1
|
Dyla M, Kjærgaard M, Poulsen H, Nissen P. Structure and Mechanism of P-Type ATPase Ion Pumps. Annu Rev Biochem 2020; 89:583-603. [PMID: 31874046 DOI: 10.1146/annurev-biochem-010611-112801] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
P-type ATPases are found in all kingdoms of life and constitute a wide range of cation transporters, primarily for H+, Na+, K+, Ca2+, and transition metal ions such as Cu(I), Zn(II), and Cd(II). They have been studied through a wide range of techniques, and research has gained very significant insight on their transport mechanism and regulation. Here, we review the structure, function, and dynamics of P2-ATPases including Ca2+-ATPases and Na,K-ATPase. We highlight mechanisms of functional transitions that are associated with ion exchange on either side of the membrane and how the functional cycle is regulated by interaction partners, autoregulatory domains, and off-cycle states. Finally, we discuss future perspectives based on emerging techniques and insights.
Collapse
Affiliation(s)
- Mateusz Dyla
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; .,Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic European Molecular Biology Laboratory (EMBL) Partnership for Molecular Medicine, 8000 Aarhus, Denmark
| | - Magnus Kjærgaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; .,Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic European Molecular Biology Laboratory (EMBL) Partnership for Molecular Medicine, 8000 Aarhus, Denmark
| | - Hanne Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; .,Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic European Molecular Biology Laboratory (EMBL) Partnership for Molecular Medicine, 8000 Aarhus, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; .,Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic European Molecular Biology Laboratory (EMBL) Partnership for Molecular Medicine, 8000 Aarhus, Denmark
| |
Collapse
|
2
|
What ATP binding does to the Ca 2+ pump and how nonproductive phosphoryl transfer is prevented in the absence of Ca 2. Proc Natl Acad Sci U S A 2020; 117:18448-18458. [PMID: 32675243 DOI: 10.1073/pnas.2006027117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Under physiological conditions, most Ca2+-ATPase (SERCA) molecules bind ATP before binding the Ca2+ transported. SERCA has a high affinity for ATP even in the absence of Ca2+, and ATP accelerates Ca2+ binding at pH values lower than 7, where SERCA is in the E2 state with low-affinity Ca2+-binding sites. Here we describe the crystal structure of SERCA2a, the isoform predominant in cardiac muscle, in the E2·ATP state at 3.0-Å resolution. In the crystal structure, the arrangement of the cytoplasmic domains is distinctly different from that in canonical E2. The A-domain now takes an E1 position, and the N-domain occupies exactly the same position as that in the E1·ATP·2Ca2+ state relative to the P-domain. As a result, ATP is properly delivered to the phosphorylation site. Yet phosphoryl transfer never takes place without the filling of the two transmembrane Ca2+-binding sites. The present crystal structure explains what ATP binding itself does to SERCA and how nonproductive phosphorylation is prevented in E2.
Collapse
|
3
|
Kaczmarski JA, Hong NS, Mukherjee B, Wey LT, Rourke L, Förster B, Peat TS, Price GD, Jackson CJ. Structural Basis for the Allosteric Regulation of the SbtA Bicarbonate Transporter by the P II-like Protein, SbtB, from Cyanobium sp. PCC7001. Biochemistry 2019; 58:5030-5039. [PMID: 31746199 DOI: 10.1021/acs.biochem.9b00880] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyanobacteria have evolved a suite of enzymes and inorganic carbon (Ci) transporters that improve photosynthetic performance by increasing the localized concentration of CO2 around the primary CO2-fixating enzyme, Rubisco. This CO2-concentrating mechanism (CCM) is highly regulated, responds to illumination/darkness cycles, and allows cyanobacteria to thrive under limiting Ci conditions. While the transcriptional control of CCM activity is well understood, less is known about how regulatory proteins might allosterically regulate Ci transporters in response to changing conditions. Cyanobacterial sodium-dependent bicarbonate transporters (SbtAs) are inhibited by PII-like regulatory proteins (SbtBs), with the inhibitory effect being modulated by adenylnucleotides. Here, we used isothermal titration calorimetry to show that SbtB from Cyanobium sp. PCC7001 (SbtB7001) binds AMP, ADP, cAMP, and ATP with micromolar-range affinities. X-ray crystal structures of apo and nucleotide-bound SbtB7001 revealed that while AMP, ADP, and cAMP have little effect on the SbtB7001 structure, binding of ATP stabilizes the otherwise flexible T-loop, and that the flexible C-terminal C-loop adopts several distinct conformations. We also show that ATP binding affinity is increased 10-fold in the presence of Ca2+, and we present an X-ray crystal structure of Ca2+ATP:SbtB7001 that shows how this metal ion facilitates additional stabilizing interactions with the apex of the T-loop. We propose that the Ca2+ATP-induced conformational change observed in SbtB7001 is important for allosteric regulation of SbtA activity by SbtB and is consistent with changing adenylnucleotide levels in illumination/darkness cycles.
