Crystal Structure of BmrR Bound to DNA at 2.4A Resolution

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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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: https://doi.org/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. 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.

  • Organizational Affiliation

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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
multidrug-efflux transporter regulatorB [auth A]278Bacillus subtilisMutation(s): 0 
Gene Names: bmrr
Find proteins for P39075 (Bacillus subtilis (strain 168))
Explore P39075 
Go to UniProtKB:  P39075
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39075
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P4P

Download Ideal Coordinates CCD File 
C24 H20 P
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B],
Q [auth A],
R [auth A],
S [auth A]
C3 H8 O3
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [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]
C3 H5 N2
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1R8E Kd: 2.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
CCP4data 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: 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
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description