3Q3D

Crystal structure of BmrR bound to puromycin

Summary for 3Q3D

• Entry DOI: 10.2210/pdb3q3d/pdb
• Related: 3D6Y 3D6Z
• Descriptor: Multidrug-efflux transporter 1 regulator, BmrR promoter DNA, PUROMYCIN, ... (4 entities in total)
• Functional Keywords: protein-dna complex, multi-drug binding, antibiotic, transcription regulator, transcription regulator-dna-antibiotic complex, transcription regulator/dna/antibiotic
• Biological source: Bacillus subtilis; More
• Total number of polymer chains: 2
• Total formula weight: 41008.25

Authors

Bachas, S.,Eginton, C.,Gunio, G.,Wade, H. (deposition date: 2010-12-21, release date: 2011-06-15, Last modification date: 2024-03-13)

Primary citation

Bachas, S.,Eginton, C.,Gunio, D.,Wade, H.
Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR.
Proc.Natl.Acad.Sci.USA, 108:11046-11051, 2011

PubMed Abstract: Current views of multidrug (MD) recognition focus on large drug-binding cavities with flexible elements. However, MD recognition in BmrR is supported by a small, rigid drug-binding pocket. Here, a detailed description of MD binding by the noncanonical BmrR protein is offered through the combined use of X-ray and solution studies. Low shape complementarity, suboptimal packing, and efficient burial of a diverse set of ligands is facilitated by an aromatic docking platform formed by a set of conformationally fixed aromatic residues, hydrophobic pincer pair that locks the different drug structures on the adaptable platform surface, and a trio of acidic residues that enables cation selectivity without much regard to ligand structure. Within the binding pocket is a set of BmrR-derived H-bonding donor and acceptors that solvate a wide range of ligand polar substituent arrangements in a manner analogous to aqueous solvent. Energetic analyses of MD binding by BmrR are consistent with structural data. A common binding orientation for the different BmrR ligands is in line with promiscuous allosteric regulation.

PubMed: 21690368
DOI: 10.1073/pnas.1104850108

Experimental method

X-RAY DIFFRACTION (2.79 Å)