2V57

Crystal structure of the TetR-like transcriptional regulator LfrR from Mycobacterium smegmatis in complex with proflavine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Plasticity and Distinct Drug-Binding Modes of Lfrr, a Mycobacterial Efflux Pump Regulator.

Bellinzoni, M.Buroni, S.Schaeffer, F.Riccardi, G.De Rossi, E.Alzari, P.M.

(2009) J.Bacteriol. 191: 7531

  • DOI: 10.1128/JB.00631-09
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The TetR-like transcriptional repressor LfrR controls the expression of the gene encoding the Mycobacterium smegmatis efflux pump LfrA, which actively extrudes fluoroquinolones, cationic dyes, and anthracyclines from the cell and promotes intrinsic a ...

    The TetR-like transcriptional repressor LfrR controls the expression of the gene encoding the Mycobacterium smegmatis efflux pump LfrA, which actively extrudes fluoroquinolones, cationic dyes, and anthracyclines from the cell and promotes intrinsic antibiotic resistance. The crystal structure of the apoprotein form of the repressor reveals a structurally asymmetric homodimer exhibiting local unfolding and a blocked drug-binding site, emphasizing the significant conformational plasticity of the protein necessary for DNA and multidrug recognition. Crystallographic and calorimetric studies of LfrR-drug complexes further confirm the intrinsic flexibility of the homodimer, which provides a dynamic mechanism to broaden multidrug binding specificity and may be a general property of transcriptional repressors regulating microbial efflux pump expression.


    Organizational Affiliation

    Institut Pasteur, Unité de Biochimie Structurale and CNRS URA 2185, Institut Pasteur, 75724 Paris Cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
A, B, C, D
190Mycobacterium smegmatisMutation(s): 0 
Gene Names: lfrR
Find proteins for Q58L87 (Mycobacterium smegmatis)
Go to UniProtKB:  Q58L87
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PRL
Query on PRL

Download SDF File 
Download CCD File 
A, C
PROFLAVIN
C13 H11 N3
WDVSHHCDHLJJJR-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, C
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PRLKd: 4300 nM BINDINGMOAD
PRLKd: 79 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.300α = 63.88
b = 62.440β = 88.34
c = 70.640γ = 88.13
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance