4ZSI

Crystal structure of the effector-binding domain of DasR (DasR-EBD) in complex with glucosamine-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.652 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors.

Fillenberg, S.B.Friess, M.D.Korner, S.Bockmann, R.A.Muller, Y.A.

(2016) Plos One 11: e0157691-e0157691

  • DOI: 10.1371/journal.pone.0157691
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small molecule effectors regulate gene transcription in bacteria by altering the DNA-binding affinities of specific repressor proteins. Although the GntR proteins represent a large family of bacterial repressors, only little is known about the allost ...

    Small molecule effectors regulate gene transcription in bacteria by altering the DNA-binding affinities of specific repressor proteins. Although the GntR proteins represent a large family of bacterial repressors, only little is known about the allosteric mechanism that enables their function. DasR from Streptomyces coelicolor belongs to the GntR/HutC subfamily and specifically recognises operators termed DasR-responsive elements (dre-sites). Its DNA-binding properties are modulated by phosphorylated sugars. Here, we present several crystal structures of DasR, namely of dimeric full-length DasR in the absence of any effector and of only the effector-binding domain (EBD) of DasR without effector or in complex with glucosamine-6-phosphate (GlcN-6-P) and N-acetylglucosamine-6-phosphate (GlcNAc-6-P). Together with molecular dynamics (MD) simulations and a comparison with other GntR/HutC family members these data allowed for a structural characterisation of the different functional states of DasR. Allostery in DasR and possibly in many other GntR/HutC family members is best described by a conformational selection model. In ligand-free DasR, an increased flexibility in the EBDs enables the attached DNA-binding domains (DBD) to sample a variety of different orientations and among these also a DNA-binding competent conformation. Effector binding to the EBDs of DasR significantly reorganises the atomic structure of the latter. However, rather than locking the orientation of the DBDs, the effector-induced formation of β-strand β* in the DBD-EBD-linker segment merely appears to take the DBDs 'on a shorter leash' thereby impeding the 'downwards' positioning of the DBDs that is necessary for a concerted binding of two DBDs of DasR to operator DNA.


    Organizational Affiliation

    Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional repressor DasR
A, B
171Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Gene Names: dasR
Find proteins for Q9K492 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9K492
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
4R1
Query on 4R1

Download SDF File 
Download CCD File 
B
beta-glucosamine-6-phosphate
C6 H14 N O8 P
XHMJOUIAFHJHBW-QZABAPFNSA-N
 Ligand Interaction
GLP
Query on GLP

Download SDF File 
Download CCD File 
A
GLUCOSAMINE 6-PHOSPHATE
C6 H14 N O8 P
XHMJOUIAFHJHBW-UKFBFLRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.652 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.267α = 90.00
b = 54.267β = 90.00
c = 220.913γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermany--

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references