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

PLoS One. 2016 Jun 23;11(6):e0157691. doi: 10.1371/journal.pone.0157691. eCollection 2016.

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.

MeSH terms

  • Allosteric Regulation
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • DNA, Bacterial / metabolism
  • Gene Expression Regulation, Bacterial
  • Ligands
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Repressor Proteins / chemistry*
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Sequence Analysis, Protein
  • Streptomyces coelicolor / genetics*
  • Streptomyces coelicolor / metabolism

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Ligands
  • Recombinant Proteins
  • Repressor Proteins

Grants and funding

This work was supported by a grant from the Deutsche Forschungsgemeinschaft, DFG (grant Mu1477/6-3, http://www.dfg.de/). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.