Structure and ion-release mechanism of PIB-4-type ATPases
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.
Reviewing Editor
- Merritt Maduke, Stanford University School of Medicine, United States
Version history
- Received: August 17, 2021
- Preprint posted: September 5, 2021 (view preprint)
- Accepted: December 17, 2021
- Accepted Manuscript published: December 24, 2021 (version 1)
- Version of Record published: February 25, 2022 (version 2)
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
-
- 1,438
- Page views
-
- 251
- Downloads
-
- 6
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
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)
Further reading
-
- Biochemistry and Chemical Biology
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named ‘L’ and ‘R,’ where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
-
- Biochemistry and Chemical Biology
Organizations that fund research are keen to ensure that their grant selection processes are fair and equitable for all applicants. In 2020, the Arnold and Mabel Beckman Foundation introduced blinding to the first stage of the process used to review applications for Beckman Young Investigator (BYI) awards: applicants were instructed to blind the technical proposal in their initial Letter of Intent by omitting their name, gender, gender-identifying pronouns, and institutional information. Here we examine the impact of this change by comparing the data on gender and institutional prestige of the applicants in the first four years of the new policy (BYI award years 2021–2024) with data on the last four years of the old policy (2017–2020). We find that under the new policy, the distribution of applicants invited to submit a full application shifted from those affiliated with institutions regarded as more prestigious to those outside of this group, and that this trend continued through to the final program awards. We did not find evidence of a shift in the distribution of applicants with respect to gender.