PDBsum entry 3e6d

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protein Protein-protein interface(s) links
Transcription regulation PDB id
Protein chains
202 a.a. *
Waters ×181
* Residue conservation analysis
PDB id:
Name: Transcription regulation
Title: Crystal structure of cprk c200s
Structure: Cyclic nucleotide-binding protein. Chain: a, b. Synonym: cprk. Engineered: yes. Mutation: yes
Source: Desulfitobacterium hafniense. Organism_taxid: 272564. Strain: dcb-2. Gene: dhaf_0678. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.233     R-free:   0.280
Authors: C.Levy
Key ref: C.Levy et al. (2008). Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator. Mol Microbiol, 70, 151-167. PubMed id: 18717788
15-Aug-08     Release date:   30-Sep-08    
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Protein chains
Pfam   ArchSchema ?
B8FW11  (B8FW11_DESHD) -  Cyclic nucleotide-binding protein
232 a.a.
202 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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


Mol Microbiol 70:151-167 (2008)
PubMed id: 18717788  
Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator.
C.Levy, K.Pike, D.J.Heyes, M.G.Joyce, K.Gabor, H.Smidt, J.van der Oost, D.Leys.
Certain bacteria are able to conserve energy via the reductive dehalogenation of halo-organic compounds in a respiration-type metabolism. The transcriptional regulator CprK from Desulfitobacterium spp. induces expression of halorespiratory genes upon binding of o-chlorophenol ligands and is reversibly inactivated by oxygen through disulphide bond formation. We report crystal structures of D. hafniense CprK in the ligand-free (both oxidation states), ligand-bound (reduced) and DNA-bound states, making it the first member of the widespread CRP-FNR superfamily for which a complete structural description of both redox-dependent and allosteric molecular rearrangements is available. In conjunction with kinetic and thermodynamic ligand binding studies, we provide a model for the allosteric mechanisms underpinning transcriptional control. Amino acids that play a key role in this mechanism are not conserved in functionally distinct CRP-FNR members. This suggests that, despite significant structural homology, distinct allosteric mechanisms are used, enabling this protein family to control a very wide range of processes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626317 H.Antelmann, and J.D.Helmann (2011).
Thiol-based redox switches and gene regulation.
  Antioxid Redox Signal, 14, 1049-1063.  
20434786 F.Maphosa, Vos, and H.Smidt (2010).
Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria.
  Trends Biotechnol, 28, 308-316.  
21118026 J.R.Haas (2010).
The potential feasibility of chlorinic photosynthesis on exoplanets.
  Astrobiology, 10, 953-963.  
19415759 G.Giardina, S.Rinaldo, N.Castiglione, M.Caruso, and F.Cutruzzolà (2009).
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
  Proteins, 77, 174-180.
PDB code: 3dkw
19805344 H.Sharma, S.Yu, J.Kong, J.Wang, and T.A.Steitz (2009).
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
  Proc Natl Acad Sci U S A, 106, 16604-16609.
PDB codes: 3fwe 3hif
19103925 M.John, R.Rubick, R.P.Schmitz, J.Rakoczy, T.Schubert, and G.Diekert (2009).
Retentive memory of bacteria: Long-term regulation of dehalorespiration in Sulfurospirillum multivorans.
  J Bacteriol, 191, 1650-1655.  
19359484 N.Popovych, S.R.Tzeng, M.Tonelli, R.H.Ebright, and C.G.Kalodimos (2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
  Proc Natl Acad Sci U S A, 106, 6927-6932.
PDB code: 2wc2
19955406 S.Mesa, L.Reutimann, H.M.Fischer, and H.Hennecke (2009).
Posttranslational control of transcription factor FixK2, a key regulator for the Bradyrhizobium japonicum-soybean symbiosis.
  Proc Natl Acad Sci U S A, 106, 21860-21865.  
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.