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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
  • Primary Citation of Related Structures:  

  • 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 PROTEIN
A
218Burkholderia 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
SAL
Query on SAL

Download SDF File 
Download CCD File 
A
2-HYDROXYBENZOIC ACID
SALICYLIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
 Ligand Interaction
PEU
Query on PEU

Download SDF File 
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
PEG 8000
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SALKd: 11800 nM BINDINGMOAD
SALKd: 3400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.698α = 90.00
b = 95.698β = 90.00
c = 67.404γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SHELXEphasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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