Collapse
Affiliation(s)
- Joe A Kaczmarski
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
| | - Nan-Sook Hong
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
| | - Bratati Mukherjee
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Laura T Wey
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Loraine Rourke
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Britta Förster
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Thomas S Peat
- CSIRO Biomedical Program , 343 Royal Parade , Parkville , VIC 3052 , Australia
| | - G Dean Price
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Colin J Jackson
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
| |
Collapse
|
4
|
Aluminum inhibits the plasma membrane and sarcoplasmic reticulum Ca 2+-ATPases by different mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1580-1588. [PMID: 29859139 DOI: 10.1016/j.bbamem.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/28/2018] [Accepted: 05/25/2018] [Indexed: 11/21/2022]
Abstract
Aluminum (Al3+) is involved in the pathophysiology of neurodegenerative disorders. The mechanisms that have been proposed to explain the action of Al3+ toxicity are linked to changes in the cellular calcium homeostasis, placing the transporting calcium pumps as potential targets. The aim of this work was to study the molecular inhibitory mechanism of Al3+ on Ca2+-ATPases such as the plasma membrane and the sarcoplasmic reticulum calcium pumps (PMCA and SERCA, respectively). These P-ATPases transport Ca2+ actively from the cytoplasm towards the extracellular medium and to the sarcoplasmic reticulum, respectively. For this purpose, we performed enzymatic measurements of the effect of Al3+ on purified preparations of PMCA and SERCA. Our results show that Al3+ is an irreversible inhibitor of PMCA and a slowly-reversible inhibitor of SERCA. The binding of Al3+ is affected by Ca2+ in SERCA, though not in PMCA. Al3+ prevents the phosphorylation of SERCA and, conversely, the dephosphorylation of PMCA. The dephosphorylation time courses of the complex formed by PMCA and Al3+ (EPAl) in the presence of ADP or ATP show that EPAl is composed mainly by the conformer E2P. This work shows for the first time a distinct mechanism of Al3+ inhibition that involves different intermediates of the reaction cycle of these two Ca2+-ATPases.
Collapse
|
5
|
Dyla M, Terry DS, Kjaergaard M, Sørensen TLM, Lauwring Andersen J, Andersen JP, Rohde Knudsen C, Altman RB, Nissen P, Blanchard SC. Dynamics of P-type ATPase transport revealed by single-molecule FRET. Nature 2017; 551:346-351. [PMID: 29144454 DOI: 10.1038/nature24296] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023]
Abstract
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled to transmembrane helices so as to expose ion binding sites to alternate sides of the membrane. Here, we have used single-molecule fluorescence resonance energy transfer to directly observe conformational changes associated with the functional transitions in the Listeria monocytogenes Ca2+-ATPase (LMCA1), an orthologue of eukaryotic Ca2+-ATPases. We identify key intermediates with no known crystal structures and show that Ca2+ efflux by LMCA1 is rate-limited by phosphoenzyme formation. The transport process involves reversible steps and an irreversible step that follows release of ADP and extracellular release of Ca2+.
Collapse
Affiliation(s)
- Mateusz Dyla
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Magnus Kjaergaard
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas L-M Sørensen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jacob Lauwring Andersen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jens P Andersen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| |
Collapse
|
6
|
Protein–phospholipid interplay revealed with crystals of a calcium pump. Nature 2017; 545:193-198. [DOI: 10.1038/nature22357] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/12/2017] [Indexed: 11/08/2022]
|
7
|
Liu M, Dong F, Zhang W, Nie X, Wei H, Sun S, Zhong X, Liu Y, Wang D. Contribution of surface functional groups and interface interaction to biosorption of strontium ions by Saccharomyces cerevisiae under culture conditions. RSC Adv 2017. [DOI: 10.1039/c7ra08416a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Surface functional group contributions to biosorption of strontium ions bySaccharomyces cerevisiaeas well as interface interactions were elucidated.
Collapse
Affiliation(s)
- Mingxue Liu
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Faqin Dong
- Key Laboratory of Solid Waste Treatment and Resource Recycle
- Ministry of Education of China
- Mianyang 621010
- China
| | - Wei Zhang
- Key Laboratory of Solid Waste Treatment and Resource Recycle
- Ministry of Education of China
- Mianyang 621010
- China
| | - Xiaoqin Nie
- China Fundamental Science on Nuclear Wastes and Environmental Safety Laboratory
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Hongfu Wei
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Shiyong Sun
- Key Laboratory of Solid Waste Treatment and Resource Recycle
- Ministry of Education of China
- Mianyang 621010
- China
| | - Xiaomei Zhong
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Yuqi Liu
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Danni Wang
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| |
Collapse
|
8
|
Bredeston LM, González Flecha FL. The promiscuous phosphomonoestearase activity of Archaeoglobus fulgidus CopA, a thermophilic Cu+ transport ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1471-8. [PMID: 27086711 DOI: 10.1016/j.bbamem.2016.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/01/2016] [Accepted: 04/13/2016] [Indexed: 11/19/2022]
Abstract
Membrane transport P-type ATPases display two characteristic enzymatic activities: a principal ATPase activity provides the driving force for ion transport across biological membranes, whereas a promiscuous secondary activity catalyzes the hydrolysis of phosphate monoesters. This last activity is usually denoted as the phosphatase activity of P-ATPases. In the present study, we characterize the phosphatase activity of the Cu(+)-transport ATPase from Archaeglobus fulgidus (Af-CopA) and compare it with the principal ATPase activity. Our results show that the phosphatase turnover number was 20 times higher than that corresponding to the ATPase activity, but it is compensated by a high value of Km, producing a less efficient catalysis for pNPP. This secondary activity is enhanced by Mg(2+) (essential activator) and phospholipids (non-essential activator), and inhibited by salts and Cu(+). Transition state analysis of the catalyzed and noncatalyzed hydrolysis of pNPP indicates that Af-CopA enhances the reaction rates by a factor of 10(5) (ΔΔG(‡)=38 kJ/mol) mainly by reducing the enthalpy of activation (ΔΔH(‡)=30 kJ/mol), whereas the entropy of activation is less negative on the enzyme than in solution. For the ATPase activity, the decrease in the enthalpic component of the barrier is higher (ΔΔH(‡)=39 kJ/mol) and the entropic component is small on both the enzyme and in solution. These results suggest that different mechanisms are involved in the transference of the phosphoryl group of p-nitrophenyl phosphate and ATP.
