1. Structural Biology and Molecular Biophysics
Download icon

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

  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  Is a corresponding author
  1. Texas A&M University, United States
  2. University of Utah School of Medicine, United States
Research Article
  • Cited 3
  • Views 970
  • Annotations
Cite this article as: eLife 2020;9:e57081 doi: 10.7554/eLife.57081

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.

Reviewing Editor

  1. Benoît Kornmann, University of Oxford, United Kingdom

Publication history

  1. Received: March 20, 2020
  2. Accepted: August 10, 2020
  3. Accepted Manuscript published: August 11, 2020 (version 1)
  4. Version of Record published: September 1, 2020 (version 2)

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

  • 970
    Page views
  • 145
    Downloads
  • 3
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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)

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

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

Further reading

    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics
    Justin D Lormand et al.
    Research Advance

    RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC employs similar structural features that distinguish these two classes as dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases indicates convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.

    1. Structural Biology and Molecular Biophysics
    Matthias Wälchli et al.
    Research Article

    The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.