7ZLA

Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the half-closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Freda, I.Exertier, C.Barile, A.Chaves-Sanjuan, A.Vega, M.V.Isupov, M.N.Harmer, N.J.Gugole, E.Swuec, P.Bolognesi, M.Scipioni, A.Savino, C.Di Salvo, M.L.Contestabile, R.Vallone, B.Tramonti, A.Montemiglio, L.C.

(2023) Nucleic Acids Res 51: 8237-8254

  • DOI: https://doi.org/10.1093/nar/gkad552
  • Primary Citation of Related Structures:  
    7PQ9, 7ZLA, 7ZN5, 7ZPA, 7ZTH

  • PubMed 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.


  • Organizational Affiliation

    Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza, University of Rome, Rome 00185, Italy.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLP-dependent aminotransferase family protein
A, B
478Shouchella clausiiMutation(s): 0 
Gene Names: CHH72_17460
UniProt
Find proteins for Q5WKW3 (Shouchella clausii (strain KSM-K16))
Explore Q5WKW3 
Go to UniProtKB:  Q5WKW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5WKW3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (48-MER)48Shouchella clausii
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (48-MER)48Shouchella clausii
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description