1
|
Abe K, Nishizawa T, Artigas P. An unusual conformation from Na +-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na +-binding. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119543. [PMID: 37482134 DOI: 10.1016/j.bbamcr.2023.119543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/29/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
The Na+,K+-ATPase (NKA) and non-gastric H+,K+- ATPase (ngHKA) share ~65 % sequence identity, and nearly identical catalytic cycles. These pumps alternate between inward-facing (E1) and outward-facing (E2) conformations and differ in their exported substrate (Na+ or H+) and stoichiometries (3 Na+:2 K+ or 1 H+:1 K+). We reported that structures of the NKA-mimetic ngHKA mutant K794S/A797P/W940/R949C (SPWC) with 2 K+ occluded in E2-Pi and 3 Na+-bound in E1·ATP states were nearly identical to NKA structures in equivalent states. Here we report the cryo-EM structures of K794A and K794S, two poorly-selective ngHKA mutants, under conditions to stabilize the E1·ATP state. Unexpectedly, the structures show a hybrid with both E1- and E2-like structural features. While transmembrane segments TM1-TM3 and TM4's extracellular half adopted an E2-like conformation, the rest of the protein assumed an E1 configuration. Two spherical densities, likely bound Na+, were observed at cation-binding sites I and III, without density at site II. This explains the E2-like conformation of TM4's exoplasmic half. In NKA, oxygen atoms derived from the unwound portion of TM4 coordinated Na+ at site II. Thus, the lack of Na+ at site II of K794A/S prevents the luminal portion of TM4 from taking an E1-like position. The K794A structure also suggests that incomplete coordination of Na+ at site III induces the halfway rotation of TM6, which impairs Na+-binding at the site II. Thus, our observations provide insight into the molecular mechanism of E2-E1 transition and cooperative Na+-binding in the NKA and other related cation pumps.
Collapse
Affiliation(s)
- Kazuhiro Abe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan; Cellular and Structural Physiology Institute, Nagoya University, Nagoya 464-8601, Japan; Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Japan.
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Sciences, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Pablo Artigas
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| |
Collapse
|
2
|
Wu M, Wu C, Song T, Pan K, Wang Y, Liu Z. Structure and transport mechanism of the human calcium pump SPCA1. Cell Res 2023; 33:533-545. [PMID: 37258749 PMCID: PMC10313705 DOI: 10.1038/s41422-023-00827-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Secretory-pathway Ca2+-ATPases (SPCAs) play critical roles in maintaining Ca2+ homeostasis, but the exact mechanism of SPCAs-mediated Ca2+ transport remains unclear. Here, we determined six cryo-electron microscopy (cryo-EM) structures of human SPCA1 (hSPCA1) in a series of intermediate states, revealing a near-complete conformational cycle. With the aid of molecular dynamics simulations, these structures offer a clear structural basis for Ca2+ entry and release in hSPCA1. We found that hSPCA1 undergoes unique conformational changes during ATP binding and phosphorylation compared to other well-studied P-type II ATPases. In addition, we observed a conformational distortion of the Ca2+-binding site induced by the separation of transmembrane helices 4L and 6, unveiling a distinct Ca2+ release mechanism. Particularly, we determined a structure of the long-sought CaE2P state of P-type IIA ATPases, providing valuable insights into the Ca2+ transport cycle. Together, these findings enhance our understanding of Ca2+ transport by hSPCA1 and broaden our knowledge of P-type ATPases.
Collapse
Affiliation(s)
- Mengqi Wu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Cang Wu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Tiefeng Song
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kewu Pan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, China.
