1UTB

DntR from Burkholderia sp. strain DNT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Development of a Bacterial Biosensor for Nitrotoluenes: The Crystal Structure of the Transcriptional Regulator Dntr

Smirnova, I.A., Dian, C., Leonard, G.A., Mcsweeney, S., Birse, D., Brzezinski, P.

(2004) J.Mol.Biol. 340: 405

  • DOI: 10.1016/j.jmb.2004.04.071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise the sensitivity o ...

    The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise the sensitivity of the biosensor for such compounds we have chosen a rational design of the inducer-binding cavity based on knowledge of the three-dimensional structure of DntR. We report two crystal structures of DntR with acetate (resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms), respectively, occupying the inducer-binding cavity. These structures allow for the construction of models of DntR in complex with salicylate (Kd approximately or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR with enhanced specificity for dinitrotoluenes. In both crystal structures DntR crystallises as a homodimer with a "head-to-tail" arrangement of monomers in the asymmetric unit. Analysis of the crystal structure has allowed the building of a full-length model of DntR in its biologically active homotetrameric form consisting of two "head-to-head" dimers. The implications of this model for the mechanism of transcription regulation by LysR proteins are discussed.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSR-TYPE REGULATORY PROTEIN
A
315Burkholderia sp. DNTMutation(s): 1 
Gene Names: dntR
Find proteins for Q7WT50 (Burkholderia sp. DNT)
Go to UniProtKB:  Q7WT50
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYSR-TYPE REGULATORY PROTEIN
B
315Burkholderia sp. DNTMutation(s): 1 
Gene Names: dntR
Find proteins for Q7WT50 (Burkholderia sp. DNT)
Go to UniProtKB:  Q7WT50
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.148α = 90.00
b = 107.148β = 90.00
c = 296.654γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance