title: Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors.
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.
authors.affiliation: Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany.
authors.forename: Simon B
authors.initials: SB
authors.lastname: Fillenberg
authors.affiliation: Computational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstr. 5, D-91058 Erlangen, Germany.
authors.forename: Mario D
authors.initials: MD
authors.lastname: Friess
authors.affiliation: Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany.
authors.forename: Samuel
authors.initials: S
authors.lastname: Körner
authors.affiliation: Computational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstr. 5, D-91058 Erlangen, Germany.
authors.forename: Rainer A
authors.initials: RA
authors.lastname: Böckmann
authors.affiliation: Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany.
authors.forename: Yves A
authors.initials: YA
authors.lastname: Muller
mesh_terms: D000494:Allosteric Regulation; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020539:Sequence Analysis, Protein; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D008024:Ligands; D011994:Recombinant Proteins; D012097:Repressor Proteins