PDBsum entry 2z69

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protein Protein-protein interface(s) links
Transcription regulator PDB id
Jmol PyMol
Protein chains
148 a.a. *
138 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
Name: Transcription regulator
Title: Crystal structure of the sensor domain of the transcriptiona regulator dnr from pseudomonas aeruginosa
Structure: Dnr protein. Chain: a, b, c. Fragment: sensor domain. Synonym: transcriptional regulator dnr, dnr dissimilative n respiration regulator. Engineered: yes
Source: Pseudomonas aeruginosa. Strain: pao1. Gene: dnr. Expressed in: escherichia coli.
2.10Å     R-factor:   0.217     R-free:   0.262
Authors: G.Giardina,K.A.Johnson,A.Di Matteo
Key ref:
G.Giardina et al. (2008). NO sensing in Pseudomonas aeruginosa: structure of the transcriptional regulator DNR. J Mol Biol, 378, 1002-1015. PubMed id: 18420222 DOI: 10.1016/j.jmb.2008.03.013
24-Jul-07     Release date:   18-Mar-08    
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Protein chains
Pfam   ArchSchema ?
Q51441  (Q51441_PSEAI) -  Cyclic nucleotide-binding domain protein
227 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
Q51441  (Q51441_PSEAI) -  Cyclic nucleotide-binding domain protein
227 a.a.
138 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/j.jmb.2008.03.013 J Mol Biol 378:1002-1015 (2008)
PubMed id: 18420222  
NO sensing in Pseudomonas aeruginosa: structure of the transcriptional regulator DNR.
G.Giardina, S.Rinaldo, K.A.Johnson, A.Di Matteo, M.Brunori, F.Cutruzzolà.
All denitrifying bacteria can keep the steady-state concentrations of nitrite and nitric oxide (NO) below cytotoxic levels, controlling the expression of the denitrification gene clusters by redox signaling, mainly through transcriptional regulators belonging either to the DNR (dissimilative nitrate respiration regulator) or to the NnrR (nitrite and nitric oxide reductase regulator) subgroups of the FNR (fumarate and nitrate reductase regulatory protein)-CRP (cAMP receptor protein) superfamily. The NO dependence of the transcriptional activity of promoters regulated by these transcription factors has suggested that they may act as NO sensors in vivo. Despite great interest in the regulation of denitrification, which in Pseudomonas aeruginosa is strictly related to virulence, functional and structural characterization of these NO sensors is still lacking. Here we present the three-dimensional structure of the sensor domain of the DNR from P. aeruginosa at 2.1 A resolution. This is the first structure of a putative NO-sensing bacterial transcriptional regulator and reveals the presence of a large hydrophobic cavity that may be the cofactor binding site. Parallel spectroscopic evidence indicates that apo-DNR binds heme in vitro and that the heme-bound form reacts with carbon monoxide and NO, thus supporting the hypothesis that NO sensing involves gas binding to the ferrous heme. Preliminary experiments indicate that heterologous expression of the heme-containing DNR yields a protein able to bind DNA in vitro.
  Selected figure(s)  
Figure 3.
Fig. 3. Conformation of the hook and conserved residues. (a) Surface representation of ΔC-DNR dimer, with subunits A and B shown in blue and orange, respectively. The blowup is a view of a 2F[o] − F[c] electron density map (contoured at 1.0σ) of the hook environment. The same color code as in panel (a) is applied to distinguish the two polypeptide chains. Side chains of Leu148, Leu150, His14 and His15 are labelled. (b) On the left is shown the position in the structure of 15 of the 26 conserved residues among the DNR subgroup that cluster around the cavity. The side chains of His15 and His14 are shown in yellow. On the right is shown the sequence alignment of ΔC-DNR with the other proteins of the DNR subgroup (DNRD, DNRE and DNRS from P. stutzeri and DNR regulators from R. sphaeroides and M. sphaeroides).
Figure 6.
Fig. 6. Spectroscopic properties and reactivity of holo-DNR with NO. (a) Spectra of a 3 μM holo-DNR solution (pH 7.5, 20 °C): ferrous derivative (dotted line) and ferrous NO-bound form (continuous line). The ferrous derivative has been recorded in the presence of 1 mM dithionite under anaerobic conditions. (b) Time course of the reaction between reduced holo-DNR and NO (pH 7.5, 20 °C). The absorbance changes at 427 nm in the presence of different concentrations of NO (88 μM, square; 175 μM, triangles; 263 μM, cross; 350 μM, open circle) are shown. The NO binding rate constant was determined by fitting the time course with a two-exponential equation; the fit obtained for the highest NO concentration is reported as a continuous line. (c) Dissociation of NO from the ferrous holo-DNR measured in the presence of dithionite and CO. The dissociation rate was measured after addition to 6.5 μM ferrous NO-bound holo-DNR (obtained anaerobically in the presence of 1 mM dithionite and 120 μM NO) of 500 μM CO and 1.5 mM dithionite; spectra were collected for vert, similar 3 h. The arrow indicates the formation of the CO-bound derivative starting from the NO-bound one. The experiment was carried out at pH 7.5 and at room temperature. The time course at 421 nm (inset) corresponds to a single exponential process, yielding an NO dissociation rate constant of 2 × 10^− 4 s^− 1.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 378, 1002-1015) copyright 2008.  
  Figures were selected by the author.  

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.  
21339081 J.A.Mayfield, C.A.Dehner, and J.L.DuBois (2011).
Recent advances in bacterial heme protein biochemistry.
  Curr Opin Chem Biol, 15, 260-266.  
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.  
19966004 A.Hartsock, and J.P.Shapleigh (2010).
Identification, functional studies, and genomic comparisons of new members of the NnrR regulon in Rhodobacter sphaeroides.
  J Bacteriol, 192, 903-911.  
20595263 A.Hartsock, and J.P.Shapleigh (2010).
Mechanisms of oxygen inhibition of nirK expression in Rhodobacter sphaeroides.
  Microbiology, 156, 3158-3165.  
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.  
20353301 M.Schobert, and P.Tielen (2010).
Contribution of oxygen-limiting conditions to persistent infection of Pseudomonas aeruginosa.
  Future Microbiol, 5, 603-621.  
20167493 N.P.Tucker, N.E.Le Brun, R.Dixon, and M.I.Hutchings (2010).
There's NO stopping NsrR, a global regulator of the bacterial NO stress response.
  Trends Microbiol, 18, 149-156.  
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
19801410 N.Barraud, D.Schleheck, J.Klebensberger, J.S.Webb, D.J.Hassett, S.A.Rice, and S.Kjelleberg (2009).
Nitric oxide signaling in Pseudomonas aeruginosa biofilms mediates phosphodiesterase activity, decreased cyclic di-GMP levels, and enhanced dispersal.
  J Bacteriol, 191, 7333-7342.  
19477902 N.Castiglione, S.Rinaldo, G.Giardina, and F.Cutruzzolà (2009).
The transcription factor DNR from Pseudomonas aeruginosa specifically requires nitric oxide and haem for the activation of a target promoter in Escherichia coli.
  Microbiology, 155, 2838-2844.  
19651860 N.E.Van Alst, M.Wellington, V.L.Clark, C.G.Haidaris, and B.H.Iglewski (2009).
Nitrite reductase NirS is required for type III secretion system expression and virulence in the human monocyte cell line THP-1 by Pseudomonas aeruginosa.
  Infect Immun, 77, 4446-4454.  
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
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.