2Y7P

DntR Inducer Binding Domain in Complex with Salicylate. Trigonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structures of Dntr Inducer Binding Domains in Complex with Salicylate Offer Insights Into the Activation of Lysr-Type Transcriptional Regulators.

Devesse, L.Smirnova, I.Lonneborg, R.Kapp, U.Brzezinski, P.Leonard, G.A.Dian, C.

(2011) Mol Microbiol 81: 354

  • DOI: 10.1111/j.1365-2958.2011.07673.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Activation of LysR-type transcription factors (LTTRs) is thought to result from conformational changes that occur when inducer molecules bind to their Inducer Binding Domains (IBDs). However, the exact nature of these changes remains to be fully eluc ...

    Activation of LysR-type transcription factors (LTTRs) is thought to result from conformational changes that occur when inducer molecules bind to their Inducer Binding Domains (IBDs). However, the exact nature of these changes remains to be fully elucidated. We present the crystal structures of two truncated constructs of the LTTR DntR in their apo- forms and in complex with its natural inducer molecule, salicylate. These provide a fuller picture of the conformational changes that can occur in LTTR IBDs and offer insights that may be relevant when considering the mechanism of activation of LTTRs. Two of the crystal structures show that DntR IBDs can bind up to two inducer molecules. The full extent of conformational changes observed is achieved only when inducer molecules are bound in both binding sites identified. Point mutations disrupting the putative secondary binding site produce DntR variants with a reduced response to salicylate in a whole cell system, suggesting that this site is functionally relevant.


    Organizational Affiliation

    Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSR-TYPE REGULATORY PROTEINA218Burkholderia sp. DNTMutation(s): 1 
Gene Names: dntR
Find proteins for Q7WT50 (Burkholderia sp. DNT)
Explore Q7WT50 
Go to UniProtKB:  Q7WT50
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEU
Query on PEU

Download CCD File 
A
2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
 Ligand Interaction
SAL
Query on SAL

Download CCD File 
A
2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SALKd :  3400   nM  PDBBind
SALKd:  11800   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.698α = 90
b = 95.698β = 90
c = 67.404γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release