Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family
- University of Zurich, Switzerland
Abstract
Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.
Data availability
The cryo-EM density maps of the EleNRM-Nb complex in absence and presence of Mg2+ have been deposited in the Electron Microscopy Data Bank under ID codes EMD-13985 and EMD-13987, respectively. The coordinates for the atomic model of the EleNRM-Nb complex in absence of Mg2+ refined against the 3.4 Å cryo-EM density and the coordinates of the EleNRMTts-Nb1,2 complex in presence of Mg2+ refined against the 4.1 Å cryo-EM density have been deposited in the Protein Data Bank under ID codes 7QIA and 7QIC. The coordinates and structure factors of the EleNRMTts-Nb1,2 complexes in Mg2+ and Mn2+ have been deposited in the Protein Data Bank with the accession codes 7QJI and 7QJJ. All datasets will be accessible upon publication. Source data files have been provided for Figures 1, Figure 1-figure supplement 1, Figure 2, Figure 2-figure supplement 1, Figure 3, Figure 2-figure supplement 2, Figure 4, Figure 4-figure supplement 1, Figure 8.
Article and author information
Author details
Karthik Ramanadane
Cristina Manatschal
Funding
Swiss National Science Foundation (NCCR TransCure)
- Raimund Dutzler
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Ramanadane 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
-
- 2,564
- views
-
- 389
- 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)
Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family
eLife 11:e74589.
https://doi.org/10.7554/eLife.74589
Further reading
-
- Computational and Systems Biology
- Structural Biology and Molecular Biophysics
Viral adhesion to host cells is a critical step in infection for many viruses, including monkeypox virus (MPXV). In MPXV, the H3 protein mediates viral adhesion through its interaction with heparan sulfate (HS), yet the structural details of this interaction have remained elusive. Using AI-based structural prediction tools and molecular dynamics (MD) simulations, we identified a novel, positively charged α-helical domain in H3 that is essential for HS binding. This conserved domain, found across orthopoxviruses, was experimentally validated and shown to be critical for viral adhesion, making it an ideal target for antiviral drug development. Targeting this domain, we designed a protein inhibitor, which disrupted the H3-HS interaction, inhibited viral infection in vitro and viral replication in vivo, offering a promising antiviral candidate. Our findings reveal a novel therapeutic target of MPXV, demonstrating the potential of combination of AI-driven methods and MD simulations to accelerate antiviral drug discovery.
-
- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