Collapse
Affiliation(s)
- Luis M Bredeston
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - F Luis González Flecha
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.
| |
Collapse
|
9
|
Yamasaki K, Daiho T, Danko S, Suzuki H. Assembly of a Tyr122 Hydrophobic Cluster in Sarcoplasmic Reticulum Ca2+-ATPase Synchronizes Ca2+ Affinity Reduction and Release with Phosphoenzyme Isomerization. J Biol Chem 2015; 290:27868-79. [PMID: 26442589 DOI: 10.1074/jbc.m115.693770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Indexed: 11/06/2022] Open
Abstract
The mechanism whereby events in and around the catalytic site/head of Ca(2+)-ATPase effect Ca(2+) release to the lumen from the transmembrane helices remains elusive. We developed a method to determine deoccluded bound Ca(2+) by taking advantage of its rapid occlusion upon formation of E1PCa2 and of stabilization afforded by a high concentration of Ca(2+). The assay is applicable to minute amounts of Ca(2+)-ATPase expressed in COS-1 cells. It was validated by measuring the Ca(2+) binding properties of unphosphorylated Ca(2+)-ATPase. The method was then applied to the isomerization of the phosphorylated intermediate associated with the Ca(2+) release process E1PCa2 → E2PCa2 → E2P + 2Ca(2+). In the wild type, Ca(2+) release occurs concomitantly with EP isomerization fitting with rate-limiting isomerization (E1PCa2 → E2PCa2) followed by very rapid Ca(2+) release. In contrast, with alanine mutants of Leu(119) and Tyr(122) on the cytoplasmic part of the second transmembrane helix (M2) and Ile(179) on the A domain, Ca(2+) release in 10 μm Ca(2+) lags EP isomerization, indicating the presence of a transient E2P state with bound Ca(2+). The results suggest that these residues function in Ca(2+) affinity reduction in E2P, likely via a structural rearrangement at the cytoplasmic part of M2 and a resulting association with the A and P domains, therefore leading to Ca(2+) release.
Collapse
Affiliation(s)
- Kazuo Yamasaki
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Takashi Daiho
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Stefania Danko
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Hiroshi Suzuki
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| |
Collapse
|
10
|
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] [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.
Collapse
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
| |
Collapse
|
11
|
Bublitz M, Musgaard M, Poulsen H, Thøgersen L, Olesen C, Schiøtt B, Morth JP, Møller JV, Nissen P. Ion pathways in the sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem 2013; 288:10759-65. [PMID: 23400778 DOI: 10.1074/jbc.r112.436550] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) is a transmembrane ion transporter belonging to the P(II)-type ATPase family. It performs the vital task of re-sequestering cytoplasmic Ca(2+) to the sarco/endoplasmic reticulum store, thereby also terminating Ca(2+)-induced signaling such as in muscle contraction. This minireview focuses on the transport pathways of Ca(2+) and H(+) ions across the lipid bilayer through SERCA. The ion-binding sites of SERCA are accessible from either the cytoplasm or the sarco/endoplasmic reticulum lumen, and the Ca(2+) entry and exit channels are both formed mainly by rearrangements of four N-terminal transmembrane α-helices. Recent improvements in the resolution of the crystal structures of rabbit SERCA1a have revealed a hydrated pathway in the C-terminal transmembrane region leading from the ion-binding sites to the cytosol. A comparison of different SERCA conformations reveals that this C-terminal pathway is exclusive to Ca(2+)-free E2 states, suggesting that it may play a functional role in proton release from the ion-binding sites. This is in agreement with molecular dynamics simulations and mutational studies and is in striking analogy to a similar pathway recently described for the related sodium pump. We therefore suggest a model for the ion exchange mechanism in P(II)-ATPases including not one, but two cytoplasmic pathways working in concert.
Collapse
Affiliation(s)
- Maike Bublitz
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Aarhus University, DK-8000 Aarhus C, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Sørensen DM, Møller AB, Jakobsen MK, Jensen MK, Vangheluwe P, Buch-Pedersen MJ, Palmgren MG. Ca2+ induces spontaneous dephosphorylation of a novel P5A-type ATPase. J Biol Chem 2012; 287:28336-48. [PMID: 22730321 DOI: 10.1074/jbc.m112.387191] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
P5 ATPases constitute the least studied group of P-type ATPases, an essential family of ion pumps in all kingdoms of life. Although P5 ATPases are present in every eukaryotic genome analyzed so far, they have remained orphan pumps, and their biochemical function is obscure. We show that a P5A ATPase from barley, HvP5A1, locates to the endoplasmic reticulum and is able to rescue knock-out mutants of P5A genes in both Arabidopsis thaliana and Saccharomyces cerevisiae. HvP5A1 spontaneously forms a phosphorylated reaction cycle intermediate at the catalytic residue Asp-488, whereas, among all plant nutrients tested, only Ca(2+) triggers dephosphorylation. Remarkably, Ca(2+)-induced dephosphorylation occurs at high apparent [Ca(2+)] (K(i) = 0.25 mM) and is independent of the phosphatase motif of the pump and the putative binding site for transported ligands located in M4. Taken together, our results rule out that Ca(2+) is a transported substrate but indicate the presence of a cytosolic low affinity Ca(2+)-binding site, which is conserved among P-type pumps and could be involved in pump regulation. Our work constitutes the first characterization of a P5 ATPase phosphoenzyme and points to Ca(2+) as a modifier of its function.
Collapse
Affiliation(s)
- Danny Mollerup Sørensen
- Centre for Membrane Pumps in Cells and Disease, PUMPKIN, Danish National Research Foundation, Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | | | | | | | | | | | | |
Collapse
|
13
|
Sacchetto R, Bertipaglia I, Giannetti S, Cendron L, Mascarello F, Damiani E, Carafoli E, Zanotti G. Crystal structure of sarcoplasmic reticulum Ca2+-ATPase (SERCA) from bovine muscle. J Struct Biol 2012; 178:38-44. [PMID: 22387132 DOI: 10.1016/j.jsb.2012.02.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 02/07/2012] [Accepted: 02/10/2012] [Indexed: 01/14/2023]
Abstract
The SERCA pump, a membrane protein of about 110kDa, transports two Ca(2+) ions per ATP hydrolyzed from the cytoplasm to the lumen of the sarcoplasmic reticulum. In muscle cells, its ability to remove Ca(2+) from the cytosol induces relaxation. The transport mechanism employed by the enzyme from rabbit muscle has been extensively studied, and several crystal structures representing different conformational states are available. However, no structure of the pump from other sources is known. In this paper we describe the crystal structure of the bovine enzyme, crystallized in the E1 conformation and determined at 2.9Å resolution. The overall molecular model is very similar to that of the rabbit enzyme, as expected by the high amino acid sequence identity. Nevertheless, the bovine enzyme has reduced catalytic activity with respect to the rabbit enzyme. Subtle structural modifications, in particular in the region of the long loop that protrudes into the SR lumen connecting transmembrane α-helices M7 and M8, may explain the difference.
Collapse
Affiliation(s)
- Roberta Sacchetto
- Department of Experimental Veterinary Sciences, Viale dell'Università 16, 35020 Legnaro, Padua, Italy
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Tlapak-Simmons VL, Medina AP, Baggenstoss BA, Nguyen L, Baron CA, Weigel PH. Clustered Conserved Cysteines in Hyaluronan Synthase Mediate Cooperative Activation by Mg 2+ Ions and Severe Inhibitory Effects of Divalent Cations. ACTA ACUST UNITED AC 2012; Suppl 1:001. [PMID: 25267933 DOI: 10.4172/2153-0637.s1-001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hyaluronan synthase (HAS) uses UDP-GlcUA and UDP-GlcNAc to make hyaluronan (HA). Streptococcus equisimilis HAS (SeHAS) contains four conserved cysteines clustered near the membrane, and requires phospholipids and Mg2+ for activity. Activity of membrane-bound or purified enzyme displayed a sigmoidal saturation profile for Mg2+ with a Hill coefficient of 2. To assess if Cys residues are important for cooperativity we examined the Mg2+ dependence of mutants with various combinations of Cys-to-Ala mutations. All Cys-mutants lost the cooperative response to Mg2+. In the presence of Mg2+, other divalent cations inhibited SeHAS with different potencies (Cu2+~Zn2+ >Co2+ >Ni2+ >Mn2+ >Ba2+ Sr2+ Ca2+). Some divalent metal ions likely inhibit by displacement of Mg2+-UDP-Sugar complexes (e.g. Ca2+, Sr2+ and Ba2+ had apparent Ki values of 2-5 mM). In contrast, Zn2+ and Cu2+ inhibited more potently (apparent Ki ≤ 0.2 mM). Inhibition of Cys-null SeHAS by Cu2+, but not Zn2+, was greatly attenuated compared to wildtype. Double and triple Cys-mutants showed differing sensitivities to Zn2+ or Cu2+. Wildtype SeHAS allowed to make HA prior to exposure to Zn2+ or Cu2+ was protected from inhibition, indicating that access of metal ions to sensitive functional groups was hindered in processively acting HA•HAS complexes. We conclude that clustered Cys residues mediate cooperative interactions with Mg2+ and that transition metal ions inhibit SeHAS very potently by interacting with one or more of these -SH groups.
Collapse
Affiliation(s)
- Valarie L Tlapak-Simmons
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| | - Andria P Medina
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| | - Bruce A Baggenstoss
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| | - Long Nguyen
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| | - Christina A Baron
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| | - Paul H Weigel
- Department of Biochemistry & Molecular Biology, The Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
| |
Collapse
|
15
|
Abstract
The sarcoplasmic (SERCA 1a) Ca2+-ATPase is a membrane protein abundantly present in skeletal muscles where it functions as an indispensable component of the excitation-contraction coupling, being at the expense of ATP hydrolysis involved in Ca2+/H+ exchange with a high thermodynamic efficiency across the sarcoplasmic reticulum membrane. The transporter serves as a prototype of a whole family of cation transporters, the P-type ATPases, which in addition to Ca2+ transporting proteins count Na+, K+-ATPase and H+, K+-, proton- and heavy metal transporting ATPases as prominent members. The ability in recent years to produce and analyze at atomic (2·3-3 Å) resolution 3D-crystals of Ca2+-transport intermediates of SERCA 1a has meant a breakthrough in our understanding of the structural aspects of the transport mechanism. We describe here the detailed construction of the ATPase in terms of one membraneous and three cytosolic domains held together by a central core that mediates coupling between Ca2+-transport and ATP hydrolysis. During turnover, the pump is present in two different conformational states, E1 and E2, with a preference for the binding of Ca2+ and H+, respectively. We discuss how phosphorylated and non-phosphorylated forms of these conformational states with cytosolic, occluded or luminally exposed cation-binding sites are able to convert the chemical energy derived from ATP hydrolysis into an electrochemical gradient of Ca2+ across the sarcoplasmic reticulum membrane. In conjunction with these basic reactions which serve as a structural framework for the transport function of other P-type ATPases as well, we also review the role of the lipid phase and the regulatory and thermodynamic aspects of the transport mechanism.
Collapse
|
16
|
Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+. Proc Natl Acad Sci U S A 2011; 108:1833-8. [PMID: 21239683 DOI: 10.1073/pnas.1017659108] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trinitrophenyl derivatives of adenine nucleotides are widely used for probing ATP-binding sites. Here we describe crystal structures of Ca(2+)-ATPase, a representative P-type ATPase, in the absence of Ca(2+) with bound ATP, trinitrophenyl-ATP, -ADP, and -AMP at better than 2.4-Å resolution, stabilized with thapsigargin, a potent inhibitor. These crystal structures show that the binding mode of the trinitrophenyl derivatives is distinctly different from the parent adenine nucleotides. The adenine binding pocket in the nucleotide binding domain of Ca(2+)-ATPase is now occupied by the trinitrophenyl group, and the side chains of two arginines sandwich the adenine ring, accounting for the much higher affinities of the trinitrophenyl derivatives. Trinitrophenyl nucleotides exhibit a pronounced fluorescence in the E2P ground state but not in the other E2 states. Crystal structures of the E2P and E2 ∼ P analogues of Ca(2+)-ATPase with bound trinitrophenyl-AMP show that different arrangements of the three cytoplasmic domains alter the orientation and water accessibility of the trinitrophenyl group, explaining the origin of "superfluorescence." Thus, the crystal structures demonstrate that ATP and its derivatives are highly adaptable to a wide range of site topologies stabilized by a variety of interactions.