| | - Zhongmin Liu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| |
Collapse
|
3
|
Multiple sub-state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle. Cell Rep 2022; 41:111760. [PMID: 36476867 DOI: 10.1016/j.celrep.2022.111760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/06/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) pumps Ca2+ into the endoplasmic reticulum (ER). Herein, we present cryo-electron microscopy (EM) structures of three intermediates of SERCA2b: Ca2+-bound phosphorylated (E1P·2Ca2+) and Ca2+-unbound dephosphorylated (E2·Pi) intermediates and another between the E2P and E2·Pi states. Our cryo-EM analysis demonstrates that the E1P·2Ca2+ state exists in low abundance and preferentially transitions to an E2P-like structure by releasing Ca2+ and that the Ca2+ release gate subsequently undergoes stepwise closure during the dephosphorylation processes. Importantly, each intermediate adopts multiple sub-state structures including those like the next one in the catalytic series, indicating conformational overlap at transition steps, as further substantiated by atomistic molecular dynamic simulations of SERCA2b in a lipid bilayer. The present findings provide insight into how enzymes accelerate catalytic cycles.
Collapse
|
4
|
Fruergaard MU, Dach I, Andersen JL, Ozol M, Shasavar A, Quistgaard EM, Poulsen H, Fedosova NU, Nissen P. The Na,K-ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state. J Biol Chem 2022; 298:102317. [PMID: 35926706 PMCID: PMC9485054 DOI: 10.1016/j.jbc.2022.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 10/29/2022] Open
Abstract
The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane via a functional cycle that includes various phosphoenzyme intermediates. However, the structure and function of these intermediates and how metal fluorides mimick them require further investigation. Here, we describe a 4.0 Å resolution crystal structure and functional properties of the pig kidney Na+,K+-ATPase stabilized by the inhibitor beryllium fluoride (denoted E2-BeFx). E2-BeFx is expected to mimic properties of the E2P phosphoenzyme, yet with unknown characteristics of ion and ligand binding. The structure resembles the E2P form obtained by phosphorylation from inorganic phosphate (Pi) and stabilized by cardiotonic steroids, including a low-affinity Mg2+ site near ion binding site II. Our anomalous Fourier analysis of the crystals soaked in Rb+ (a K+ congener) followed by a low-resolution rigid-body refinement (6.9-7.5 Å) revealed pre-occlusion transitions leading to activation of the dephosphorylation reaction. We show that the Mg2+ location indicates a site of initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Furthermore, using binding and activity studies, we find that the BeFx-inhibited enzyme is also able to bind ADP/ATP and Na+. These results relate the E2-BeFx complex to a transient K+- and ADP-sensitive E*P intermediate of the functional cycle of the Na+,K+-ATPase, prior to E2P.
Collapse
Affiliation(s)
- Marlene U Fruergaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Ingrid Dach
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Jacob L Andersen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark; Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark
| | - Mette Ozol
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Azadeh Shasavar
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Esben M Quistgaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Hanne Poulsen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Natalya U Fedosova
- Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark.
| | - Poul Nissen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark.
| |
Collapse
|
5
|
Dieudonné T, Herrera SA, Laursen MJ, Lejeune M, Stock C, Slimani K, Jaxel C, Lyons JA, Montigny C, Pomorski TG, Nissen P, Lenoir G. Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders. eLife 2022; 11:75272. [PMID: 35416773 PMCID: PMC9045818 DOI: 10.7554/elife.75272] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
P4-ATPases flip lipids from the exoplasmic to the cytosolic leaflet, thus maintaining lipid asymmetry in eukaryotic cell membranes. Mutations in several human P4-ATPase genes are associated with severe diseases, for example in ATP8B1 causing progressive familial intrahepatic cholestasis, a rare inherited disorder progressing toward liver failure. ATP8B1 forms a binary complex with CDC50A and displays a broad specificity to glycerophospholipids, but regulatory mechanisms are unknown. Here, we report functional studies and the cryo-EM structure of the human lipid flippase ATP8B1-CDC50A at 3.1 Å resolution. We find that ATP8B1 is autoinhibited by its N- and C-terminal tails, which form extensive interactions with the catalytic sites and flexible domain interfaces. Consistently, ATP hydrolysis is unleashed by truncation of the C-terminus, but also requires phosphoinositides, most markedly phosphatidylinositol-3,4,5-phosphate (PI(3,4,5)P3), and removal of both N- and C-termini results in full activation. Restored inhibition of ATP8B1 truncation constructs with a synthetic peptide mimicking the C-terminal segment further suggests molecular communication between N- and C-termini in the autoinhibition and demonstrates that the regulatory mechanism can be interfered with by exogenous compounds. A recurring (G/A)(Y/F)AFS motif of the C-terminal segment suggests that this mechanism is employed widely across P4-ATPase lipid flippases in plasma membrane and endomembranes.
Collapse
Affiliation(s)
- Thibaud Dieudonné
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Sara Abad Herrera
- Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
| | | | - Maylis Lejeune
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Charlott Stock
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kahina Slimani
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Christine Jaxel
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Joseph A Lyons
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cédric Montigny
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Guillaume Lenoir
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| |
Collapse
|
6
|
Fedosova NU, Habeck M, Nissen P. Structure and Function of Na,K-ATPase-The Sodium-Potassium Pump. Compr Physiol 2021; 12:2659-2679. [PMID: 34964112 DOI: 10.1002/cphy.c200018] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Na,K-ATPase is an ubiquitous enzyme actively transporting Na-ions out of the cell in exchange for K-ions, thereby maintaining their concentration gradients across the cell membrane. Since its discovery more than six decades ago the Na-pump has been studied extensively and its vital physiological role in essentially every cell has been established. This article aims at providing an overview of well-established biochemical properties with a focus on Na,K-ATPase isoforms, its transport mechanism and principle conformations, inhibitors, and insights gained from crystal structures. © 2021 American Physiological Society. Compr Physiol 11:1-21, 2021.
Collapse
Affiliation(s)
| | - Michael Habeck
- Department of Molecular Biology and Genetics, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| |
Collapse
|
7
|
Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca 2+-ATPase. Proc Natl Acad Sci U S A 2021; 118:2105507118. [PMID: 34593638 PMCID: PMC8501872 DOI: 10.1073/pnas.2105507118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/05/2023] Open
Abstract
Ion pumps (or P-type ATPases) are membrane proteins, which transport ions through biological membranes against a concentration gradient, a function essential for many biological processes, such as muscle contraction, neurotransmission, and metabolism. Molecular mechanisms underlying active ion transport by ion pumps have been investigated by biochemical experiments and high-resolution structure analyses. Here, the transition of sarcoplasmic reticulum Ca2+-ATPase upon dissociation of Ca2+ is investigated using atomistic molecular dynamics simulations. We find intermediate structures along the pathway are stabilized by transient interactions between A- and P-domains as well as lipid molecules in the transmembrane helices. Sarcoplasmic reticulum (SR) Ca2+-ATPase transports two Ca2+ ions from the cytoplasm to the SR lumen against a large concentration gradient. X-ray crystallography has revealed the atomic structures of the protein before and after the dissociation of Ca2+, while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca2+ and E2P. Here, we explore the pathway and free energy profile of the transition using atomistic molecular dynamics simulations with the mean-force string method and umbrella sampling. The simulations suggest that a series of structural changes accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca2+ ions toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization. Free energy profiles of the transition assuming different protonation states suggest rapid exchanges between Ca2+ ions and protons when the Ca2+ ions are released toward the SR lumen.
Collapse
|
8
|
Abe K, Yamamoto K, Irie K, Nishizawa T, Oshima A. Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun 2021; 12:5709. [PMID: 34588453 PMCID: PMC8481561 DOI: 10.1038/s41467-021-26024-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
The gastric H+,K+-ATPase mediates electroneutral exchange of 1H+/1K+ per ATP hydrolysed across the membrane. Previous structural analysis of the K+-occluded E2-P transition state of H+,K+-ATPase showed a single bound K+ at cation-binding site II, in marked contrast to the two K+ ions occluded at sites I and II of the closely-related Na+,K+-ATPase which mediates electrogenic 3Na+/2K+ translocation across the membrane. The molecular basis of the different K+ stoichiometry between these K+-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H+,K+-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K+ bound H+,K+-ATPase, achieved by five mutations, including amino acids directly coordinating K+ (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K+-occluded conformation (Tyr799Trp). This quintuple mutant in the K+-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K+ accommodated at their cation-binding site. The gastric H+,K+-ATPase is a proton pump that creates the acidic environment of the stomach lumen, maintaining high proton gradient across the gastric mucosa cell membrane. Here, structural analysis of rationally designed H+,K+-ATPase mutants provides insight into this and other P-type ATPases cation binding stoichiometry and mechanisms.
