1
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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2
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Faraj SE, Valsecchi WM, Ferreira-Gomes M, Centeno M, Saint Martin EM, Fedosova NU, Rossi JPFC, Montes MR, Rossi RC. Measurements of Na +-occluded intermediates during the catalytic cycle of the Na +/K +-ATPase provide novel insights into the mechanism of Na + transport. J Biol Chem 2022; 299:102811. [PMID: 36539036 PMCID: PMC9860123 DOI: 10.1016/j.jbc.2022.102811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The Na+/K+-ATPase is an integral plasma membrane glycoprotein of all animal cells that couples the exchange of intracellular Na+ for extracellular K+ to the hydrolysis of ATP. The asymmetric distribution of Na+ and K+ is essential for cellular life and constitutes the physical basis of a series of fundamental biological phenomena. The pumping mechanism is explained by the Albers-Post model. It involves the presence of gates alternatively exposing Na+/K+-ATPase transport sites to the intracellular and extracellular sides and includes occluded states in which both gates are simultaneously closed. Unlike for K+, information is lacking about Na+-occluded intermediates, as occluded Na+ was only detected in states incapable of performing a catalytic cycle, including two Na+-containing crystallographic structures. The current knowledge is that intracellular Na+ must bind to the transport sites and become occluded upon phosphorylation by ATP to be transported to the extracellular medium. Here, taking advantage of epigallocatechin-3-gallate to instantaneously stabilize native Na+-occluded intermediates, we isolated species with tightly bound Na+ in an enzyme able to perform a catalytic cycle, consistent with a genuine occluded state. We found that Na+ becomes spontaneously occluded in the E1 dephosphorylated form of the Na+/K+-ATPase, exhibiting positive interactions between binding sites. In fact, the addition of ATP does not produce an increase in Na+ occlusion as it would have been expected; on the contrary, occluded Na+ transiently decreases, whereas ATP lasts. These results reveal new properties of E1 intermediates of the Albers-Post model for explaining the Na+ transport pathway.
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Affiliation(s)
- Santiago E. Faraj
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Wanda M. Valsecchi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Mariela Ferreira-Gomes
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Mercedes Centeno
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Elina Malén Saint Martin
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina
| | | | - Juan Pablo FC. Rossi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Mónica R. Montes
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina
| | - Rolando C. Rossi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), Buenos Aires, Argentina,For correspondence: Rolando C. Rossi
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3
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Orädd F, Steffen JH, Gourdon P, Andersson M. Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B. PLoS Comput Biol 2022; 18:e1010074. [PMID: 36070320 PMCID: PMC9484656 DOI: 10.1371/journal.pcbi.1010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/19/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
ATP7B is a human copper-transporting P1B-type ATPase that is involved in copper homeostasis and resistance to platinum drugs in cancer cells. ATP7B consists of a copper-transporting core and a regulatory N-terminal tail that contains six metal-binding domains (MBD1-6) connected by linker regions. The MBDs can bind copper, which changes the dynamics of the regulatory domain and activates the protein, but the underlying mechanism remains unknown. To identify possible copper-specific structural dynamics involved in transport regulation, we constructed a model of ATP7B spanning the N-terminal tail and core catalytic domains and performed molecular dynamics (MD) simulations with (holo) and without (apo) copper ions bound to the MBDs. In the holo protein, MBD2, MBD3 and MBD5 showed enhanced mobilities, which resulted in a more extended N-terminal regulatory region. The observed separation of MBD2 and MBD3 from the core protein supports a mechanism where copper binding activates the ATP7B protein by reducing interactions among MBD1-3 and between MBD1-3 and the core protein. We also observed an increased interaction between MBD5 and the core protein that brought the copper-binding site of MBD5 closer to the high-affinity internal copper-binding site in the core protein. The simulation results assign specific, mechanistic roles to the metal-binding domains involved in ATP7B