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Sitsel O, Wang Z, Janning P, Kroczek L, Wagner T, Raunser S. Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations. Nat Microbiol 2024; 9:390-404. [PMID: 38238469 PMCID: PMC10847048 DOI: 10.1038/s41564-023-01571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/29/2023] [Indexed: 02/04/2024]
Abstract
Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogen Yersinia entomophaga, we demonstrate that a specialized subset of these cells produces a complex toxin cocktail, including the nearly ribosome-sized Tc toxin YenTc, which is subsequently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the Tc toxin export process by a T10SS, identifying that T10SSs operate via a previously unknown lytic mode of action and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major pathogens, we anticipate that our findings may model an important aspect of pathogenesis in bacteria with substantial impact on agriculture and healthcare.
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Affiliation(s)
- Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lara Kroczek
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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2
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Parker JL, Kato T, Kuteyi G, Sitsel O, Newstead S. Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1. Nat Struct Mol Biol 2023; 30:1786-1793. [PMID: 37482561 PMCID: PMC10643130 DOI: 10.1038/s41594-023-01039-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023]
Abstract
In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Takafumi Kato
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Oleg Sitsel
- Department of Biochemistry, University of Oxford, Oxford, UK
- Max Planck Institute of Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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3
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Rice G, Wagner T, Stabrin M, Sitsel O, Prumbaum D, Raunser S. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods 2023:10.1038/s41592-023-01878-z. [PMID: 37188953 DOI: 10.1038/s41592-023-01878-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.
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Affiliation(s)
- Gavin Rice
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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4
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Vinayagam D, Quentin D, Yu-Strzelczyk J, Sitsel O, Merino F, Stabrin M, Hofnagel O, Yu M, Ledeboer MW, Nagel G, Malojcic G, Raunser S. Structural basis of TRPC4 regulation by calmodulin and pharmacological agents. eLife 2020; 9:e60603. [PMID: 33236980 PMCID: PMC7735759 DOI: 10.7554/elife.60603] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca2+ signaling. Inhibition of TRPCs by small molecules was shown to be promising in treating renal diseases. In cells, the channels are regulated by calmodulin (CaM). Molecular details of both CaM and drug binding have remained elusive so far. Here, we report structures of TRPC4 in complex with three pyridazinone-based inhibitors and CaM. The structures reveal that all the inhibitors bind to the same cavity of the voltage-sensing-like domain and allow us to describe how structural changes from the ligand-binding site can be transmitted to the central ion-conducting pore of TRPC4. CaM binds to the rib helix of TRPC4, which results in the ordering of a previously disordered region, fixing the channel in its closed conformation. This represents a novel CaM-induced regulatory mechanism of canonical TRP channels.
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Affiliation(s)
| | - Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Jing Yu-Strzelczyk
- Department of Neurophysiology, Physiological Institute, Julius-Maximilians-Universität WürzburgWürzburgGermany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | | | | | - Georg Nagel
- Department of Neurophysiology, Physiological Institute, Julius-Maximilians-Universität WürzburgWürzburgGermany
| | | | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
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5
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Abstract
Lifeact is a short actin-binding peptide that is used to visualize filamentous actin (F-actin) structures in live eukaryotic cells using fluorescence microscopy. However, this popular probe has been shown to alter cellular morphology by affecting the structure of the cytoskeleton. The molecular basis for such artefacts is poorly understood. Here, we determined the high-resolution structure of the Lifeact-F-actin complex using electron cryo-microscopy (cryo-EM). The structure reveals that Lifeact interacts with a hydrophobic binding pocket on F-actin and stretches over 2 adjacent actin subunits, stabilizing the DNase I-binding loop (D-loop) of actin in the closed conformation. Interestingly, the hydrophobic binding site is also used by actin-binding proteins, such as cofilin and myosin and actin-binding toxins, such as the hypervariable region of TccC3 (TccC3HVR) from Photorhabdus luminescens and ExoY from Pseudomonas aeruginosa. In vitro binding assays and activity measurements demonstrate that Lifeact indeed competes with these proteins, providing an explanation for the altering effects of Lifeact on cell morphology in vivo. Finally, we demonstrate that the affinity of Lifeact to F-actin can be increased by introducing mutations into the peptide, laying the foundation for designing improved actin probes for live cell imaging.
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Affiliation(s)
- Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- * E-mail:
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6
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Roderer D, Bröcker F, Sitsel O, Kaplonek P, Leidreiter F, Seeberger PH, Raunser S. Glycan-dependent cell adhesion mechanism of Tc toxins. Nat Commun 2020; 11:2694. [PMID: 32483155 PMCID: PMC7264150 DOI: 10.1038/s41467-020-16536-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/11/2020] [Indexed: 01/19/2023] Open
Abstract
Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor–toxin interaction and membrane permeation, TcB and TcC form a toxin-encapsulating cocoon. While the mechanisms of holotoxin assembly and pore formation have been described, little is known about receptor binding of TcAs. Here, we identify heparins/heparan sulfates and Lewis antigens as receptors for different TcAs from insect and human pathogens. Glycan array screening reveals that all tested TcAs bind negatively charged heparins. Cryo-EM structures of Morganella morganii TcdA4 and Xenorhabdus nematophila XptA1 reveal that heparins/heparan sulfates unexpectedly bind to different regions of the shell domain, including receptor-binding domains. In addition, Photorhabdus luminescens TcdA1 binds to Lewis antigens with micromolar affinity. Here, the glycan interacts with the receptor-binding domain D of the toxin. Our results suggest a glycan dependent association mechanism of Tc toxins on the host cell surface. Although Tc toxins are a major class of bacterial toxin translocation systems, little is known about their receptor binding. Here, the authors identify heparins/heparan sulfates and Lewis antigens as receptors for different Tc toxins, determine cryo-EM structures of three toxin-glycan complexes and propose a two-step cell adhesion mechanism for Tc toxins.
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Affiliation(s)
- Daniel Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Felix Bröcker
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany.,Vaxxilon Deutschland GmbH, 12489, Berlin, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Paulina Kaplonek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Franziska Leidreiter
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.
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7
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Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P, Sitsel O, Raisch T, Prumbaum D, Quentin D, Roderer D, Tacke S, Siebolds B, Schubert E, Shaikh TR, Lill P, Gatsogiannis C, Raunser S. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun Biol 2019; 2:218. [PMID: 31240256 PMCID: PMC6584505 DOI: 10.1038/s42003-019-0437-z] [Citation(s) in RCA: 622] [Impact Index Per Article: 124.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/24/2019] [Indexed: 11/23/2022] Open
Abstract
Selecting particles from digital micrographs is an essential step in single-particle electron cryomicroscopy (cryo-EM). As manual selection of complete datasets-typically comprising thousands of particles-is a tedious and time-consuming process, numerous automatic particle pickers have been developed. However, non-ideal datasets pose a challenge to particle picking. Here we present the particle picking software crYOLO which is based on the deep-learning object detection system You Only Look Once (YOLO). After training the network with 200-2500 particles per dataset it automatically recognizes particles with high recall and precision while reaching a speed of up to five micrographs per second. Further, we present a general crYOLO network able to pick from previously unseen datasets, allowing for completely automated on-the-fly cryo-EM data preprocessing during data acquisition. crYOLO is available as a standalone program under http://sphire.mpg.de/ and is distributed as part of the image processing workflow in SPHIRE.
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Affiliation(s)
- Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Toshio Moriya
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Claudia Antoni
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Amir Apelbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Philine Hagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Daniel Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sebastian Tacke
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Birte Siebolds
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Evelyn Schubert
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Tanvir R. Shaikh
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Pascal Lill
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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8
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9
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Grønberg C, Sitsel O, Lindahl E, Gourdon P, Andersson M. Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport. Biophys J 2016; 111:2417-2429. [PMID: 27926843 PMCID: PMC5153542 DOI: 10.1016/j.bpj.2016.10.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 12/23/2022] Open
Abstract
Cu+-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu+-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu+ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu+ delivery. Mutational analyses and simulations in the presence and absence of Cu+ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu+-transporting P-type ATPases.
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Affiliation(s)
| | | | - Erik Lindahl
- Biochemistry & Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Pontus Gourdon
- University of Copenhagen, Copenhagen, Denmark; Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Magnus Andersson
- Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
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10
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Abstract
Determining structures of membrane proteins remains a significant challenge. A technique utilizing high lipid-detergent concentrations ("HiLiDe") circumvents the major bottlenecks of current membrane protein crystallization methods. During HiLiDe, the protein-lipid-detergent ratio is varied in a controlled way in order to yield initial crystal hits, which may be subsequently optimized by variation of the crystallization conditions and/or utilizing secondary detergents. HiLiDe preserves the advantages of classical lipid-based methods, yet is compatible with both the vapor diffusion and batch crystallization techniques. The method has been applied with particular success to P-type ATPases.
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Affiliation(s)
- Oleg Sitsel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Germany
| | - Xiangyu Liu
- School of Medicine, Tsinghua University, Beijing, China
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Germany
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-22184, Lund, Sweden
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11
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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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12
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Bublitz M, Nass K, Drachmann ND, Markvardsen AJ, Gutmann MJ, Barends TRM, Mattle D, Shoeman RL, Doak RB, Boutet S, Messerschmidt M, Seibert MM, Williams GJ, Foucar L, Reinhard L, Sitsel O, Gregersen JL, Clausen JD, Boesen T, Gotfryd K, Wang KT, Olesen C, Møller JV, Nissen P, Schlichting I. Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser. IUCrJ 2015; 2:409-20. [PMID: 26175901 PMCID: PMC4491313 DOI: 10.1107/s2052252515008969] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/08/2015] [Indexed: 05/24/2023]
Abstract
Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein-ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.
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Affiliation(s)
- Maike Bublitz
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Karol Nass
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Nikolaj D. Drachmann
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | | | - Matthias J. Gutmann
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot OX11 0QX, England
| | - Thomas R. M. Barends
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Daniel Mattle
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marvin M. Seibert
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Linda Reinhard
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Oleg Sitsel
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Jonas L. Gregersen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Johannes D. Clausen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Kai-Tuo Wang
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
| | - Claus Olesen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Jesper V. Møller
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Centre for Membrane Pumps in Cells and Disease – PUMPkin, Danish National Research Foundation, Aarhus University, Gustav Wieds Vej 10c, 8000 Aarhus C, Denmark
- DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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13
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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 DOI: 10.15252/embr.201439927] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [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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14
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Nass K, Foucar L, Barends TRM, Hartmann E, Botha S, Shoeman RL, Doak RB, Alonso-Mori R, Aquila A, Bajt S, Barty A, Bean R, Beyerlein KR, Bublitz M, Drachmann N, Gregersen J, Jönsson HO, Kabsch W, Kassemeyer S, Koglin JE, Krumrey M, Mattle D, Messerschmidt M, Nissen P, Reinhard L, Sitsel O, Sokaras D, Williams GJ, Hau-Riege S, Timneanu N, Caleman C, Chapman HN, Boutet S, Schlichting I. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. J Synchrotron Radiat 2015; 22:225-38. [PMID: 25723924 DOI: 10.1107/s1600577515002349] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/03/2015] [Indexed: 05/23/2023]
Abstract
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.
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Affiliation(s)
- Karol Nass
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Elisabeth Hartmann
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Sabine Botha
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Robert L Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - R Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Saša Bajt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maike Bublitz
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Nikolaj Drachmann
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Jonas Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - H Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala 75120, Sweden
| | - Wolfgang Kabsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Stephan Kassemeyer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Jason E Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Krumrey
- Physikalisch-Technische Bundesanstalt (PTB), Abbestrasse 2-12, 10587 Berlin, Germany
| | - Daniel Mattle
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Marc Messerschmidt
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Linda Reinhard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Oleg Sitsel
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Dimosthenis Sokaras
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan Hau-Riege
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala 75120, Sweden
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Andersson M, Mattle D, Sitsel O, Nielsen AM, Lindahl E, White SH, Nissen P, Gourdon P. Transport Pathway in Cu+ P-Type ATPases. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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17
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Mattle D, Sitsel O, Autzen HE, Meloni G, Gourdon P, Nissen P. On allosteric modulation of P-type Cu(+)-ATPases. J Mol Biol 2013; 425:2299-308. [PMID: 23500486 DOI: 10.1016/j.jmb.2013.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
P-type ATPases perform active transport of various compounds across biological membranes and are crucial for ion homeostasis and the asymmetric composition of lipid bilayers. Although their functional cycle share principles of phosphoenzyme intermediates, P-type ATPases also show subclass-specific sequence motifs and structural elements that are linked to transport specificity and mechanistic modulation. Here we provide an overview of the Cu(+)-transporting ATPases (of subclass PIB) and compare them to the well-studied sarco(endo)plasmic reticulum Ca(2+)-ATPase (of subclass PIIA). Cu(+) ions in the cell are delivered by soluble chaperones to Cu(+)-ATPases, which expose a putative "docking platform" at the intracellular interface. Cu(+)-ATPases also contain heavy-metal binding domains providing a basis for allosteric control of pump activity. Database analysis of Cu(+) ligating residues questions a two-site model of intramembranous Cu(+) binding, and we suggest an alternative role for the proposed second site in copper translocation and proton exchange. The class-specific features demonstrate that topological diversity in P-type ATPases may tune a general energy coupling scheme to the translocation of compounds with remarkably different properties.
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Affiliation(s)
- Daniel Mattle
- 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
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18
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Abstract
Abstract
The human copper exporters ATP7A and ATP7B contain domains common to all P-type ATPases as well as class-specific features such as six sequential heavy-metal binding domains (HMBD1–HMBD6) and a type-specific constellation of transmembrane helices. Despite the medical significance of ATP7A and ATP7B related to Menkes and Wilson diseases, respectively, structural information has only been available for isolated, soluble domains. Here we present homology models based on the existing structures of soluble domains and the recently determined structure of the homologous LpCopA from the bacterium Legionella pneumophila. The models and sequence analyses show that the domains and residues involved in the catalytic phosphorylation events and copper transfer are highly conserved. In addition, there are only minor differences in the core structures of the two human proteins and the bacterial template, allowing protein-specific properties to be addressed. Furthermore, the mapping of known disease-causing missense mutations indicates that among the heavy-metal binding domains, HMBD5 and HMBD6 are the most crucial for function, thus mimicking the single or dual HMBDs found in most copper-specific P-type ATPases. We propose a structural arrangement of the HMBDs and how they may interact with the core of the proteins to achieve autoinhibition.
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