Collapse
Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.
| | - Kenta Yamamoto
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Katsumasa Irie
- Department of Biophysical Chemistry, Faculty of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama, 640-8156, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| |
Collapse
|
9
|
Woodbury DJ, Whitt EC, Coffman RE. A review of TNP-ATP in protein binding studies: benefits and pitfalls. BIOPHYSICAL REPORTS 2021; 1:100012. [PMID: 36425312 PMCID: PMC9680771 DOI: 10.1016/j.bpr.2021.100012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/03/2021] [Indexed: 06/16/2023]
Abstract
We review 50 years of use of 2',3'-O-trinitrophenyl (TNP)-ATP, a fluorescently tagged ATP analog. It has been extensively used to detect binding interactions of ATP to proteins and to measure parameters of those interactions such as the dissociation constant, Kd, or inhibitor dissociation constant, Ki. TNP-ATP has also found use in other applications, for example, as a fluorescence marker in microscopy, as a FRET pair, or as an antagonist (e.g., of P2X receptors). However, its use in protein binding studies has limitations because the TNP moiety often enhances binding affinity, and the fluorescence changes that occur with binding can be masked or mimicked in unexpected ways. The goal of this review is to provide a clear perspective of the pros and cons of using TNP-ATP to allow for better experimental design and less ambiguous data in future experiments using TNP-ATP and other TNP nucleotides.
Collapse
Affiliation(s)
- Dixon J. Woodbury
- Department of Cell Biology and Physiology
- Neuroscience Center, Brigham Young University, Provo, Utah
| | | | | |
Collapse
|
10
|
Angle change of the A-domain in a single SERCA1a molecule detected by defocused orientation imaging. Sci Rep 2021; 11:13672. [PMID: 34211016 PMCID: PMC8249593 DOI: 10.1038/s41598-021-92986-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
The sarcoendoplasmic reticulum Ca2+-ATPase (SERCA) transports Ca2+ ions across the membrane coupled with ATP hydrolysis. Crystal structures of ligand-stabilized molecules indicate that the movement of actuator (A) domain plays a crucial role in Ca2+ translocation. However, the actual structural movements during the transitions between intermediates remain uncertain, in particular, the structure of E2PCa2 has not been solved. Here, the angle of the A-domain was measured by defocused orientation imaging using isotropic total internal reflection fluorescence microscopy. A single SERCA1a molecule, labeled with fluorophore ReAsH on the A-domain in fixed orientation, was embedded in a nanodisc, and stabilized on Ni–NTA glass. Activation with ATP and Ca2+ caused angle changes of the fluorophore and therefore the A-domain, motions lost by inhibitor, thapsigargin. Our high-speed set-up captured the motion during EP isomerization, and suggests that the A-domain rapidly rotates back and forth from an E1PCa2 position to a position close to the E2P state. This is the first report of the detection in the movement of the A-domain as an angle change. Our method provides a powerful tool to investigate the conformational change of a membrane protein in real-time.
Collapse
|
11
|
Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
Collapse
Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | |
Collapse
|
12
|
Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM. Cell Rep 2020; 32:108208. [DOI: 10.1016/j.celrep.2020.108208] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
|
13
|
Ravishankar H, Pedersen MN, Eklund M, Sitsel A, Li C, Duelli A, Levantino M, Wulff M, Barth A, Olesen C, Nissen P, Andersson M. Tracking Ca 2+ ATPase intermediates in real time by x-ray solution scattering. SCIENCE ADVANCES 2020; 6:eaaz0981. [PMID: 32219166 PMCID: PMC7083613 DOI: 10.1126/sciadv.aaz0981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/23/2019] [Indexed: 05/14/2023]
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.
Collapse
Affiliation(s)
- Harsha Ravishankar
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
| | | | | | - Aljona Sitsel
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Chenge Li
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen. Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matteo Levantino
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
- Department of Physics and Chemistry, University of Palermo, Viale delle Scienze -Ed 18, 90128 Palermo, Italy
| | - Michael Wulff
- European Synchrotron Radiation Facility, Grenoble, Cedex 38043, BP 220, France
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius Väg 16C, 106 91 Stockholm, Sweden
| | - Claus Olesen
- Department of Biomedicine, Aarhus University, Vest Ole Worms Allé 3, 113 8000 Aarhus C, Denmark
| | - Poul Nissen
- DANDRITE–Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University. Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden
- Corresponding author.
| |
Collapse
|
14
|
Saffioti NA, de Sautu M, Ferreira-Gomes MS, Rossi RC, Berlin J, Rossi JPFC, Mangialavori IC. E2P-like states of plasma membrane Ca 2+‑ATPase characterization of vanadate and fluoride-stabilized phosphoenzyme analogues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:366-379. [PMID: 30419189 DOI: 10.1016/j.bbamem.2018.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/22/2018] [Accepted: 11/01/2018] [Indexed: 01/18/2023]
Abstract
The plasma membrane Ca2+‑ATPase (PMCA) belongs to the family of P-type ATPases, which share the formation of an acid-stable phosphorylated intermediate as part of their reaction cycle. The crystal structure of PMCA is currently lacking. Its abundance is approximately 0.1% of the total protein in the membrane, hampering efforts to produce suitable crystals for X-ray structure analysis. In this work we characterized the effect of beryllium fluoride (BeFx), aluminium fluoride (AlFx) and magnesium fluoride (MgFx) on PMCA. These compounds are known inhibitors of P-type ATPases that stabilize E2P ground, E2·P phosphoryl transition and E2·Pi product states. Our results show that the phosphate analogues BeFx, AlFx and MgFx inhibit PMCA Ca2+‑ATPase activity, phosphatase activity and phosphorylation with high apparent affinity. Ca2+‑ATPase inhibition by AlFx and BeFx depended on Mg2+ concentration indicating that this ion stabilizes the complex between these inhibitors and the enzyme. Low pH increases AlFx and BeFx but not MgFx apparent affinity. Eosin fluorescent probe binds with high affinity to the nucleotide binding site of PMCA. The fluorescence of eosin decreases when fluoride complexes bind to PMCA indicating that the environment of the nucleotide binding site is less hydrophobic in E2P-like states. Finally, measuring the time course of E → E2P-like conformational change, we proposed a kinetic model for the binding of fluoride complexes and vanadate to PMCA. In summary, our results show that these fluoride complexes reveal different states of phosphorylated intermediates belonging to the mechanism of hydrolysis of ATP by the PMCA.
Collapse
Affiliation(s)
- Nicolás A Saffioti
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina
| | - Marilina de Sautu
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina
| | - Mariela S Ferreira-Gomes
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina
| | - Rolando C Rossi
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina
| | - Joshua Berlin
- Department of Pharmacology and Physiology, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Juan Pablo F C Rossi
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina
| | - Irene C Mangialavori
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Facultad de Farmacia y Bioquímica, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina.
| |
Collapse
|
15
|
Danko S, Yamasaki K, Daiho T, Suzuki H. Membrane Perturbation of ADP-insensitive Phosphoenzyme of Ca 2+-ATPase Modifies Gathering of Transmembrane Helix M2 with Cytoplasmic Domains and Luminal Gating. Sci Rep 2017; 7:41172. [PMID: 28117348 PMCID: PMC5259720 DOI: 10.1038/srep41172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/16/2016] [Indexed: 11/25/2022] Open
Abstract
Ca2+ transport by sarcoplasmic reticulum Ca2+-ATPase involves ATP-dependent phosphorylation of a catalytic aspartic acid residue. The key process, luminal Ca2+ release occurs upon phosphoenzyme isomerization, abbreviated as E1PCa2 (reactive to ADP regenerating ATP and with two occluded Ca2+ at transport sites) → E2P (insensitive to ADP and after Ca2+ release). The isomerization involves gathering of cytoplasmic actuator and phosphorylation domains with second transmembrane helix (M2), and is epitomized by protection of a Leu119-proteinase K (prtK) cleavage site on M2. Ca2+ binding to the luminal transport sites of E2P, producing E2PCa2 before Ca2+-release exposes the prtK-site. Here we explore E2P structure to further elucidate luminal gating mechanism and effect of membrane perturbation. We find that ground state E2P becomes cleavable at Leu119 in a non-solubilizing concentration of detergent C12E8 at pH 7.4, indicating a shift towards a more E2PCa2-like state. Cleavage is accelerated by Mg2+ binding to luminal transport sites and blocked by their protonation at pH 6.0. Results indicate that possible disruption of phospholipid-protein interactions strongly favors an E2P species with looser head domain interactions at M2 and responsive to specific ligand binding at the transport sites, likely an early flexible intermediate in the development towards ground state E2P.
Collapse
Affiliation(s)
- Stefania Danko
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Kazuo Yamasaki
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Takashi Daiho
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Hiroshi Suzuki
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| |
Collapse
|
16
|
Daiho T, Yamasaki K, Danko S, Suzuki H. Glycine 105 as Pivot for a Critical Knee-like Joint between Cytoplasmic and Transmembrane Segments of the Second Transmembrane Helix in Ca2+-ATPase. J Biol Chem 2016; 291:24688-24701. [PMID: 27733680 DOI: 10.1074/jbc.m116.759704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/11/2016] [Indexed: 11/06/2022] Open
Abstract
The cytoplasmic actuator domain of the sarco(endo)plasmic reticulum Ca2+-ATPase undergoes large rotational movements that influence the distant transmembrane transport sites, and a long second transmembrane helix (M2) connected with this domain plays critical roles in transmitting motions between the cytoplasmic catalytic domains and transport sites. Here we explore possible structural roles of Gly105 between the cytoplasmic (M2c) and transmembrane (M2m) segments of M2 by introducing mutations that limit/increase conformational freedom. Alanine substitution G105A markedly retards isomerization of the phosphoenzyme intermediate (E1PCa2 → E2PCa2 → E2P + 2Ca2+), and disrupts Ca2+ occlusion in E1PCa2 and E2PCa2 at the transport sites uncoupling ATP hydrolysis and Ca2+ transport. In contrast, this substitution accelerates the ATPase activation (E2 → E1Ca2). Introducing a glycine by substituting another residue on M2 in the G105A mutant (i.e. "G-shift substitution") identifies the glycine positions required for proper Ca2+ handling and kinetics in each step. All wild-type kinetic properties, including coupled transport, are fully restored in the G-shift substitution at position 112 (G105A/A112G) located on the same side of the M2c helix as Gly105 facing M4/phosphorylation domain. Results demonstrate that Gly105 functions as a flexible knee-like joint during the Ca2+ transport cycle, so that cytoplasmic domain motions can bend and strain M2 in the correct direction or straighten the helix for proper gating and coupling of Ca2+ transport and ATP hydrolysis.
Collapse
Affiliation(s)
- Takashi Daiho
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
| | - Kazuo Yamasaki
- 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
|
17
|
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
|
18
|
Pedersen JT, Falhof J, Ekberg K, Buch-Pedersen MJ, Palmgren M. Metal Fluoride Inhibition of a P-type H+ Pump: STABILIZATION OF THE PHOSPHOENZYME INTERMEDIATE CONTRIBUTES TO POST-TRANSLATIONAL PUMP ACTIVATION. J Biol Chem 2015; 290:20396-406. [PMID: 26134563 DOI: 10.1074/jbc.m115.639385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Indexed: 11/06/2022] Open
Abstract
The plasma membrane H(+)-ATPase is a P-type ATPase responsible for establishing electrochemical gradients across the plasma membrane in fungi and plants. This essential proton pump exists in two activity states: an autoinhibited basal state with a low turnover rate and a low H(+)/ATP coupling ratio and an activated state in which ATP hydrolysis is tightly coupled to proton transport. Here we characterize metal fluorides as inhibitors of the fungal enzyme in both states. In contrast to findings for other P-type ATPases, inhibition of the plasma membrane H(+)-ATPase by metal fluorides was partly reversible, and the stability of the inhibition varied with the activation state. Thus, the stability of the ATPase inhibitor complex decreased significantly when the pump transitioned from the activated to the basal state, particularly when using beryllium fluoride, which mimics the bound phosphate in the E2P conformational state. Taken together, our results indicate that the phosphate bond of the phosphoenzyme intermediate of H(+)-ATPases is labile in the basal state, which may provide an explanation for the low H(+)/ATP coupling ratio of these pumps in the basal state.
