Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR

DOI: 10.1093/nar/gkad552

Authors: Ida Freda (Sapienza University of Rome) , Cécile Exertier (National Research Council (Italy)) , Anna Barile (National Research Council (Italy)) , Antonio Chaves-Sanjuan (University of Milano) , Mirella Vivoli Vega (University of Bristol) , Misha N. Isupov (University of Exeter) , Nicholas J. Harmer (University of Exeter) , Elena Gugole (National Research Council (Italy)) , Paolo Swuec (Human Technopole) , Martino Bolognesi (University of Milano) , Anita Scipioni (Sapienza University of Rome) , Carmelinda Savino (National Research Council (Italy)) , Martino luigi Di salvo (Sapienza University of Rome) , Roberto Contestabile (Sapienza University of Rome) , Beatrice Vallone (Sapienza University of Rome) , Angela Tramonti (National Research Council (Italy)) , Linda Celeste Montemiglio (National Research Council (Italy))
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nucleic Acids Research , VOL 33

State: Published (Approved)
Published: June 2023
Diamond Proposal Number(s): 11945

Abstract: Specificity in protein–DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5′-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR–DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR–DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.

Subject Areas: Biology and Bio-materials, Chemistry


Instruments: I03-Macromolecular Crystallography

Added On: 03/07/2023 08:54

Documents:
gkad552.pdf

Discipline Tags:

Biochemistry Chemistry Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)