Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates

Abstract
Data availability
Article and author information
Metrics

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.

The following data sets were generated

1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 in low pH (protonated state)
Protein Data Bank, 7MH6.

https://www.rcsb.org/structure/7MH6
1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 and methyl viologen
Protein Data Bank, 7MGX.

https://www.rcsb.org/structure/7MGX
1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 and harmane
Protein Data Bank, 7SVX.

https://www.rcsb.org/structure/7SVX
1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 and methyltriphenylphosphonium
Protein Data Bank, 7SSU.

https://www.rcsb.org/structure/7SSU
1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 and TPP
Protein Data Bank, 7SV9.

https://www.rcsb.org/structure/7SV9
1. Kermani AA
2. Stockbridge RB
(2022) Structure of EmrE-D3 mutant in complex with monobody L10 and benzyltrimethylammonium
Protein Data Bank, 7T00.

https://www.rcsb.org/structure/7T00
(2022) https://www.rcsb.org/structure/7SZT
Protein Data Bank, 7SZT.

https://www.rcsb.org/structure/7SZT

Article and author information

Author details

Ali A Kermani

Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States

Competing interests
No competing interests declared.
Olive E Burata

Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-8450-8930
B Ben Koff

Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-3276-143X
Akiko Koide

Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States

Competing interests
Akiko Koide, is listed as inventor for patents (US9512199 B2 and related patents and applications) covering aspects of the monobody technology filed by the University of Chicago and Novartis..
Shohei Koide

Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States

Competing interests
Shohei Koide, is listed as inventor for patents (US9512199 B2 and related patents and applications) covering aspects of the monobody technology filed by the University of Chicago and Novartis. Is a scientific advisory board member and holds equity in and receives consulting fees from Black Diamond Therapeutics; receives research funding from Puretech Health and Argenx BVBA..
Randy B Stockbridge

Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States

For correspondence
stockbr@umich.edu

Competing interests
Randy B Stockbridge, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0001-8848-3032

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

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.