Structure and ion-release mechanism of PIB-4-type ATPases
- University of Copenhagen, Denmark
- Umeå University, Sweden
- Lund University, Sweden
- The University of Texas at Dallas, United States
- University of Cambridge, United Kingdom
Abstract
Transition metals, such as zinc, are essential micronutrients in all organisms, but also highly toxic in excessive amounts. Heavy-metal transporting P-type (PIB) ATPases are crucial for homeostasis, conferring cellular detoxification and redistribution through transport of these ions across cellular membranes. No structural information is available for the PIB-4-ATPases, the subclass with the broadest cargo scope, and hence even their topology remains elusive. Here we present structures and complementary functional analyses of an archetypal PIB‑4‑ATPase, sCoaT from Sulfitobacter sp. NAS14-1. The data disclose the architecture, devoid of classical so-called heavy metal binding domains, and provides fundamentally new insights into the mechanism and diversity of heavy-metal transporters. We reveal several novel P-type ATPase features, including a dual role in heavy-metal release and as an internal counter ion of an invariant histidine. We also establish that the turn-over of PIB‑ATPases is potassium independent, contrasting to many other P-type ATPases. Combined with new inhibitory compounds, our results open up for efforts in e.g. drug discovery, since PIB-4-ATPases function as virulence factors in many pathogens.
Data availability
Atomic coordinates and structure factors for the sCoaT AlF4-- and BeF3--stabilized crystal structures have been deposited at the Protein Data Bank (PDB) under accession codes 7QBZ and 7QC0.
-
Structure and ion-release mechanism of PIB-4-type ATPasesProtein Data Bank, 7QBZ.
-
Structure and ion-release mechanism of PIB-4-type ATPasesProtein Data Bank, 7QC0.
Article and author information
Author details
Funding
Novo Nordisk Fonden (NNF18SA0034956)
- Christina Grønberg
Lundbeckfonden (R313-2019-774,R218-2016-1548,R133-A12689)
- Pontus Gourdon
Knut och Alice Wallenbergs Stiftelse (2020.0194,2015.0131)
- Pontus Gourdon
Carlsbergfondet (CF15-0542,2013_01_0641)
- Pontus Gourdon
Novo Nordisk Fonden (NNF13OC0007471)
- Pontus Gourdon
Brodrene Hartmann (A29519)
- Pontus Gourdon
Agnes og Poul Friis Fond
- Pontus Gourdon
Augustinus Fonden (16-1992)
- Pontus Gourdon
Crafoord (20180652,20170818)
- Pontus Gourdon
Per-Eric and Ulla Schyberg (38267)
- Pontus Gourdon
Swedish Research Council (2016-04474)
- Pontus Gourdon
The memorial foundation of manufacturer Vilhelm Pedersen and wife - and the Aarhus Wilson consortium
- Christina Grønberg
The Independent Research Fund Denmark (9039-00273A)
- Pontus Gourdon
China Scholarship Council
- Qiaoxia Hu
Carl Tryggers Stiftelse för Vetenskaplig Forskning (CTS 17:22)
- Dhani Ram Mahato
Swedish Research Council Starting Grant (2016-03610)
- Magnus Andersson
Robert A. Welke Cancer Research Foundation (AT-1935-20170325 and AT-2073-20210327)
- Gabriele Meloni
National Institute of General Medical Sciences (R35GM128704))
- Gabriele Meloni
National Science Foundation (CHE- 2045984)
- Gabriele Meloni
Swedish Heart-Lung Foundation (20200378)
- Gabriela Godaly
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Grønberg 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
-
- 1,621
- views
-
- 271
- downloads
-
- 9
- 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)
Structure and ion-release mechanism of PIB-4-type ATPases
eLife 10:e73124.
https://doi.org/10.7554/eLife.73124
Further reading
-
- Biochemistry and Chemical Biology
N 6,2’-O-dimethyladenosine (m6Am) is a modified nucleotide located at the first transcribed position in mRNA and snRNA that is essential for diverse physiological processes. m6Am mapping methods assume each gene uses a single start nucleotide. However, gene transcription usually involves multiple start sites, generating numerous 5’ isoforms. Thus, gene-level annotations cannot capture the diversity of m6Am modification in the transcriptome. Here, we describe CROWN-seq, which simultaneously identifies transcription-start nucleotides and quantifies m6Am stoichiometry for each 5’ isoform that initiates with adenosine. Using CROWN-seq, we map the m6Am landscape in nine human cell lines. Our findings reveal that m6Am is nearly always a high stoichiometry modification, with only a small subset of cellular mRNAs showing lower m6Am stoichiometry. We find that m6Am is associated with increased transcript expression and provide evidence that m6Am may be linked to transcription initiation associated with specific promoter sequences and initiation mechanisms. These data suggest a potential new function for m6Am in influencing transcription.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.
