A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins

Abstract

Yeast Sfh5 is an unusual member of the Sec14-like phosphatidylinositol transfer protein (PITP) family. Whereas PITPs are defined by their abilities to transfer phosphatidylinositol between membranes in vitro, and to stimulate phosphoinositide signaling in vivo, Sfh5 does not exhibit these activities. Rather, Sfh5 is a redox-active penta-coordinate high spin FeIII hemoprotein with an unusual heme-binding arrangement that involves a co-axial tyrosine/histidine coordination strategy and a complex electronic structure connecting the open shell iron d-orbitals with three aromatic ring systems. That Sfh5 is not a PITP is supported by demonstrations that heme is not a readily exchangeable ligand, and that phosphatidylinositol-exchange activity is resuscitated in heme binding-deficient Sfh5 mutants. The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct ligands to the control of diverse sets of cellular activities.

Data availability

Diffraction data have been deposited in PDB under the accession code 6W32.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. Danish Khan

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0650-3990
  2. Dongju Lee

    Department of Molecular and Cellular Medicine, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Gulcin Gulten

    Biochemistry, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Anup Aggarwal

    Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Joshua Wofford

    Chemistry, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Inna Krieger

    Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Ashutosh Tripathi

    Department of Molecular and Cellular Medicine, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. John W Patrick

    Chemistry, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Debra M Eckert

    Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Arthur Laganowsky

    Department of Chemistry, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. James Sacchettini

    Biochemistry/Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5767-2367
  12. Paul Lindahl

    Chemistry, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Vytas A Bankaitis

    molecular & cellular medicine, Texas A&M University, College Station, United States
    For correspondence
    vytas@tamu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1654-6759

Funding

National Institute of General Medical Sciences (R35 GM131804)

  • Vytas A Bankaitis

Welch Foundation (BE-0017)

  • Vytas A Bankaitis

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

Copyright

© 2020, Khan 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

  • 1,564
    views
  • 213
    downloads
  • 11
    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. Danish Khan
  2. Dongju Lee
  3. Gulcin Gulten
  4. Anup Aggarwal
  5. Joshua Wofford
  6. Inna Krieger
  7. Ashutosh Tripathi
  8. John W Patrick
  9. Debra M Eckert
  10. Arthur Laganowsky
  11. James Sacchettini
  12. Paul Lindahl
  13. Vytas A Bankaitis
(2020)
A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins
eLife 9:e57081.
https://doi.org/10.7554/eLife.57081

Share this article

https://doi.org/10.7554/eLife.57081

Further reading

    1. Structural Biology and Molecular Biophysics
    Chuchu Wang, Chunyu Zhao ... Cong Liu
    Research Advance

    Previously, we reported that α-synuclein (α-syn) clusters synaptic vesicles (SV) Diao et al., 2013, and neutral phospholipid lysophosphatidylcholine (LPC) can mediate this clustering Lai et al., 2023. Meanwhile, post-translational modifications (PTMs) of α-syn such as acetylation and phosphorylation play important yet distinct roles in regulating α-syn conformation, membrane binding, and amyloid aggregation. However, how PTMs regulate α-syn function in presynaptic terminals remains unclear. Here, based on our previous findings, we further demonstrate that N-terminal acetylation, which occurs under physiological conditions and is irreversible in mammalian cells, significantly enhances the functional activity of α-syn in clustering SVs. Mechanistic studies reveal that this enhancement is caused by the N-acetylation-promoted insertion of α-syn’s N-terminus and increased intermolecular interactions on the LPC-containing membrane. N-acetylation in our work is shown to fine-tune the interaction between α-syn and LPC, mediating α-syn’s role in synaptic vesicle clustering.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Raji E Joseph, Thomas E Wales ... Amy H Andreotti
    Research Advance

    Inhibition of Bruton’s tyrosine kinase (BTK) has proven to be highly effective in the treatment of B-cell malignancies such as chronic lymphocytic leukemia (CLL), autoimmune disorders, and multiple sclerosis. Since the approval of the first BTK inhibitor (BTKi), Ibrutinib, several other inhibitors including Acalabrutinib, Zanubrutinib, Tirabrutinib, and Pirtobrutinib have been clinically approved. All are covalent active site inhibitors, with the exception of the reversible active site inhibitor Pirtobrutinib. The large number of available inhibitors for the BTK target creates challenges in choosing the most appropriate BTKi for treatment. Side-by-side comparisons in CLL have shown that different inhibitors may differ in their treatment efficacy. Moreover, the nature of the resistance mutations that arise in patients appears to depend on the specific BTKi administered. We have previously shown that Ibrutinib binding to the kinase active site causes unanticipated long-range effects on the global conformation of BTK (Joseph et al., 2020). Here, we show that binding of each of the five approved BTKi to the kinase active site brings about distinct allosteric changes that alter the conformational equilibrium of full-length BTK. Additionally, we provide an explanation for the resistance mutation bias observed in CLL patients treated with different BTKi and characterize the mechanism of action of two common resistance mutations: BTK T474I and L528W.