Collapse
|
17
|
Daiho T, Danko S, Yamasaki K, Suzuki H. Stable structural analog of Ca2+-ATPase ADP-insensitive phosphoenzyme with occluded Ca2+ formed by elongation of A-domain/M1'-linker and beryllium fluoride binding. J Biol Chem 2010; 285:24538-47. [PMID: 20529842 DOI: 10.1074/jbc.m110.144535] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have developed a stable analog for the ADP-insensitive phosphoenzyme intermediate with two occluded Ca(2+) at the transport sites (E2PCa(2)) of sarcoplasmic reticulum Ca(2+)-ATPase. This is normally a transient intermediate state during phosphoenzyme isomerization from the ADP-sensitive to ADP-insensitive form and Ca(2+) deocclusion/release to the lumen; E1PCa(2) --> E2PCa(2) --> E2P + 2Ca(2+). Stabilization was achieved by elongation of the Glu(40)-Ser(48) loop linking the Actuator domain and M1 (1st transmembrane helix) with four glycine insertions at Gly(46)/Lys(47) and by binding of beryllium fluoride (BeF(x)) to the phosphorylation site of the Ca(2+)-bound ATPase (E1Ca(2)). The complex E2Ca(2)xBeF(3)(-) was also produced by lumenal Ca(2+) binding to E2xBeF(3)(-) (E2P ground state analog) of the elongated linker mutant. The complex was stable for at least 1 week at 25 degrees C. Only BeF(x), but not AlF(x) or MgF(x), produced the E2PCa(2) structural analog. Complex formation required binding of Mg(2+), Mn(2+), or Ca(2+) at the catalytic Mg(2+) site. Results reveal that the phosphorylation product E1PCa(2) and the E2P ground state (but not the transition states) become competent to produce the E2PCa(2) transient state during forward and reverse phosphoenzyme isomerization. Thus, isomerization and lumenal Ca(2+) release processes are strictly coupled with the formation of the acylphosphate covalent bond at the catalytic site. Results also demonstrate the critical structural roles of the Glu(40)-Ser(48) linker and of Mg(2+) at the catalytic site in these processes.
Collapse
Affiliation(s)
- Takashi Daiho
- Department of Biochemistry, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | | | | | | |
Collapse
|
18
|
Møller JV, Olesen C, Winther AML, Nissen P. What can be learned about the function of a single protein from its various X-ray structures: the example of the sarcoplasmic calcium pump. Methods Mol Biol 2010; 654:119-40. [PMID: 20665264 DOI: 10.1007/978-1-60761-762-4_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Improvements in the handling of membrane proteins for crystallization, combined with better synchrotron sources for X-ray diffraction analysis, are leading to clarification of the structural details of an ever increasing number of membrane transporters and receptors. Here we describe how this development has resulted in the elucidation at atomic resolution of a large number of structures of the sarcoplasmic Ca(2+)-ATPase (SERCA1a) present in skeletal muscle. The structures corresponding to the various intermediary states have been obtained after stabilization with structural analogues of ATP and of metal fluorides as mimicks of inorganic phosphate. From these results it is possible, in accordance with previous biochemical and molecular biology data, to give a detailed structural description of both ATP hydrolysis and Ca(2+) transport through the membrane, to serve as the starting point for a fuller understanding of the pump mechanism and, in future studies, on the regulatory role of this ubiquitous intracellular Ca(2+)-ATPase in cellular Ca(2+) metabolism in normal and pathological conditions.
Collapse
Affiliation(s)
- Jesper Vuust Møller
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Copenhagen, Denmark.
| | | | | | | |
Collapse
|
19
|
Danko S, Daiho T, Yamasaki K, Liu X, Suzuki H. Formation of the stable structural analog of ADP-sensitive phosphoenzyme of Ca2+-ATPase with occluded Ca2+ by beryllium fluoride: structural changes during phosphorylation and isomerization. J Biol Chem 2009; 284:22722-35. [PMID: 19561071 DOI: 10.1074/jbc.m109.029702] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As a stable analog for ADP-sensitive phosphorylated intermediate of sarcoplasmic reticulum Ca(2+)-ATPase E1PCa(2).Mg, a complex of E1Ca(2).BeF(x), was successfully developed by addition of beryllium fluoride and Mg(2+) to the Ca(2+)-bound state, E1Ca(2). In E1Ca(2).BeF(x), most probably E1Ca(2).BeF(3)(-), two Ca(2+) are occluded at high affinity transport sites, its formation required Mg(2+) binding at the catalytic site, and ADP decomposed it to E1Ca(2), as in E1PCa(2).Mg. Organization of cytoplasmic domains in E1Ca(2).BeF(x) was revealed to be intermediate between those in E1Ca(2).AlF(4)(-) ADP (transition state of E1PCa(2) formation) and E2.BeF(3)(-).(ADP-insensitive phosphorylated intermediate E2P.Mg). Trinitrophenyl-AMP (TNP-AMP) formed a very fluorescent (superfluorescent) complex with E1Ca(2).BeF(x) in contrast to no superfluorescence of TNP-AMP bound to E1Ca(2).AlF(x). E1Ca(2).BeF(x) with bound TNP-AMP slowly decayed to E1Ca(2), being distinct from the superfluorescent complex of TNP-AMP with E2.BeF(3)(-), which was stable. Tryptophan fluorescence revealed that the transmembrane structure of E1Ca(2).BeF(x) mimics E1PCa(2).Mg, and between those of E1Ca(2).AlF(4)(-).ADP and E2.BeF(3)(-). E1Ca(2).BeF(x) at low 50-100 microm Ca(2+) was converted slowly to E2.BeF(3)(-) releasing Ca(2+), mimicking E1PCa(2).Mg --> E2P.Mg + 2Ca(2+). Ca(2+) replacement of Mg(2+) at the catalytic site at approximately millimolar high Ca(2+) decomposed E1Ca(2).BeF(x) to E1Ca(2). Notably, E1Ca(2).BeF(x) was perfectly stabilized for at least 12 days by 0.7 mm lumenal Ca(2+) with 15 mm Mg(2+). Also, stable E1Ca(2).BeF(x) was produced from E2.BeF(3)(-) at 0.7 mm lumenal Ca(2+) by binding two Ca(2+) to lumenally oriented low affinity transport sites, as mimicking the reverse conversion E2P. Mg + 2Ca(2+) --> E1PCa(2).Mg.
Collapse
Affiliation(s)
- Stefania Danko
- Department of Biochemistry, Asahikawa Medical College, Asahikawa 078-8510, Japan
| | | | | | | | | |
Collapse
|
20
|
Tsuda T, Toyoshima C. Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase. EMBO J 2009; 28:1782-91. [PMID: 19478797 DOI: 10.1038/emboj.2009.143] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 04/30/2009] [Indexed: 11/09/2022] Open
Abstract
Heavy metal pumps constitute a large subgroup in P-type ion-transporting ATPases. One of the outstanding features is that the nucleotide binding N-domain lacks residues critical for ATP binding in other well-studied P-type ATPases. Instead, they possess an HP-motif and a Gly-rich sequence in the N-domain, and their mutations impair ATP binding. Here, we describe 1.85 A resolution crystal structures of the P- and N-domains of CopA, an archaeal Cu(+)-transporting ATPase, with bound nucleotides. These crystal structures show that CopA recognises the adenine ring completely differently from other P-type ATPases. The crystal structure of the His462Gln mutant, in the HP-motif, a disease-causing mutation in human Cu(+)-ATPases, shows that the Gln side chain mimics the imidazole ring, but only partially, explaining the reduction in ATPase activity. These crystal structures lead us to propose a role of the His and a mechanism for removing Mg(2+) from ATP before phosphoryl transfer.
Collapse
Affiliation(s)
- Takeo Tsuda
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | | |
Collapse
|
21
|
Characterization of Ca2+uptake in a subcellular membrane fraction ofHerpetomonassp. promastigotes. Parasitology 2009; 136:657-63. [DOI: 10.1017/s0031182009005903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
SUMMARYATP-dependent Ca2+uptake was studied in a subcellular fraction fromHerpetomonassp. prepared by mechanical disruption and using45Ca2+as a tracer. The uptake was stimulated by Ca2+with a K0·5of 0·1 μmand a Hill number (nH)=2·8±0·4. The Ca2+-dependent ATP hydrolysis was optimal at pH 7·0 and had a Ca2+dependence identical to uptake. The uptake was highly stimulated by oxalate whereas calmodulin had no activating effect. ATP stimulated Ca2+uptake with a biphasic pattern that resembled the curves described for the purified preparations of rabbit sarcoplasmic reticulum. The ATP stimulation is described as the sum of two Michaelis-Menten curves with Km1=0·25±0·19 μmand Km2=29·6±6·8 μm. GTP or UTP could also promote Ca2+uptake, but with less efficiency than ATP. Vanadate inhibited the uptake with low apparent affinity. Thapsigargin and cyclopiazonic acid were almost ineffective. The Ca2+uptake was insensitive to H+ionophores and to bafilomycin suggesting no participation of acidocalcisomes. The results are comparable to those obtained using cells permeabilized with digitonin and using arsenaze III as Ca2+indicator. The Ca2+uptake activity described here seems to belong to the endoplasmic reticulum ofHerpetomonassp. and is suitable for further studies on the mechanisms of calcium homeostasis in parasites.
Collapse
|
22
|
Montigny C, Arnou B, Marchal E, Champeil P. Use of glycerol-containing media to study the intrinsic fluorescence properties of detergent-solubilized native or expressed SERCA1a. Biochemistry 2008; 47:12159-74. [PMID: 18947188 DOI: 10.1021/bi8006498] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid irreversible inactivation of Ca (2+)-free states of detergent-solubilized SERCA1a (sarco-endoplasmic reticulum calcium ATPase 1a) has so far prevented the use of Trp fluorescence for functional characterization of this ATPase after its solubilization in various detergents. Here we show that using 20-40% glycerol for protection makes this fluorescence characterization possible. Most of the ligand-induced Trp fluorescence changes previously demonstrated to occur for SERCA1a embedded in native sarcoplasmic reticulum membranes were observed in the combined presence of glycerol and detergent, although the results greatly depended on the detergent used, namely, octaethylene glycol mono- n-dodecyl ether (C 12E 8) or dodecyl maltoside (DDM). In particular, at pH 6, we found a C 12E 8-dependent unexpectedly huge reduction in SERCA1a affinity for Ca (2+). We suggest that a major reason for the different effects of the two detergents is that high concentrations of C 12E 8, but not of DDM, slow down the E2 to E1 transition in solubilized and delipidated SERCA1a. Independently of the characterization of the specific effects of various detergents on SR vesicles, our results open the way to functional characterization by Trp fluorescence of heterologously expressed and purified mutants of SERCA1a in the presence of detergent, without their preliminary reconstitution into liposomes. As an example, we used the E309Q mutant to demonstrate our previous suspicion that Ca (2+) binding to Site I of SERCA1a in fact slightly reduces Trp fluorescence, and consequently that the rise in this fluorescence generally observed when two Ca (2+) ions bind to WT SERCA1a mainly reflects Ca (2+) binding at Site II of SERCA1a.
Collapse
Affiliation(s)
- Cédric Montigny
- CNRS, URA 2096, Systemes membranaires, photobiologie, stress et detoxication, F-91191 Gif-sur-Yvette, France
| | | | | | | |
Collapse
|
23
|
Cura CI, Corradi GR, Rinaldi DE, Adamo HP. High sensibility to reactivation by acidic lipids of the recombinant human plasma membrane Ca2+-ATPase isoform 4xb purified from Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2757-64. [PMID: 18822268 DOI: 10.1016/j.bbamem.2008.08.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Revised: 08/25/2008] [Accepted: 08/26/2008] [Indexed: 11/17/2022]
Abstract
The human plasma membrane Ca2+ pump (isoform 4xb) was expressed in Saccharomyces cerevisiae and purified by calmodulin-affinity chromatography. Under optimal conditions the recombinant enzyme (yPMCA) hydrolyzed ATP in a Ca2+ dependent manner at a rate of 15 micromol/mg/min. The properties of yPMCA were compared to those of the PMCA purified from human red cells (ePMCA). The mobility of yPMCA in SDS-PAGE was the expected for the hPMCA4xb protein but slightly lower than that of ePMCA. Both enzymes achieved maximal activity when supplemented with acidic phospholipids. However, while ePMCA in mixed micelles of phosphatidylcholine-detergent had 30% of its maximal activity, the yPMCA enzyme was nearly inactive. Increasing the phosphatidylcholine content of the micelles did not increase the activity of yPMCA but the activity in the presence of phosphatidylcholine improved by partially removing the detergent. The reactivation of the detergent solubilized yPMCA required specifically acidic lipids and, as judged by the increase in the level of phosphoenzyme, it involved the increase in the amount of active enzyme. These results indicate that the function of yPMCA is highly sensitive to delipidation and the restitution of acidic lipids is needed for a functional enzyme.
Collapse
Affiliation(s)
- Carolina I Cura
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB)-Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113 Ciudad de Buenos Aires, Argentina.
| | | | | | | |
Collapse
|
24
|
Structural aspects of ion pumping by Ca2+-ATPase of sarcoplasmic reticulum. Arch Biochem Biophys 2008; 476:3-11. [PMID: 18455499 DOI: 10.1016/j.abb.2008.04.017] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 04/09/2008] [Indexed: 11/22/2022]
Abstract
Ca2+-ATPase of muscle sarcoplasmic reticulum is an ATP-powered Ca2+-pump that establishes a >10,000-fold concentration gradient across the membrane. Its crystal structures have been determined for nine different states that cover nearly the entire reaction cycle. Presented here is a brief structural account of the ion pumping process, which is achieved by a series of very large domain rearrangements.
Collapse
|
25
|
Marchand A, Winther AML, Holm PJ, Olesen C, Montigny C, Arnou B, Champeil P, Clausen JD, Vilsen B, Andersen JP, Nissen P, Jaxel C, Møller JV, le Maire M. Crystal structure of D351A and P312A mutant forms of the mammalian sarcoplasmic reticulum Ca(2+) -ATPase reveals key events in phosphorylation and Ca(2+) release. J Biol Chem 2008; 283:14867-82. [PMID: 18356161 DOI: 10.1074/jbc.m710165200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In recent years crystal structures of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1a), stabilized in various conformations with nucleotide and phosphate analogs, have been obtained. However, structural analysis of mutant forms would also be valuable to address key mechanistic aspects. We have worked out a procedure for affinity purification of SERCA1a heterologously expressed in yeast cells, producing sufficient amounts for crystallization and biophysical studies. We present here the crystal structures of two mutant forms, D351A and P312A, to address the issue whether the profound functional changes seen for these mutants are caused by major structural changes. We find that the structure of P312A with ADP and AlF(4)(-) bound (3.5-A resolution) and D351A with AMPPCP or ATP bound (3.4- and 3.7-A resolution, respectively) deviate only slightly from the complexes formed with that of wild-type ATPase. ATP affinity of the D351A mutant was very high, whereas the affinity for cytosolic Ca(2+) was similar to that of the wild type. We conclude from an analysis of data that the extraordinary affinity of the D351A mutant for ATP is caused by the electrostatic effects of charge removal and not by a conformational change. P312A exhibits a profound slowing of the Ca(2+)-translocating Ca(2)E1P-->E2P transition, which seems to be due to a stabilization of Ca(2)E1P rather than a destabilization of E2P. This can be accounted for by the strain that the Pro residue induces in the straight M4 helix of the wild type, which is removed upon the replacement of Pro(312) with alanine in P312A.
Collapse
Affiliation(s)
- Alexandre Marchand
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie et de Technologies de Saclay, SBSM, URA CNRS 2096, Laboratoire de Recherche Associé, 17V University of Paris-Sud, Gif sur Yvette, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Montigny C, Picard M, Lenoir G, Gauron C, Toyoshima C, Champeil P. Inhibitors bound to Ca(2+)-free sarcoplasmic reticulum Ca(2+)-ATPase lock its transmembrane region but not necessarily its cytosolic region, revealing the flexibility of the loops connecting transmembrane and cytosolic domains. Biochemistry 2007; 46:15162-74. [PMID: 18052080 DOI: 10.1021/bi701855r] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ca2+-free crystals of sarcoplasmic reticulum Ca2+-ATPase have, up until now, been obtained in the presence of inhibitors such as thapsigargin (TG), bound to the transmembrane region of this protein. Here, we examined the consequences of such binding for the protein. We found that, after TG binding, an active site ligand such as beryllium fluoride can still bind to the ATPase and change the conformation or dynamics of the cytosolic domains (as revealed by the protection afforded against proteolysis), but it becomes unable to induce any change in the transmembrane domain (as revealed by the intrinsic fluorescence of the membranous tryptophan residues). TG also obliterates the Trp fluorescence changes normally induced by binding of MgATP or metal-free ATP, as well as those induced by binding of Mg2+ alone. In the nucleotide binding domain, the environment of Lys515 (as revealed by fluorescein isothiocyanate fluorescence after specific labeling of this residue) is significantly different in the ATPase complex with aluminum fluoride and in the ATPase complex with beryllium fluoride, and in the latter case it is modified by TG. All these facts document the flexibility of the loops connecting the transmembrane and cytosolic domains in the ATPase. In the absence of active site ligands, TG protects the ATPase from cleavage by proteinase K at Thr242-Glu243, suggesting TG-induced reduction in the mobility of these loops. 2,5-Di-tert-butyl-1,4-dihydroxybenzene or cyclopiazonic acid, inhibitors which also bind in or near the transmembrane region, also produce similar overall effects on Ca2+-free ATPase.