Collapse
Affiliation(s)
- Jesper Torbøl Pedersen
- From the Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Janus Falhof
- From the Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Kira Ekberg
- From the Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark kiek@
| | - Morten Jeppe Buch-Pedersen
- From the Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Michael Palmgren
- From the Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| |
Collapse
|
19
|
Daiho T, Yamasaki K, Danko S, Suzuki H. Second transmembrane helix (M2) and long range coupling in Ca²⁺-ATPase. J Biol Chem 2014; 289:31241-52. [PMID: 25246522 DOI: 10.1074/jbc.m114.584086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The actuator (A) domain of sarco(endo)plasmic reticulum Ca(2+)-ATPase not only plays a catalytic role but also undergoes large rotational movements that influence the distant transport sites through connections with transmembrane helices M1 and M2. Here we explore the importance of long helix M2 and its junction with the A domain by disrupting the helix structure and elongating with insertions of five glycine residues. Insertions into the membrane region of M2 and the top junctional segment impair Ca(2+) transport despite reasonable ATPase activity, indicating that they are uncoupled. These mutants fail to occlude Ca(2+). Those at the top segment also exhibited accelerated phosphoenzyme isomerization E1P → E2P. Insertions into the middle of M2 markedly accelerate E2P hydrolysis and cause strong resistance to inhibition by luminal Ca(2+). Insertions along almost the entire M2 region inhibit the dephosphorylated enzyme transition E2 → E1. The results pinpoint which parts of M2 control cytoplasm gating and which are critical for luminal gating at each stage in the transport cycle and suggest that proper gate function requires appropriate interactions, tension, and/or rigidity in the M2 region at appropriate times for coupling with A domain movements and catalysis.
Collapse
Affiliation(s)
- Takashi Daiho
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Kazuo Yamasaki
- 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
|
20
|
Toyoshima C, Cornelius F. New crystal structures of PII-type ATPases: excitement continues. Curr Opin Struct Biol 2013; 23:507-14. [PMID: 23871101 DOI: 10.1016/j.sbi.2013.06.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 11/29/2022]
Abstract
P-type ATPases are ATP-powered ion pumps, classified into five subfamilies (PI-PV). Of these, PII-type ATPases, including Ca2+-ATPase, Na+,K+-ATPase and gastric H+,K+-ATPase, among others, have been the most intensively studied. Best understood structurally and biochemically is Ca2+-ATPase from sarcoplasmic reticulum of fast twitch skeletal muscle (sarco(endo)plasmic reticulum Ca2+-ATPase 1a, SERCA1a). Since publication of the first crystal structure in 2000, it has continuously been a source of excitement, as crystal structures for new reaction intermediates always show large structural changes. Crystal structures now exist for most of the reaction intermediates, almost covering the entire reaction cycle. This year the crystal structure of a missing link, the E1·Mg2+ state, finally appeared, bringing another surprise: bound sarcolipin (SLN). The current status of two other important PII-type ATPases, Na+,K+-ATPase and H+,K+-ATPase, is also briefly described.