regulation that are testable in experimental settings. Living organisms depend upon active transport against gradients across biological membranes for survival. Such transport can be accomplished by ATP-dependent membrane protein transporters for which the activity must be regulated to maintain optimal concentrations in the cellular compartments. The regulatory mechanisms often involve structural responses inherent to the protein structure, which because of their dynamic nature can be hard to assess experimentally. A prime example is regulation of cellular copper levels by a copper-binding tail in the human copper transporter ATP7B. Dysregulation can cause severe diseases, for example the copper metabolism disorder Wilson’s disease, which is caused by mutations in ATP7B regulation machinery. Due to the practical difficulties in working with membrane proteins, most studies of ATP7B have been conducted in the absence of the membrane-bound protein core. Here, we used computer simulations of full-length ATP7B to study how structural dynamics in the regulatory tail differ between copper-bound and copper-free states. Copper induced increased dynamics in the tail, resulting in an overall movement towards the ion-binding site in the protein core. The simulations identified several, hitherto not reported, interactions between the regulatory tail and the protein core that can be targeted experimentally to enhance our understanding of this medically relevant regulatory mechanism.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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4
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Grønberg C, Hu Q, Mahato DR, Longhin E, Salustros N, Duelli A, Lyu P, Bågenholm V, Eriksson J, Rao KU, Henderson DI, Meloni G, Andersson M, Croll T, Godaly G, Wang K, Gourdon P. Structure and ion-release mechanism of P IB-4-type ATPases. eLife 2021; 10:73124. [PMID: 34951590 PMCID: PMC8880997 DOI: 10.7554/elife.73124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Christina Grønberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Qiaoxia Hu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Elena Longhin
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pin Lyu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Viktoria Bågenholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | | | | | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States
| | | | - Tristan Croll
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Gabriela Godaly
- Department of Laboratory Medicine, Umeå University, Umeå, Sweden
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
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5
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Abeyrathna N, Abeyrathna S, Morgan MT, Fahrni CJ, Meloni G. Transmembrane Cu(I) P-type ATPase pumps are electrogenic uniporters. Dalton Trans 2021; 49:16082-16094. [PMID: 32469032 DOI: 10.1039/d0dt01380c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cu(i) P-type ATPases are transmembrane primary active ion pumps that catalyze the extrusion of copper ions across cellular membranes. Their activity is critical in controlling copper levels in all kingdoms of life. Biochemical and structural characterization established the structural framework by which Cu-pumps perform their function. However, the details of the overall mechanism of transport (uniporter vs. cotransporter) and electrogenicity still remain elusive. In this work, we developed a platform to reconstitute the model Cu(i)-pump from E. coli (EcCopA) in artificial lipid bilayer small unilamellar vesicles (SUVs) to quantitatively characterize the metal substrate, putative counter-ions and charge translocation. By encapsulating in the liposome lumen fluorescence detector probes (CTAP-3, pyranine and oxonol VI) responsive to diverse stimuli (Cu(i), pH and membrane potential), we correlated substrate, secondary-ion translocation and charge movement events in EcCopA proteoliposomes. This platform centered on multiple fluorescence reporters allowed study of the mechanism and translocation kinetic parameters in real-time for wild-type EcCopA and inactive mutants. The maximal initial Cu(i) transport rate of 165 nmol Cu(i) mg-1 min-1 and KM, Cu(I) = 0.15 ± 0.07 μM was determined with this analysis. We reveal that Cu(i) pumps are primary-active uniporters and electrogenic. The Cu(i) translocation cycle does not require proton counter-transport resulting in electrogenic generation of transmembrane potential upon translocation of one Cu(i) per ATP hydrolysis cycle. Thus, mechanistic differences between Cu(i) pumps and other better characterized P-type ATPases are discussed. The platform opens the venue to study translocation events and mechanisms of transport in other transition metal P-type ATPase pumps.