Collapse
Affiliation(s)
- Cédric Montigny
- CNRS, URA 2096 (Protéines Membranaires Transductrices d'Energie), F-91191 Gif-sur-Yvette, France
| | | | | | | | | | | |
Collapse
|
27
|
Daiho T, Yamasaki K, Danko S, Suzuki H. Critical role of Glu40-Ser48 loop linking actuator domain and first transmembrane helix of Ca2+-ATPase in Ca2+ deocclusion and release from ADP-insensitive phosphoenzyme. J Biol Chem 2007; 282:34429-47. [PMID: 17881350 DOI: 10.1074/jbc.m707665200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functional importance of the length of the A/M1 linker (Glu(40)-Ser(48)) connecting the actuator domain and the first transmembrane helix of sarcoplasmic reticulum Ca(2+)-ATPase was explored by its elongation with glycine insertion at Pro(42)/Ala(43) and Gly(46)/Lys(47). Two or more glycine insertions at each site completely abolished ATPase activity. The isomerization of phosphoenzyme (EP) intermediate from the ADP-sensitive form (E1P) to the ADP-insensitive form (E2P) was markedly accelerated, but the decay of EP was completely blocked in these mutants. The E2P accumulated was therefore demonstrated to be E2PCa(2) possessing two occluded Ca(2+) ions at the transport sites, and the Ca(2+) deocclusion and release into lumen were blocked in the mutants. By contrast, the hydrolysis of the Ca(2+)-free form of E2P produced from P(i) without Ca(2+) was as rapid in the mutants as in the wild type. Analysis of resistance against trypsin and proteinase K revealed that the structure of E2PCa(2) accumulated is an intermediate state between E1PCa(2) and the Ca(2+)-released E2P state. Namely in E2PCa(2), the actuator domain is already largely rotated from its position in E1PCa(2) and associated with the phosphorylation domain as in the Ca(2+)-released E2P state; however, in E2PCa(2), the hydrophobic interactions among these domains and Leu(119)/Tyr(122) on the top of second transmembrane helix are not yet formed properly. This is consistent with our previous finding that these interactions at Tyr(122) are critical for formation of the Ca(2+)-released E2P structure. Results showed that the EP isomerization/Ca(2+)-release process consists of the following two steps: E1PCa(2) --> E2PCa(2) --> E2P + 2Ca(2+); and the intermediate state E2PCa(2) was identified for the first time. Results further indicated that the A/M1 linker with its appropriately short length, probably because of the strain imposed in E2PCa(2), is critical for the correct positioning and interactions of the actuator and phosphorylation domains to cause structural changes for the Ca(2+) deocclusion and release.
Collapse
Affiliation(s)
- Takashi Daiho
- Department of Biochemistry, Asahikawa Medical College, Midorigaoka-higashi, Asahikawa, Japan.
| | | | | | | |
Collapse
|
28
|
Löf D, Schillén K, Jönsson B, Evilevitch A. Dynamic and static light scattering analysis of DNA ejection from the phage lambda. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:011914. [PMID: 17677501 DOI: 10.1103/physreve.76.011914] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Revised: 04/27/2007] [Indexed: 05/16/2023]
Abstract
With the aid of time-resolved dynamic light scattering (DLS) and static light scattering (SLS), we have analyzed the ejection kinetics from the bacterial virus bacteriophage (or phage) lambda , triggered in vitro by its receptor. We have used DLS to investigate the kinetics in such a system. Furthermore, we have shown that both SLS and DLS can be interchangeably used to study the process of phage DNA release. DLS is superior to SLS in that it also allows the change in the light scattering arising from each of the components in the system to be monitored under conditions such that the relaxation times are separable. With help of these two methods we present a model explaining the reason for the observed decrease in the scattering intensity accompanying DNA ejection from phage. We emphasize that ejection from phage capsid occurs through a very long tail (which is nearly three times longer than the capsid diameter), which significantly separates ejected DNA from the scattering volume of the capsid. The scattering intensity recorded during the DNA ejection process is the result of a change in the form factor of the phage particle, i.e., the change in the interference effects between the phage capsid and the DNA confined in the phage particle. When the DNA molecule is completely ejected it remains in the proximity of the phage for some time, thus contributing to the scattering signal as it diffuses away from the phage capsid, into the scattering volume and returns to its unperturbed chain conformation in bulk solution. The free DNA chain does not contribute to the scattered intensity, when measured at a large angle, due to the DNA form factor and the low concentration. Although the final diffusion-controlled step can lead to overestimation of the real ejection time, we can still use both scattering methods to estimate the initial DNA ejection rates, which are mainly dependent on the pressure-driven DNA ejection from the phage, allowing studies of the effects of various parameters affecting the ejection.
Collapse
Affiliation(s)
- David Löf
- Division of Physical Chemistry 1, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | | | | | | |
Collapse
|