Abstract

ABC transporters facilitate the movement of diverse molecules across cellular membranes, but how their activity is regulated post-translationally is not well understood. Here we report the crystal structure of MlaFB from E. coli, the cytoplasmic portion of the larger MlaFEDB ABC transporter complex, which drives phospholipid trafficking across the bacterial envelope to maintain outer membrane integrity. MlaB, a STAS domain protein, binds the ABC nucleotide binding domain, MlaF, and is required for its stability. Our structure also implicates a unique C-terminal tail of MlaF in self-dimerization. Both the C-terminal tail of MlaF and the interaction with MlaB are required for the proper assembly of the MlaFEDB complex and its function in cells. This work leads to a new model for how an important bacterial lipid transporter may be regulated by small proteins, and raises the possibility that similar regulatory mechanisms may exist more broadly across the ABC transporter family.

Data availability

The structure factors and coordinates for crystal structures were deposited in the Protein Data Bank with accession codes 6XGY (dimeric MlaFB with ADP+Mg) and 6XGZ (monomeric MlaFB in apo state). Plasmids generated in this study have been deposited in Addgene. All data generated or analysed during this study are included in the manuscript and supporting files.

The following data sets were generated

Article and author information

Author details

  1. Ljuvica R Kolich

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6696-9645
  2. Ya-Ting Chang

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Nicolas Coudray

    Department of Cell Biology and Applied Bioinformatics Laboratory, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Sabrina I Giacometti

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Mark R MacRae

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4941-9526
  6. Georgia L Isom

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Evelyn M Teran

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Gira Bhabha

    Department of Cell Biology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0624-6178
  9. Damian C Ekiert

    Department of Cell Biology and Department of Microbiology, New York University School of Medicine, New York, United States
    For correspondence
    damian.ekiert@EKIERTLAB.ORG
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2570-0404

Funding

American Heart Association (20POST35210202)

  • Georgia L Isom

National Institutes of Health (T32 GM088118)

  • Mark R MacRae

National Institutes of Health (R35GM128777)

  • Damian C Ekiert

Damon Runyon Cancer Research Foundation (DFS‐20‐16)

  • Gira Bhabha

National Institutes of Health (R00GM112982)

  • Gira Bhabha

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2020, Kolich 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.

Metrics

  • 2,004
    views
  • 316
    downloads
  • 34
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ljuvica R Kolich
  2. Ya-Ting Chang
  3. Nicolas Coudray
  4. Sabrina I Giacometti
  5. Mark R MacRae
  6. Georgia L Isom
  7. Evelyn M Teran
  8. Gira Bhabha
  9. Damian C Ekiert
(2020)
Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation
eLife 9:e60030.
https://doi.org/10.7554/eLife.60030

Share this article

https://doi.org/10.7554/eLife.60030

Further reading

    1. Structural Biology and Molecular Biophysics
    Chris van Hoorn, Andrew P Carter
    Research Article

    Ciliary rootlets are striated bundles of filaments that connect the base of cilia to internal cellular structures. Rootlets are critical for the sensory and motile functions of cilia. However, the mechanisms underlying these functions remain unknown, in part due to a lack of structural information of rootlet organization. In this study, we obtain 3D reconstructions of membrane-associated and purified rootlets from mouse retina using cryo-electron tomography. We show that flexible protrusions on the rootlet surface, which emanate from the cross-striations, connect to intracellular membranes. In purified rootlets, the striations were classified into amorphous (A)-bands, associated with accumulations on the rootlet surface, and discrete (D)-bands corresponding to punctate lines of density that run through the rootlet. These striations connect a flexible network of longitudinal filaments. Subtomogram averaging suggests the filaments consist of two intertwined coiled coils. The rootlet’s filamentous architecture, with frequent membrane-connecting cross-striations, lends itself well for anchoring large membranes in the cell.

    1. Structural Biology and Molecular Biophysics
    Jian Wu, Nisha A Jonniya ... Susan S Taylor
    Research Article

    Although the αC-β4 loop is a stable feature of all protein kinases, the importance of this motif as a conserved element of secondary structure, as well as its links to the hydrophobic architecture of the kinase core, has been underappreciated. We first review the motif and then describe how it is linked to the hydrophobic spine architecture of the kinase core, which we first discovered using a computational tool, local spatial Pattern (LSP) alignment. Based on NMR predictions that a mutation in this motif abolishes the synergistic high-affinity binding of ATP and a pseudo substrate inhibitor, we used LSP to interrogate the F100A mutant. This comparison highlights the importance of the αC-β4 loop and key residues at the interface between the N- and C-lobes. In addition, we delved more deeply into the structure of the apo C-subunit, which lacks ATP. While apo C-subunit showed no significant changes in backbone dynamics of the αC-β4 loop, we found significant differences in the side chain dynamics of K105. The LSP analysis suggests disruption of communication between the N- and C-lobes in the F100A mutant, which would be consistent with the structural changes predicted by the NMR spectroscopy.