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Affiliation(s)
- Nisansala Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
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6
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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7
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Tadini-Buoninsegni F. Protein Adsorption on Solid Supported Membranes: Monitoring the Transport Activity of P-Type ATPases. Molecules 2020; 25:molecules25184167. [PMID: 32933017 PMCID: PMC7570688 DOI: 10.3390/molecules25184167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
P-type ATPases are a large family of membrane transporters that are found in all forms of life. These enzymes couple ATP hydrolysis to the transport of various ions or phospholipids across cellular membranes, thereby generating and maintaining crucial electrochemical potential gradients. P-type ATPases have been studied by a variety of methods that have provided a wealth of information about the structure, function, and regulation of this class of enzymes. Among the many techniques used to investigate P-type ATPases, the electrical method based on solid supported membranes (SSM) was employed to investigate the transport mechanism of various ion pumps. In particular, the SSM method allows the direct measurement of charge movements generated by the ATPase following adsorption of the membrane-bound enzyme on the SSM surface and chemical activation by a substrate concentration jump. This kind of measurement was useful to identify electrogenic partial reactions and localize ion translocation in the reaction cycle of the membrane transporter. In the present review, we discuss how the SSM method has contributed to investigate some key features of the transport mechanism of P-type ATPases, with a special focus on sarcoplasmic reticulum Ca2+-ATPase, mammalian Cu+-ATPases (ATP7A and ATP7B), and phospholipid flippase ATP8A2.
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Lekeux G, Crowet JM, Nouet C, Joris M, Jadoul A, Bosman B, Carnol M, Motte P, Lins L, Galleni M, Hanikenne M. Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:329-341. [PMID: 30418580 PMCID: PMC6305203 DOI: 10.1093/jxb/ery353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/01/2018] [Indexed: 05/26/2023]
Abstract
The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.
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Affiliation(s)
- Gilles Lekeux
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, Liège, Belgium
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Jean-Marc Crowet
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Cécile Nouet
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Marine Joris
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Alice Jadoul
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Bernard Bosman
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Monique Carnol
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Patrick Motte
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, Liège, Belgium
| | - Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
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Tadini-Buoninsegni F, Sordi G, Smeazzetto S, Natile G, Arnesano F. Effect of cisplatin on the transport activity of P II-type ATPases. Metallomics 2018. [PMID: 28636017 DOI: 10.1039/c7mt00100b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cisplatin (cis-diamminedichlorido-Pt(ii)) is extensively used as a chemotherapeutic agent against various types of tumors. However, cisplatin administration causes serious side effects, including nephrotoxicity, ototoxicity and neurotoxicity. It has been shown that cisplatin can interact with P-type ATPases, e.g., Cu+-ATPases (ATP7A and ATP7B) and Na+,K+-ATPase. Cisplatin-induced inhibition of Na+,K+-ATPase has been related to the nephrotoxic effect of the drug. To investigate the inhibitory effects of cisplatin on the pumping activity of PII-type ATPases, electrical measurements were performed on sarcoplasmic reticulum Ca2+-ATPase (SERCA) and Na+,K+-ATPase embedded in vesicles/membrane fragments adsorbed on a solid-supported membrane. We found that cisplatin inhibits SERCA and Na+,K+-ATPase only when administered without a physiological reducing agent (GSH); in contrast, inhibition was also observed in the case of Cu+-ATPases in the presence of 1 mM GSH. Our results indicate that cisplatin is a much stronger inhibitor of SERCA (with an IC50 value of 1.3 μM) than of Na+,K+-ATPase (with an IC50 value of 11.1 μM); moreover, cisplatin inhibition of Na+,K+-ATPase is reversible, whereas it is irreversible in the case of SERCA. In the absence of a physiological substrate, while Cu+-ATPases are able to translocate cisplatin, SERCA and Na+,K+-ATPase do not perform ATP-dependent cisplatin displacement.
