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: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.3 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: https://doi.org/10.1371/journal.pone.0157691
  • Primary Citation of Related Structures:  
    4ZS8, 4ZSB, 4ZSI, 4ZSK

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional repressor DasR
A, B
171Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: dasRSCO5231SC7E4.28c
UniProt
Find proteins for Q9K492 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9K492 
Go to UniProtKB:  Q9K492
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K492
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.267α = 90
b = 54.267β = 90
c = 220.913γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary