3d6y

From Proteopedia

Crystal structure of R275E mutant of BMRR bound to DNA and berberine

PDB ID 3d6y

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Structural highlights

3d6y is a 2 chain structure with sequence from Bacillus subtilis and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BMRR_BACSU Activates transcription of the bmr gene in response to structurally dissimilar drugs. Binds rhodamine as an inducer.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.,Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG J Biol Chem. 2008 Sep 26;283(39):26795-804. Epub 2008 Jul 25. PMID:18658145^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG. Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion. J Biol Chem. 2008 Sep 26;283(39):26795-804. Epub 2008 Jul 25. PMID:18658145 doi:10.1074/jbc.M804191200