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10
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Solioz M. Copper Homeostasis in Gram-Positive Bacteria. SPRINGERBRIEFS IN MOLECULAR SCIENCE 2018. [DOI: 10.1007/978-3-319-94439-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation. Proc Natl Acad Sci U S A 2017; 114:13661-13666. [PMID: 29229866 DOI: 10.1073/pnas.1708563115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation. This histidine switch-mediated cooperation between site 1 and site 2 enables ZitR to adjust its DNA-binding affinity in response to a broad range of zinc fluctuation, which may allow the fine tuning of transcriptional regulation.
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12
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Characterization of ATP7A missense mutants suggests a correlation between intracellular trafficking and severity of Menkes disease. Sci Rep 2017; 7:757. [PMID: 28389643 PMCID: PMC5428812 DOI: 10.1038/s41598-017-00618-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Menkes disease (MD) is caused by mutations in ATP7A, encoding a copper-transporting P-type ATPase which exhibits copper-dependent trafficking. ATP7A is found in the Trans-Golgi Network (TGN) at low copper concentrations, and in the post-Golgi compartments and the plasma membrane at higher concentrations. Here we have analyzed the effect of 36 ATP7A missense mutations identified in phenotypically different MD patients. Nine mutations identified in patients with severe MD, virtually eliminated ATP7A synthesis, in most cases due to aberrant RNA splicing. A group of 21 predominantly severe mutations led to trapping of the protein in TGN and displayed essentially no activity in a yeast-based functional assay. These were predicted to inhibit the catalytic phosphorylation of the protein. Four mutants showed diffuse post-TGN localization, while two displayed copper dependent trafficking. These six variants were identified in patients with mild MD and typically displayed activity in the yeast assay. The four post-TGN located mutants were presumably affected in the catalytic dephosphorylation of the protein. Together these results indicate that the severity of MD correlate with cellular localization of ATP7A and support previous studies indicating that phosphorylation is crucial for the exit of ATP7A from TGN, while dephosphorylation is crucial for recycling back to TGN.
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13
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Tadini-Buoninsegni F, Smeazzetto S. Mechanisms of charge transfer in human copper ATPases ATP7A and ATP7B. IUBMB Life 2017; 69:218-225. [PMID: 28164426 DOI: 10.1002/iub.1603] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022]
Abstract
ATP7A and ATP7B are Cu+ -transporting ATPases of subclass IB and play a fundamental role in intracellular copper homeostasis. ATP7A/B transfer Cu+ ions across the membrane from delivery to acceptor proteins without establishing a free Cu+ gradient. Transfer of copper across the membrane is coupled to ATP hydrolysis. Current measurements on solid supported membranes (SSM) were performed to investigate the mechanism of copper-related charge transfer across ATP7A and ATP7B. SSM measurements demonstrated that electrogenic copper displacement occurs within ATP7A/B following addition of ATP and formation of the phosphorylated intermediate. Comparison of the time constants for cation displacement in ATP7A/B and sarcoplasmic reticulum Ca2+ -ATPase is consistent with the slower phosphoenzyme formation in copper ATPases. Moreover, ATP-dependent copper transfer in ATP7A/B is not affected by varying the pH, suggesting that net proton counter-transport may not occur in copper ATPases. Platinum anticancer drugs activate ATP7A/B and are subjected to ATP-dependent vectorial displacement with a mechanism analogous to that of copper. © 2016 IUBMB Life, 69(4):218-225, 2017.
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Affiliation(s)
| | - Serena Smeazzetto
- Department of Chemistry "Ugo Schiff,", University of Florence, Sesto Fiorentino, Italy
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14
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Öhrvik H, Aaseth J, Horn N. Orchestration of dynamic copper navigation – new and missing pieces. Metallomics 2017; 9:1204-1229. [DOI: 10.1039/c7mt00010c] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A general principle in all cells in the body is that an essential metal – here copper – is taken up at the plasma membrane, directed through cellular compartments for use in specific enzymes and pathways, stored in specific scavenging molecules if in surplus, and finally expelled from the cells.
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Affiliation(s)
- Helena Öhrvik
- Medical Biochemistry and Microbiology
- Uppsala University
- Sweden
| | - Jan Aaseth
- Innlandet Hospital Trust and Inland Norway University of Applied Sciences
- Norway
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15
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Zinati Z, Alemzadeh A, KayvanJoo AH. Computational approaches for classification and prediction of P-type ATPase substrate specificity in Arabidopsis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:163-174. [PMID: 27186030 PMCID: PMC4840148 DOI: 10.1007/s12298-016-0351-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/15/2016] [Accepted: 03/28/2016] [Indexed: 06/05/2023]
Abstract
As an extended gamut of integral membrane (extrinsic) proteins, and based on their transporting specificities, P-type ATPases include five subfamilies in Arabidopsis, inter alia, P4ATPases (phospholipid-transporting ATPase), P3AATPases (plasma membrane H(+) pumps), P2A and P2BATPases (Ca(2+) pumps) and P1B ATPases (heavy metal pumps). Although, many different computational methods have been developed to predict substrate specificity of unknown proteins, further investigation needs to improve the efficiency and performance of the predicators. In this study, various attribute weighting and supervised clustering algorithms were employed to identify the main amino acid composition attributes, which can influence the substrate specificity of ATPase pumps, classify protein pumps and predict the substrate specificity of uncharacterized ATPase pumps. The results of this study indicate that both non-reduced coefficients pertaining to absorption and Cys extinction within 280 nm, the frequencies of hydrogen, Ala, Val, carbon, hydrophilic residues, the counts of Val, Asn, Ser, Arg, Phe, Tyr, hydrophilic residues, Phe-Phe, Ala-Ile, Phe-Leu, Val-Ala and length are specified as the most important amino acid attributes through applying the whole attribute weighting models. Here, learning algorithms engineered in a predictive machine (Naive Bays) is proposed to foresee the Q9LVV1 and O22180 substrate specificities (P-type ATPase like proteins) with 100 % prediction confidence. For the first time, our analysis demonstrated promising application of bioinformatics algorithms in classifying ATPases pumps. Moreover, we suggest the predictive systems that can assist towards the prediction of the substrate specificity of any new ATPase pumps with the maximum possible prediction confidence.
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Affiliation(s)
- Zahra Zinati
- />Department of Agroecology, College of Agriculture and Natural Resources of Darab, Shiraz University, Shiraz, Iran
| | - Abbas Alemzadeh
- />Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Amir Hossein KayvanJoo
- />Bonn-Aachen International Center for Information Technology B-IT, University of Bonn, Bonn, Germany
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16
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Sitsel O, Grønberg C, Autzen HE, Wang K, Meloni G, Nissen P, Gourdon P. Structure and Function of Cu(I)- and Zn(II)-ATPases. Biochemistry 2015; 54:5673-83. [PMID: 26132333 DOI: 10.1021/acs.biochem.5b00512] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper and zinc are micronutrients essential for the function of many enzymes while also being toxic at elevated concentrations. Cu(I)- and Zn(II)-transporting P-type ATPases of subclass 1B are of key importance for the homeostasis of these transition metals, allowing ion transport across cellular membranes at the expense of ATP. Recent biochemical studies and crystal structures have significantly improved our understanding of the transport mechanisms of these proteins, but many details about their structure and function remain elusive. Here we compare the Cu(I)- and Zn(II)-ATPases, scrutinizing the molecular differences that allow transport of these two distinct metal types, and discuss possible future directions of research in the field.
