3DKW

Crystal Structure of DNR from Pseudomonas aeruginosa.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.326 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.

Giardina, G.Rinaldo, S.Castiglione, N.Caruso, M.Cutruzzola, F.

(2009) Proteins --: --

  • DOI: 10.1002/prot.22428

  • PubMed 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, ...

    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.


    Organizational Affiliation

    Department of Biochemical Sciences A. Rossi Fanelli, University of Rome La Sapienza, 00185 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNR protein
A, B, C, D, E, F, G, H, I, J
227Pseudomonas aeruginosaMutation(s): 0 
Gene Names: dnr
Find proteins for Q51441 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q51441
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.326 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 245.282α = 90.00
b = 121.466β = 97.53
c = 82.554γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-06-26 
  • Released Date: 2009-05-19 
  • Deposition Author(s): Giardina, G.

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance