3F8F

Crystal structure of multidrug binding transcriptional regulator LmrR complexed with Daunomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.

Madoori, P.K.Agustiandari, H.Driessen, A.J.Thunnissen, A.M.

(2009) EMBO J 28: 156-166

  • DOI: https://doi.org/10.1038/emboj.2008.263
  • Primary Citation of Related Structures:  
    3F8B, 3F8C, 3F8F

  • PubMed Abstract: 

    LmrR is a PadR-related transcriptional repressor that regulates the production of LmrCD, a major multidrug ABC transporter in Lactococcus lactis. Transcriptional regulation is presumed to follow a drug-sensitive induction mechanism involving the direct binding of transporter ligands to LmrR. Here, we present crystal structures of LmrR in an apo state and in two drug-bound states complexed with Hoechst 33342 and daunomycin. LmrR shows a common topology containing a typical beta-winged helix-turn-helix domain with an additional C-terminal helix involved in dimerization. Its dimeric organization is highly unusual with a flat-shaped hydrophobic pore at the dimer centre serving as a multidrug-binding site. The drugs bind in a similar manner with their aromatic rings sandwiched in between the indole groups of two dimer-related tryptophan residues. Multidrug recognition is facilitated by conformational plasticity and the absence of drug-specific hydrogen bonds. Combined analyses using site-directed mutagenesis, fluorescence-based drug binding and protein-DNA gel shift assays reveal an allosteric coupling between the multidrug- and DNA-binding sites of LmrR that most likely has a function in the induction mechanism.


  • Organizational Affiliation

    Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, PadR-like family
A, B
126Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: lmrR
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RI36 
Go to UniProtKB:  A2RI36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RI36
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DM1
Query on DM1

Download Ideal Coordinates CCD File 
C [auth A]DAUNOMYCIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DM1 PDBBind:  3F8F Kd: 236 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.45α = 90
b = 53.025β = 90
c = 147.116γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-04-09
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description