Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates
- University of Michigan, United States
- New York University Langone Medical Center, United States
Abstract
Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of the Escherichia coli transporter, EmrE, has been studied extensively, but a lack of high-resolution structural information has impeded a structural description of its molecular mechanism. Here we apply a novel approach, multipurpose crystallization chaperones, to solve several structures of EmrE, including a 2.9 Å structure at low pH without substrate. We report five additional structures in complex with structurally diverse transported substrates, including quaternary phosphonium, quaternary ammonium, and planar polyaromatic compounds. These structures show that binding site tryptophan and glutamate residues adopt different rotamers to conform to disparate structures without requiring major rearrangements of the backbone structure. Structural and functional comparison to Gdx-Clo, an SMR protein that transports a much narrower spectrum of substrates, suggests that in EmrE, a relatively sparse hydrogen bond network among binding site residues permits increased sidechain flexibility.
Data availability
Atomic coordinates for the crystal structures have been deposited in the Protein Data Bank under accession numbers 7MH6 (EmrE3/L10), 7MGX (EmrE3/L10/methyl viologen), 7SVX (EmrE3/L10/harmane), 7SSU (EmrE3/L10/MeTPP+), 7SV9 (EmrE3/L10/TPP+), 7T00 (EmrE3/L10/benzyltrimethylammonium) and 7SZT (Gdx-Clo/L10). All other data generated or analyzed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures 1 and 5.
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Structure of EmrE-D3 mutant in complex with monobody L10 and harmaneProtein Data Bank, 7SVX.
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Structure of EmrE-D3 mutant in complex with monobody L10 and TPPProtein Data Bank, 7SV9.
Article and author information
Author details
Randy B Stockbridge
Funding
National Institutes of Health (CA194864)
- Shohei Koide
National Science Foundation (CAREER 1845012)
- Randy B Stockbridge
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Kermani et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates
eLife 11:e76766.
https://doi.org/10.7554/eLife.76766
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