1EXI

CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the transcription activator BmrR bound to DNA and a drug.

Heldwein, E.E.Brennan, R.G.

(2001) Nature 409: 378-382

  • DOI: 10.1038/35053138
  • Primary Citation of Related Structures:  1EXJ

  • PubMed Abstract: 
  • The efflux of chemically diverse drugs by multidrug transporters that span the membrane is one mechanism of multidrug resistance in bacteria. The concentrations of many of these transporters are controlled by transcription regulators, such as BmrR in ...

    The efflux of chemically diverse drugs by multidrug transporters that span the membrane is one mechanism of multidrug resistance in bacteria. The concentrations of many of these transporters are controlled by transcription regulators, such as BmrR in Bacillus subtilis, EmrR in Escherichia coli and QacR in Staphylococcus aureus. These proteins promote transporter gene expression when they bind toxic compounds. BmrR activates transcription of the multidrug transporter gene, bmr, in response to cellular invasion by certain lipophilic cationic compounds (drugs). BmrR belongs to the MerR family, which regulates response to stress such as exposure to toxic compounds or oxygen radicals in bacteria. MerR proteins have homologous amino-terminal DNA-binding domains but different carboxy-terminal domains, which enable them to bind specific 'coactivator' molecules. When bound to coactivator, MerR proteins upregulate transcription by reconfiguring the 19-base-pair spacer found between the -35 and -10 promoter elements to allow productive interaction with RNA polymerase. Here we report the 3.0 A resolution structure of BmrR in complex with the drug tetraphenylphosphonium (TPP) and a 22-base-pair oligodeoxynucleotide encompassing the bmr promoter. The structure reveals an unexpected mechanism for transcription activation that involves localized base-pair breaking, and base sliding and realignment of the -35 and -10 operator elements.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
A
278Bacillus subtilis (strain 168)Gene Names: bmrR (bmr1R)
Find proteins for P39075 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39075
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')M21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
118
Query on 118

Download SDF File 
Download CCD File 
A
TETRAPHENYLANTIMONIUM ION
C24 H20 Sb
SZOUUWBVOLRGQM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.268 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.150α = 90.00
b = 110.150β = 90.00
c = 144.590γ = 90.00
Software Package:
Software NamePurpose
bioteXdata reduction
TNTrefinement
TNTphasing
bioteXdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Refinement description