1R8E

Crystal Structure of BmrR Bound to DNA at 2.4A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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This is version 1.2 of the entry. See complete history


Literature

The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.

Newberry, K.J.Brennan, R.G.

(2004) J Biol Chem 279: 20356-20362

  • DOI: 10.1074/jbc.M400960200
  • Primary Citation of Related Structures:  
    1R8D, 1R8E

  • PubMed Abstract: 
  • Transcription regulators of the MerR family respond to myriad stress signals to activate sigma70/sigmaA-targeted genes, which contain suboptimal 19-bp spacers between their -35 and -10 promoter elements. The crystal structure of a BmrR-TPP(+)-DNA complex provided initial insight into the transcription activation mechanism of the MerR family, which involves base pair distortion, DNA undertwisting and shortening of the spacer, and realignment of the -35 and -10 boxes ...

    Transcription regulators of the MerR family respond to myriad stress signals to activate sigma70/sigmaA-targeted genes, which contain suboptimal 19-bp spacers between their -35 and -10 promoter elements. The crystal structure of a BmrR-TPP(+)-DNA complex provided initial insight into the transcription activation mechanism of the MerR family, which involves base pair distortion, DNA undertwisting and shortening of the spacer, and realignment of the -35 and -10 boxes. Here, we describe the crystal structure of MerR family member MtaN bound to the mta promoter. Although the global DNA binding modes of MtaN and BmrR differ somewhat, homologous protein-DNA interactions are maintained. Moreover, despite their different sequences, the mta promoter conformation is essentially identical to that of the BmrR-TPP(+)-bound bmr promoter, indicating that this DNA distortion mechanism is common to the entire MerR family. Interestingly, DNA binding experiments reveal that the identity of the two central bases of the mta and bmr promoters, which are conserved as either a thymidine or an adenine in nearly all MerR promoters, is not important for DNA affinity. Comparison of the free and DNA-bound MtaN structures reveals that a conformational hinge, centered at residues N-terminal to the ubiquitous coiled coil, is key for mta promoter binding. Analysis of the structures of BmrR, CueR, and ZntR indicates that this hinge may be common to all MerR family members.


    Related Citations: 
    • Crystal structure of the transcription activator BmrR bound to DNA and a drug
      Heldwein, E.E., Brennan, R.G.
      (2001) Nature 409: 378

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239-3098, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
multidrug-efflux transporter regulatorB [auth A]278Bacillus subtilisMutation(s): 0 
Gene Names: bmrR
UniProt
Find proteins for P39075 (Bacillus subtilis (strain 168))
Explore P39075 
Go to UniProtKB:  P39075
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'A [auth B]23N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4P (Subject of Investigation/LOI)
Query on P4P

Download Ideal Coordinates CCD File 
E [auth A]TETRAPHENYLPHOSPHONIUM
C24 H20 P
USFPINLPPFWTJW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B], D [auth B], Q [auth A], R [auth A], S [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , 
F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1R8E Kd: 2.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.28α = 90
b = 107.28β = 90
c = 145.7γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance