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Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.
Freda, Ida; Exertier, Cécile; Barile, Anna; Chaves-Sanjuan, Antonio; Vega, Mirella Vivoli; Isupov, Michail N; Harmer, Nicholas J; Gugole, Elena; Swuec, Paolo; Bolognesi, Martino; Scipioni, Anita; Savino, Carmelinda; Di Salvo, Martino Luigi; Contestabile, Roberto; Vallone, Beatrice; Tramonti, Angela; Montemiglio, Linda Celeste.
Affiliation
  • Freda I; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.
  • Exertier C; Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy.
  • Barile A; Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy.
  • Chaves-Sanjuan A; Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy.
  • Vega MV; School of Biochemistry, University of Bristol, University Walk, BS8 1TD Bristol, UK.
  • Isupov MN; Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
  • Harmer NJ; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
  • Gugole E; Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy.
  • Swuec P; Cryo-Electron Microscopy Core Facility, Human Technopole, Milano 20157, Italy.
  • Bolognesi M; Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy.
  • Scipioni A; Department of Chemistry, Sapienza, University of Rome, Rome 00185, Italy.
  • Savino C; Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy.
  • Di Salvo ML; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.
  • Contestabile R; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.
  • Vallone B; Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome 00185, Italy.
  • Tramonti A; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.
  • Montemiglio LC; Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy.
Nucleic Acids Res ; 51(15): 8237-8254, 2023 08 25.
Article in En | MEDLINE | ID: mdl-37378428
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(s)

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacterial Proteins / Transcription Factors Language: En Journal: Nucleic Acids Res Year: 2023 Document type: Article Affiliation country:

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacterial Proteins / Transcription Factors Language: En Journal: Nucleic Acids Res Year: 2023 Document type: Article Affiliation country:
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