHPA-CprK complex and orange for the ligand free CprK. Bound CHPA molecules in the CHPA-CprK structure are represented in atom-colored spheres. To illustrate the motion of the NH[2]-terminal -barrel with respect to the putative position of the HTH motifs in the DNA binding state (by analogy to CRP), the putative HTH motifs are represented in gray.
Figure 7.
FIGURE 7. Binding of ortho-chlorophenolic compounds causes structural rearrangement. A, overlay of a single CHPA-binding site of the ligand-free CprK (color coding same as described for Fig. 1) with a hybrid CprK structure (in gray; see "Results and Discussion"). This clearly illustrates the induced fit in both the NH[2]-terminal -barrel and the C helix residues upon binding of CHPA. B, similar view to A, but only the hybrid structure is displayed, colored-coded as described for Fig. 1. The hydrophobic pocket created by the C helix residues is depicted as a transparent surface. H-bonds between CHPA and CprK are depicted in dashed lines. No direct interaction can be made between CHPA and Lys-133, while the CHPA chloride atom is not ideally placed in the binding pocket. C, similar view to B but for the CHPA-CprK crystal structure. The reorientation of the -barrel has allowed for an additional interaction between CHPA and Lys-133 while positioning the CHPA chloride atom in the center of the hydrophobic cavity.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 28318-28325) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265791 G.Giardina, N.Castiglione, M.Caruso, F.Cutruzzolà, and S.Rinaldo (2011).
The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms.
  Biochem Soc Trans, 39, 294-298.  
20626317 H.Antelmann, and J.D.Helmann (2011).
Thiol-based redox switches and gene regulation.
  Antioxid Redox Signal, 14, 1049-1063.  
20177947 N.Nagahara (2011).
Intermolecular disulfide bond to modulate protein function as a redox-sensing switch.
  Amino Acids, 41, 59-72.  
19193643 D.T.Gallagher, N.Smith, S.K.Kim, H.Robinson, and P.T.Reddy (2009).
Profound asymmetry in the structure of the cAMP-free cAMP Receptor Protein (CRP) from Mycobacterium tuberculosis.
  J Biol Chem, 284, 8228-8232.  
18717788 C.Levy, K.Pike, D.J.Heyes, M.G.Joyce, K.Gabor, H.Smidt, J.van der Oost, and D.Leys (2008).
Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator.
  Mol Microbiol, 70, 151-167.
PDB codes: 3e5q 3e5u 3e5x 3e6b 3e6c 3e6d
18424517 J.Esbelin, Y.Jouanneau, J.Armengaud, and C.Duport (2008).
ApoFnr binds as a monomer to promoters regulating the expression of enterotoxin genes of Bacillus cereus.
  J Bacteriol, 190, 4242-4251.  
19047736 K.Gábor, K.Hailesellasse Sene, H.Smidt, Vos, and J.van der Oost (2008).
Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression.
  Microbiology, 154, 3686-3696.  
18076763 N.Kannan, J.Wu, G.S.Anand, S.Yooseph, A.F.Neuwald, C.J.Venter, and S.S.Taylor (2007).
Evolution of allostery in the cyclic nucleotide binding module.
  Genome Biol, 8, R264.  
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 codes are shown on the right.