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Affiliation(s)
- Oleg Sitsel
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Christina Grønberg
- Department of Biomedical Sciences, University of Copenhagen , Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Henriette Elisabeth Autzen
- Department of Biomedical Sciences, University of Copenhagen , Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen , Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Gabriele Meloni
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen , Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.,Department of Experimental Medical Science, Lund University , Sölvegatan 19, SE-221 84 Lund, Sweden
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17
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Jen FEC, Djoko KY, Bent SJ, Day CJ, McEwan AG, Jennings MP. A genetic screen reveals a periplasmic copper chaperone required for nitrite reductase activity in pathogenicNeisseria. FASEB J 2015; 29:3828-38. [DOI: 10.1096/fj.15-270751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/18/2015] [Indexed: 01/21/2023]
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18
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Smith AT, Barupala D, Stemmler TL, Rosenzweig AC. A new metal binding domain involved in cadmium, cobalt and zinc transport. Nat Chem Biol 2015; 11:678-84. [PMID: 26192600 PMCID: PMC4543396 DOI: 10.1038/nchembio.1863] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
Abstract
The P1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P1B-ATPases is the presence of soluble metal binding domains that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. Here we report the biochemical, structural, and functional characterization of a new MBD from the Cupriavidus metallidurans P1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd2+, Co2+, or Zn2+ ions in distinct and unique sites, and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full length CzcP, truncated CzcP, and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Taken together, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P1B-ATPases.
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Affiliation(s)
- Aaron T Smith
- 1] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [2] Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Dulmini Barupala
- Department of Pharmaceutical Sciences and Cardiovascular Research Institute, Wayne State University, School of Medicine, Detroit, Michigan, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences and Cardiovascular Research Institute, Wayne State University, School of Medicine, Detroit, Michigan, USA
| | - Amy C Rosenzweig
- 1] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [2] Department of Chemistry, Northwestern University, Evanston, Illinois, USA
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19
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Chen Y, Yang F, Sun Z, Wang Q, Mi K, Deng H. Proteomic Analysis of Drug-Resistant Mycobacteria: Co-Evolution of Copper and INH Resistance. PLoS One 2015; 10:e0127788. [PMID: 26035302 PMCID: PMC4452738 DOI: 10.1371/journal.pone.0127788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/19/2015] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis, caused by the pathogen Mycobacterium tuberculosis, is a worldwide public health threat. Mycobacterium tuberculosis is capable of resisting various stresses in host cells, including high levels of ROS and copper ions. To better understand the resistance mechanisms of mycobacteria to copper, we generated a copper-resistant strain of Mycobacterium smegmatis, mc2155-Cu from the selection of copper sulfate treated-bacteria. The mc2155-Cu strain has a 5-fold higher resistance to copper sulfate and a 2-fold higher resistance to isoniazid (INH) than its parental strain mc2155, respectively. Quantitative proteomics was carried out to find differentially expressed proteins between mc2155 and mc2155-Cu. Among 345 differentially expressed proteins, copper-translocating P-type ATPase was up-regulated, while all other ABC transporters were down-regulated in mc2155-Cu, suggesting copper-translocating P-type ATPase plays a crucial role in copper resistance. Results also indicated that the down-regulation of metabolic enzymes and decreases in cellular NAD, FAD, mycothiol, and glutamine levels in mc2155-Cu were responsible for its slowing growth rate as compared to mc2155. Down-regulation of KatG2 expression in both protein and mRNA levels indicates the co-evolution of copper and INH resistance in copper resistance bacteria, and provides new evidence to understanding of the molecular mechanisms of survival of mycobacteria under stress conditions.
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Affiliation(s)
- Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhongyuan Sun
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qingtao Wang
- Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing, 100101, China
- * E-mail: (HTD); (KXM)
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (HTD); (KXM)
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20
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Mattle D, Zhang L, Sitsel O, Pedersen LT, Moncelli MR, Tadini-Buoninsegni F, Gourdon P, Rees DC, Nissen P, Meloni G. A sulfur-based transport pathway in Cu+-ATPases. EMBO Rep 2015; 16:728-40. [PMID: 25956886 PMCID: PMC4467857 DOI: 10.15252/embr.201439927] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/13/2015] [Accepted: 03/31/2015] [Indexed: 11/09/2022] Open
Abstract
Cells regulate copper levels tightly to balance the biogenesis and integrity of copper centers in vital enzymes against toxic levels of copper. PIB -type Cu(+)-ATPases play a central role in copper homeostasis by catalyzing the selective translocation of Cu(+) across cellular membranes. Crystal structures of a copper-free Cu(+)-ATPase are available, but the mechanism of Cu(+) recognition, binding, and translocation remains elusive. Through X-ray absorption spectroscopy, ATPase activity assays, and charge transfer measurements on solid-supported membranes using wild-type and mutant forms of the Legionella pneumophila Cu(+)-ATPase (LpCopA), we identify a sulfur-lined metal transport pathway. Structural analysis indicates that Cu(+) is bound at a high-affinity transmembrane-binding site in a trigonal-planar coordination with the Cys residues of the conserved CPC motif of transmembrane segment 4 (C382 and C384) and the conserved Met residue of transmembrane segment 6 (M717 of the MXXXS motif). These residues are also essential for transport. Additionally, the studies indicate essential roles of other conserved intramembranous polar residues in facilitating copper binding to the high-affinity site and subsequent release through the exit pathway.
