3VW2

Crystal Strucuture of The Berberine-bound Form of RamR (Transcriptional Regurator of TetR Family) from Salmonella Typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of multidrug-resistance regulator RamR with multiple drugs

Yamasaki, S.Nikaido, E.Nakashima, R.Sakurai, K.Fujiwara, D.Fujii, I.Nishino, K.

(2013) Nat Commun 4: 2078-2078

  • DOI: https://doi.org/10.1038/ncomms3078
  • Primary Citation of Related Structures:  
    3VVX, 3VVY, 3VVZ, 3VW0, 3VW1, 3VW2

  • PubMed Abstract: 

    RamR is a transcriptional repressor of the gene-encoding RamA protein, which controls the expression of the multidrug efflux system genes acrAB-tolC. RamR is an important multidrug-resistance factor, however, its structure and the identity of the molecules to which it responds have been unknown. Here, we report the crystal structure of RamR in complex with multiple drugs, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6G. All compounds are found to interact with Phe155 of RamR, and each compound is surrounded by different amino acid residues. Binding of these compounds to RamR reduces its DNA-binding affinity, which results in the increased expression of ramA. Our results reveal significant flexibility in the substrate-recognition region of RamR, which regulates the bacterial efflux participating in multidrug resistance.


  • Organizational Affiliation

    Laboratory of Microbiology and Infectious Diseases, Division of Special Projects, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative regulatory protein
A, B, C, D
194Salmonella enterica subsp. enterica serovar Typhimurium str. 14028SMutation(s): 0 
Gene Names: STM0580STM14_0676
UniProt
Find proteins for A0A0F6AY66 (Salmonella typhimurium (strain 14028s / SGSC 2262))
Explore A0A0F6AY66 
Go to UniProtKB:  A0A0F6AY66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6AY66
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.817α = 104.97
b = 54.623β = 97.74
c = 92.291γ = 90.04
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations