7B5W

RCK_C domain of S.agalactiae BusR in ligand-free state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture.

Bandera, A.M.Bartho, J.Lammens, K.Drexler, D.J.Kleinschwarzer, J.Hopfner, K.P.Witte, G.

(2021) Nucleic Acids Res 49: 10166-10177

  • DOI: https://doi.org/10.1093/nar/gkab736
  • Primary Citation of Related Structures:  
    7B5T, 7B5U, 7B5W, 7B5Y, 7OZ3

  • PubMed Abstract: 

    The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.


  • Organizational Affiliation

    Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GntR family transcriptional regulator98Streptococcus agalactiaeMutation(s): 0 
Gene Names: BM110_ORF1201DX05_06300F5F86_05185NCTC6175_01043
UniProt
Find proteins for I7JWA3 (Streptococcus agalactiae)
Explore I7JWA3 
Go to UniProtKB:  I7JWA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7JWA3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.26α = 90
b = 40.41β = 103.21
c = 41.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3717/3-1
German Research Foundation (DFG)GermanyGRK1721

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2021-10-13
    Changes: Data collection
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description