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Affiliation(s)
- Daniel Mattle
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Limei Zhang
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Oleg Sitsel
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Lotte Thue Pedersen
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Maria Rosa Moncelli
- Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | | | - Pontus Gourdon
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark
| | - Gabriele Meloni
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Department of Molecular Biology and Genetics, Danish National Research Foundation Aarhus University, Aarhus C, Denmark Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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21
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Evolution of a plant-specific copper chaperone family for chloroplast copper homeostasis. Proc Natl Acad Sci U S A 2014; 111:E5480-7. [PMID: 25468978 DOI: 10.1073/pnas.1421545111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Metallochaperones traffic copper (Cu(+)) from its point of entry at the plasma membrane to its destination. In plants, one destination is the chloroplast, which houses plastocyanin, a Cu-dependent electron transfer protein involved in photosynthesis. We present a previously unidentified Cu(+) chaperone that evolved early in the plant lineage by an alternative-splicing event of the pre-mRNA encoding the chloroplast P-type ATPase in Arabidopsis 1 (PAA1). In several land plants, recent duplication events created a separate chaperone-encoding gene coincident with loss of alternative splicing. The plant-specific Cu(+) chaperone delivers Cu(+) with specificity for PAA1, which is flipped in the envelope relative to prototypical bacterial ATPases, compatible with a role in Cu(+) import into the stroma and consistent with the canonical catalytic mechanism of these enzymes. The ubiquity of the chaperone suggests conservation of this Cu(+)-delivery mechanism and provides a unique snapshot into the evolution of a Cu(+) distribution pathway. We also provide evidence for an interaction between PAA2, the Cu(+)-ATPase in thylakoids, and the Cu(+)-chaperone for Cu/Zn superoxide dismutase (CCS), uncovering a Cu(+) network that has evolved to fine-tune Cu(+) distribution.
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22
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Wang K, Sitsel O, Meloni G, Autzen HE, Andersson M, Klymchuk T, Nielsen AM, Rees DC, Nissen P, Gourdon P. Structure and mechanism of Zn2+-transporting P-type ATPases. Nature 2014; 514:518-22. [PMID: 25132545 PMCID: PMC4259247 DOI: 10.1038/nature13618] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/25/2014] [Indexed: 12/23/2022]
Abstract
Zinc is an essential micronutrient for all living organisms. It is required for signalling and proper functioning of a range of proteins involved in, for example, DNA binding and enzymatic catalysis. In prokaryotes and photosynthetic eukaryotes, Zn(2+)-transporting P-type ATPases of class IB (ZntA) are crucial for cellular redistribution and detoxification of Zn(2+) and related elements. Here we present crystal structures representing the phosphoenzyme ground state (E2P) and a dephosphorylation intermediate (E2·Pi) of ZntA from Shigella sonnei, determined at 3.2 Å and 2.7 Å resolution, respectively. The structures reveal a similar fold to Cu(+)-ATPases, with an amphipathic helix at the membrane interface. A conserved electronegative funnel connects this region to the intramembranous high-affinity ion-binding site and may promote specific uptake of cellular Zn(2+) ions by the transporter. The E2P structure displays a wide extracellular release pathway reaching the invariant residues at the high-affinity site, including C392, C394 and D714. The pathway closes in the E2·Pi state, in which D714 interacts with the conserved residue K693, which possibly stimulates Zn(2+) release as a built-in counter ion, as has been proposed for H(+)-ATPases. Indeed, transport studies in liposomes provide experimental support for ZntA activity without counter transport. These findings suggest a mechanistic link between PIB-type Zn(2+)-ATPases and PIII-type H(+)-ATPases and at the same time show structural features of the extracellular release pathway that resemble PII-type ATPases such as the sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPase (SERCA) and Na(+), K(+)-ATPase. These findings considerably increase our understanding of zinc transport in cells and represent new possibilities for biotechnology and biomedicine.
