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PDBsum entry 3dkw

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protein Protein-protein interface(s) links
Transcription regulator PDB id
3dkw
Jmol
Contents
Protein chains
(+ 4 more) 227 a.a. *
* Residue conservation analysis
PDB id:
3dkw
Name: Transcription regulator
Title: Crystal structure of dnr from pseudomonas aeruginosa.
Structure: Dnr protein. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: transcriptional regulator dnr. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pao1. Gene: dnr, pa0527. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.60Å     R-factor:   0.328     R-free:   0.374
Authors: G.Giardina
Key ref:
G.Giardina et al. (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. PubMed id: 19415759 DOI: 10.1002/prot.22428
Date:
26-Jun-08     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q51441  (Q51441_PSEAI) -  Cyclic nucleotide-binding domain protein
Seq:
Struc:
227 a.a.
227 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     response to nitric oxide   5 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1002/prot.22428 Proteins 77:174-180 (2009)
PubMed id: 19415759  
 
 
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
G.Giardina, S.Rinaldo, N.Castiglione, M.Caruso, F.Cutruzzolà.
 
  ABSTRACT  
 
The opportunistic pathogen Pseudomonas aeruginosa can grow in low oxygen, because it is capable of anaerobic respiration using nitrate as a terminal electron acceptor (denitrification). An intermediate of the denitrification pathway is nitric oxide, a compound that may become cytotoxic at high concentration. The intracellular levels of nitric oxide are tightly controlled by regulating the expression of the enzymes responsible for its synthesis and degradation (nitrite and nitric oxide reductases). In this article, we present the crystallographic structure of the wild-type dissimilative nitrate respiration regulator (DNR), a master regulator controlling expression of the denitrification machinery and a putative target for new therapeutic strategies. Comparison with other structures among the CRP-FNR class of regulators reveals that DNR has crystallized in a conformation that has never been observed before. In particular, the sensing domain of DNR has undergone a rotation of more than 50 degrees with respect to the other structures. This suggests that DNR may undergo an unexpected and very large conformational rearrangement on activation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of wtDNR from P. aeruginosa. (A) 3D structure of wtDNR dimer, side and top views. The monomer domains are highlighted with different colors: green the sensing domain; blue the dimerization helix; salmon the DNA binding domain (the recognition helix -G is shown in red). The structural features hinge and flap are highlighted by red circles. The same color code is used throughout the figure. (B) Sequence and corresponding secondary structure of wtDNR. (C) 3D structure of CRP from E. coli in complex with DNA[27] (pdb id:1run).
Figure 2.
Figure 2. wtDNR peculiar fully OFF conformation. (A) Different positions of the sensing domains (surface representation) of wtDNR (blue), C-DNR[15] (red;pdb id 2z69), and CRP[27] (yellow; pdb id:1run) showing the angles of rotation around an axis perpendicular to the direction of the superposed dimerization helices. The DNA binding domains have been removed for clarity. (B) Superposition of the dimerization helices of wtDNR (in blue) and CRP[27] (in yellow; pdb id:1run) monomers showing the different positions of the DNA binding domains and sensing domains in the active ON conformation (CRP) and in the inactive fully OFF conformation (wtDNR). (C) Superposition of the dimerization helices of wtDNR (in blue) and CooA OFF[28] and ON[33] conformations (in magenta and salmon, respectively, pdb id: 1ft9 and 2hkx) showing different positions of the DNA binding domains and sensing domains. (D) Superposition of the dimerization helices of wtDNR (in blue) and CprK OFF[30] and ON[30] conformations (in light and dark grey, respectively, pdb id: 3e6d and 3e6c) showing the different positions of the DNA binding domains and sensing domains.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 77, 174-180) copyright 2009.  

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.  
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.  
21265792 M.Kern, C.Winkler, and J.Simon (2011).
Respiratory nitrogen metabolism and nitrosative stress defence in ϵ-proteobacteria: the role of NssR-type transcription regulators.
  Biochem Soc Trans, 39, 299-302.  
20553552 K.Trunk, B.Benkert, N.Quäck, R.Münch, M.Scheer, J.Garbe, L.Jänsch, M.Trost, J.Wehland, J.Buer, M.Jahn, M.Schobert, and D.Jahn (2010).
Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons.
  Environ Microbiol, 12, 1719-1733.  
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.  
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