Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41239.61 
• Atom Count: 2832 
• Residue Count: 301 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1R8E

Crystal Structure of BmrR Bound to DNA at 2.4A Resolution

• DOI: 10.2210/pdb1R8E/pdb
• NDB: PD0483

• Classification: TRANSCRIPTION/DNA
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli


• Deposited: 2003-10-23 Released: 2004-08-17 
• Deposition Author(s): Newberry, K.J., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 

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

• PubMed: 14985361 
• DOI: 10.1074/jbc.M400960200
• Primary Citation of Related Structures:  
  1R8D


• 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.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
multidrug-efflux transporter regulator	A	278	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: bmrR (bmr1R)
Find proteins for P39075 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P39075

Entity ID: 1
Molecule	Chains	Length	Organism
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'	B	23	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
P4P	A	TETRAPHENYLPHOSPHONIUM C24 H20 P USFPINLPPFWTJW-UHFFFAOYSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	A	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DNA	Kd: 2.4 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• Space Group: P 4₃ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 107.280	α = 90.00
b = 107.280	β = 90.00
c = 145.700	γ = 90.00

Software Package:

Software Name	Purpose
EPMR	phasing
MOSFLM	data reduction
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-23 
• Released Date: 2004-08-17 
• Deposition Author(s): Newberry, K.J., Brennan, R.G.

Revision History 

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