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Structure paper

TitleStructural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 15, Page 8237-8254, Year 2023
Publish dateAug 25, 2023
AuthorsIda Freda / Cécile Exertier / Anna Barile / Antonio Chaves-Sanjuan / Mirella Vivoli Vega / Michail N Isupov / Nicholas J Harmer / Elena Gugole / Paolo Swuec / Martino Bolognesi / Anita Scipioni / Carmelinda Savino / Martino Luigi Di Salvo / Roberto Contestabile / Beatrice Vallone / Angela Tramonti / Linda Celeste Montemiglio /
PubMed AbstractSpecificity 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 ...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.
External linksNucleic Acids Res / PubMed:37378428 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.8 - 4.0 Å
Structure data

14778

7zla

EMDB-14778, PDB-7zla:
Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the half-closed conformation
Method: EM (single particle) / Resolution: 3.99 Å

14801

7zn5

EMDB-14801: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C2 symmetry
PDB-7zn5: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C2 symmetry.
Method: EM (single particle) / Resolution: 3.7 Å

14852

7zpa

EMDB-14852, PDB-7zpa:
Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C1 symmetry
Method: EM (single particle) / Resolution: 3.9 Å

14960

7zth

EMDB-14960, PDB-7zth:
Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the open conformation
Method: EM (single particle) / Resolution: 4.0 Å

PDB-7pq9:
Crystal structure of Bacillus clausii pdxR at 2.8 Angstroms resolution
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-HOH:
WATER / Water

Source
  • alkalihalobacillus clausii (bacteria)
KeywordsDNA BINDING PROTEIN / Bacillus clausii; MocR; PdxR; pyridoxal 5'-phosphate biosynthesis; transcriptional regulation; apo / transcription factor / PLP-binding protein / domain-swap homodimer

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