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

  1. Ali A Kermani
  2. Olive E Burata
  3. B Ben Koff
  4. Akiko Koide
  5. Shohei Koide
  6. Randy B Stockbridge  Is a corresponding author
  1. University of Michigan, United States
  2. 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.

The following data sets were generated

Article and author information

Author details

  1. Ali A Kermani

    Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  2. Olive E Burata

    Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8450-8930
  3. B Ben Koff

    Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3276-143X
  4. 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..
  5. 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..
  6. 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.
    ORCID icon "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.

Reviewing Editor

  1. Nir Ben-Tal, Tel Aviv University, Israel

Version history

  1. Received: January 4, 2022
  2. Preprint posted: January 11, 2022 (view preprint)
  3. Accepted: March 6, 2022
  4. Accepted Manuscript published: March 7, 2022 (version 1)
  5. Version of Record published: April 11, 2022 (version 2)

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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  1. Ali A Kermani
  2. Olive E Burata
  3. B Ben Koff
  4. Akiko Koide
  5. Shohei Koide
  6. Randy B Stockbridge
(2022)
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

Share this article

https://doi.org/10.7554/eLife.76766

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