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Affiliation(s)
- Kaituo Wang
- 1] Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark [2] Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark (K.W. and P.G.); Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden (P.G.). [3]
| | - Oleg Sitsel
- 1] Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark [2]
| | - Gabriele Meloni
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Henriette Elisabeth Autzen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Magnus Andersson
- Science for Life Laboratory, Department of Theoretical Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, SE-171 21 Solna, Sweden
| | - Tetyana Klymchuk
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Anna Marie Nielsen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering and Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Pontus Gourdon
- 1] Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark [2] Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark (K.W. and P.G.); Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden (P.G.)
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Smith AT, Smith KP, Rosenzweig AC. Diversity of the metal-transporting P1B-type ATPases. J Biol Inorg Chem 2014; 19:947-60. [PMID: 24729073 PMCID: PMC4119550 DOI: 10.1007/s00775-014-1129-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/21/2014] [Indexed: 01/23/2023]
Abstract
The P1B-ATPases are integral membrane proteins that couple ATP hydrolysis to metal cation transport. Widely distributed across all domains of life, these enzymes have been previously shown to transport copper, zinc, cobalt, and other thiophilic heavy metals. Recent data suggest that these enzymes may also be involved in nickel and/or iron transport. Here we have exploited large amounts of genomic data to examine and classify the various P1B-ATPase subfamilies. Specifically, we have combined new methods of data partitioning and network visualization known as Transitivity Clustering and Protein Similarity Networks with existing biochemical data to examine properties such as length, speciation, and metal-binding motifs of the P1B-ATPase subfamily sequences. These data reveal interesting relationships among the enzyme sequences of previously established subfamilies, indicate the presence of two new subfamilies, and suggest the existence of new regulatory elements in certain subfamilies. Taken together, these findings underscore the importance of P1B-ATPases in homeostasis of nearly every biologically relevant transition metal and provide an updated framework for future studies.
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Affiliation(s)
- Aaron T. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Kyle P. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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24
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Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol 2013; 21:43-8. [PMID: 24317491 DOI: 10.1038/nsmb.2721] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/11/2013] [Indexed: 11/09/2022]
Abstract
Heavy metals in cells are typically regulated by PIB-type ATPases. The first structure of the class, a Cu(+)-ATPase from Legionella pneumophila (LpCopA), outlined a copper transport pathway across the membrane, which was inferred to be occluded. Here we show by molecular dynamics simulations that extracellular water solvated the transmembrane (TM) domain, results indicative of a Cu(+)-release pathway. Furthermore, a new LpCopA crystal structure determined at 2.8-Å resolution, trapped in the preceding E2P state, delineated the same passage, and site-directed-mutagenesis activity assays support a functional role for the conduit. The structural similarities between the TM domains of the two conformations suggest that Cu(+)-ATPases couple dephosphorylation and ion extrusion differently than do the well-characterized PII-type ATPases. The ion pathway explains why certain Menkes' and Wilson's disease mutations impair protein function and points to a site for inhibitors targeting pathogens.
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25
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Kalodimos C. Regulation of Biological Function by Allosteric Interactions. J Mol Biol 2013; 425:2277-8. [DOI: 10.1016/j.jmb.2013.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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