Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR

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.

Structures of a Na + -coupled, substrate-bound MATE multidrug transporter

“…The substrates bury ∼70% of their accessible surface area on binding the transporter, which is consistent with values obtained from multidrug-binding transcription factor BmrR (17). Also similar to BmrR (17,18), the structures of NorM-NG revealed similar docking locations for all three substrates, which are located near the membrane-periplasm interface ( Fig. 2A).…”

“…The unexpected paucity of aromatic and nonpolar residues, on the other hand, may allow NorM-NG to avoid the deleterious consequences of tight association with hydrophobic drugs when the transporter is poised to release its bound substrate (30,31). Moreover, there are no significant alterations in the positions of amino acid side chains on binding different substrates in NorM-NG, similar to what had been observed in BmrR (17,18). As in BmrR, the presence of multiple acidic residues may enable versatile orientation and charge complementation of structurally dissimilar cationic drugs in NorM-NG without the need to revamp the drugbinding site.…”

Transported Substrate Determines Exchange Rate in the Multidrug Resistance Transporter EmrE

“…Multidrug recognition in a single small binding pocket has already been established in one case, the MDR transcription factor BmrR (13). In BmrR, the same set of active site residues interacts with its full array of ligands in a highly rigid binding pocket (13). This is in contrast to the canonical concept of multidrug recognition (11,12), which postulates a key role for flexibility in accommodating diverse ligands in a single site.…”

“…As a member of the smallest family of MDR transporters, EmrE has a small binding pocket that must accommodate its entire wide range of substrates within a limited space. Multidrug recognition in a single small binding pocket has already been established in one case, the MDR transcription factor BmrR (13). In BmrR, the same set of active site residues interacts with its full array of ligands in a highly rigid binding pocket (13).…”

Unconventional Coupling between Ligand Recognition and Allosteric Control in the Multidrug Resistance Gene Regulator, BmrR

“…Protection of this type is universal and essential for the functioning of normal cells. [5] However,o ur understanding of how polyspecific interactions control the conformations and functions of MDR systems at the molecular and mechanistic levels remains incomplete. MDR efflux pumps,r egulators and other sensory proteins share two salient features that appear to be essential to their abilities to protectc ells from lethal doses of unrelated agents.…”