PDBsum entry 3d6z

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protein dna_rna ligands links
Transcription regulator/DNA PDB id
Protein chain
277 a.a. *
GOL ×4
Waters ×86
* Residue conservation analysis
PDB id:
Name: Transcription regulator/DNA
Title: Crystal structure of r275e mutant of bmrr bound to DNA and r
Structure: Multidrug-efflux transporter 1 regulator. Chain: a. Fragment: residues 1-278. Engineered: yes. Mutation: yes. Bmr promoter DNA. Chain: b. Engineered: yes
Source: Bacillus subtilis. Gene: bmrr, bmr1r. Expressed in: escherichia coli. Synthetic: yes
2.60Å     R-factor:   0.226     R-free:   0.263
Authors: K.J.Newberry,R.G.Brennan
Key ref:
K.J.Newberry et al. (2008). Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion. J Biol Chem, 283, 26795-26804. PubMed id: 18658145 DOI: 10.1074/jbc.M804191200
20-May-08     Release date:   26-Aug-08    
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Protein chain
Pfam   ArchSchema ?
P39075  (BMRR_BACSU) -  Multidrug-efflux transporter 1 regulator
278 a.a.
277 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     1 term  


DOI no: 10.1074/jbc.M804191200 J Biol Chem 283:26795-26804 (2008)
PubMed id: 18658145  
Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.
K.J.Newberry, J.L.Huffman, M.C.Miller, N.Vazquez-Laslop, A.A.Neyfakh, R.G.Brennan.
BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal structures of BmrR bound to rhodamine 6G (R6G) or berberine (Ber) and cognate DNA. These structures reveal each drug stacks against multiple aromatic residues with their positive charges most proximal to the carboxylate group of Glu-253 and that, unlike other multidrug binding pockets, that of BmrR is rigid. Substitution of Glu-253 with either alanine (E253A) or glutamine (E253Q) results in unpredictable binding affinities for R6G, Ber, and tetraphenylphosphonium. Moreover, these drug binding studies reveal that the negative charge of Glu-253 is not important for high affinity binding to Ber and tetraphenylphosphonium but plays a more significant, but unpredictable, role in R6G binding. In vitro transcription data show that E253A and E253Q are constitutively active, and structures of the drug-free E253A-DNA and E253Q-DNA complexes support a transcription activation mechanism requiring the expulsion of Tyr-152 from the multidrug binding pocket. In sum, these data delineate the mechanism by which BmrR binds lipophilic, monovalent cationic compounds and suggest the importance of the redundant negative electrostatic nature of this rigid drug binding pocket that can be used to discriminate against molecules that are not substrates of the Bmr multidrug efflux pump.
  Selected figure(s)  
Figure 2.
FIGURE 2. Drug binding to BmrR. Key residues are labeled and shown as pale blue sticks with the oxygen atoms colored red and nitrogen atoms colored blue. Secondary structural elements are depicted as pale blue ribbons (coils, helices; arrows, β strands). A, wtBmrR-imidazole-DNA complex (21). Imidazole molecules are shown as green sticks, and dashed lines denote hydrogens bonds. B, wtBmrR-R6G-DNA complex. R6G is shown as red sticks with its positive charge depicted by a red +. Electrostatic interactions are shown as dashed lines. C, wtBmrR-Ber-DNA complex. Ber is shown as yellow sticks, and its positive charge depicted by a blue +. Electrostatic interactions are shown as dashed lines. D, superposition of the BmrR-imidazole-DNA and BmrR-R6G-DNA complexes. E, superposition of all BmrR-drug-DNA complexes. TPP^+ is shown as green sticks with its positively charged phosphorus atom colored purple. F, superposition of E253Q-DNA and BmrR-R6G-DNA structures. E253Q-DNA is shown as green ribbons and sticks. Dashed lines indicate potential clashes between R6G and residues in the E253Q structure. Figs. 2, 3, 4, 5 and 6 were made with PyMol (Delano, W. L. (2002)).
Figure 6.
FIGURE 6. Electrostatic surface representation of wild type and mutant BmrR drug binding pockets. Electropositive surfaces are shown in blue, and electronegative surfaces are shown in red. The left panel shows the electrostatic surface potential of the wtBmrR-R6G-DNA complex with R6G depicted as cyan sticks within the pocket. The middle panel depicts the E253A surface, and the right panel the E253Q surface.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 26795-26804) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21390267 C.N.Deshpande, S.J.Harrop, Y.Boucher, K.A.Hassan, R.Di Leo, X.Xu, H.Cui, A.Savchenko, C.Chang, M.Labbate, I.T.Paulsen, H.W.Stokes, P.M.Curmi, and B.C.Mabbutt (2011).
Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module.
  PLoS One, 6, e16934.
PDB code: 3gk6
21264225 K.M.Peters, B.E.Brooks, M.A.Schumacher, R.A.Skurray, R.G.Brennan, and M.H.Brown (2011).
A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.
  PLoS One, 6, e15974.
PDB code: 3pm1
20580544 H.Wade (2010).
MD recognition by MDR gene regulators.
  Curr Opin Struct Biol, 20, 489-496.  
20230832 M.Kumaraswami, K.J.Newberry, and R.G.Brennan (2010).
Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR.
  J Mol Biol, 398, 264-275.
PDB code: 3iao
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
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