Collapse
Affiliation(s)
- Chikashi Toyoshima
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.
| | | |
Collapse
|
21
|
Yamasaki K, Daiho T, Danko S, Suzuki H. Roles of long-range electrostatic domain interactions and K+ in phosphoenzyme transition of Ca2+-ATPase. J Biol Chem 2013; 288:20646-57. [PMID: 23737524 DOI: 10.1074/jbc.m113.482711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sarcoplasmic reticulum Ca(2+)-ATPase couples the motions and rearrangements of three cytoplasmic domains (A, P, and N) with Ca(2+) transport. We explored the role of electrostatic force in the domain dynamics in a rate-limiting phosphoenzyme (EP) transition by a systematic approach combining electrostatic screening with salts, computer analysis of electric fields in crystal structures, and mutations. Low KCl concentration activated and increasing salt above 0.1 m inhibited the EP transition. A plot of the logarithm of the transition rate versus the square of the mean activity coefficient of the protein gave a linear relationship allowing division of the activation energy into an electrostatic component and a non-electrostatic component in which the screenable electrostatic forces are shielded by salt. Results show that the structural change in the transition is sterically restricted, but that strong electrostatic forces, when K(+) is specifically bound at the P domain, come into play to accelerate the reaction. Electric field analysis revealed long-range electrostatic interactions between the N and P domains around their hinge. Mutations of the residues directly involved and other charged residues at the hinge disrupted in parallel the electric field and the structural transition. Favorable electrostatics evidently provides a low energy path for the critical N domain motion toward the P domain, overcoming steric restriction. The systematic approach employed here is, in general, a powerful tool for understanding the structural mechanisms of enzymes.
Collapse
Affiliation(s)
- Kazuo Yamasaki
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
| | | | | | | |
Collapse
|
22
|
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
|
23
|
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
|
24
|
Yamasaki K, Daiho T, Danko S, Suzuki H. Ca2+ release to lumen from ADP-sensitive phosphoenzyme E1PCa2 without bound K+ of sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem 2010; 285:38674-83. [PMID: 20937807 PMCID: PMC2992300 DOI: 10.1074/jbc.m110.183343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 10/04/2010] [Indexed: 11/06/2022] Open
Abstract
During Ca(2+) transport by sarcoplasmic reticulum Ca(2+)-ATPase, the conformation change of ADP-sensitive phosphoenzyme (E1PCa(2)) to ADP-insensitive phosphoenzyme (E2PCa(2)) is followed by rapid Ca(2+) release into the lumen. Here, we find that in the absence of K(+), Ca(2+) release occurs considerably faster than E1PCa(2) to E2PCa(2) conformation change. Therefore, the lumenal Ca(2+) release pathway is open to some extent in the K(+)-free E1PCa(2) structure. The Ca(2+) affinity of this E1P is as high as that of the unphosphorylated ATPase (E1), indicating the Ca(2+) binding sites are not disrupted. Thus, bound K(+) stabilizes the E1PCa(2) structure with occluded Ca(2+), keeping the Ca(2+) pathway to the lumen closed. We found previously (Yamasaki, K., Wang, G., Daiho, T., Danko, S., and Suzuki, H. (2008) J. Biol. Chem. 283, 29144-29155) that the K(+) bound in E2P reduces the Ca(2+) affinity essential for achieving the high physiological Ca(2+) gradient and to fully open the lumenal Ca(2+) gate for rapid Ca(2+) release (E2PCa(2) → E2P + 2Ca(2+)). These findings show that bound K(+) is critical for stabilizing both E1PCa(2) and E2P structures, thereby contributing to the structural changes that efficiently couple phosphoenzyme processing and Ca(2+) handling.
Collapse
Affiliation(s)
- Kazuo Yamasaki
- Department of Biochemistry, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | | | | | | |
Collapse
|
25
|
In and out of the cation pumps: P-type ATPase structure revisited. Curr Opin Struct Biol 2010; 20:431-9. [PMID: 20634056 DOI: 10.1016/j.sbi.2010.06.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 06/08/2010] [Accepted: 06/15/2010] [Indexed: 12/12/2022]
Abstract
Active transport across membranes is a crucial requirement for life. P-type ATPases build up electrochemical gradients at the expense of ATP by forming and splitting a covalent phosphoenzyme intermediate, coupled to conformational changes in the transmembrane section where the ions are translocated. The marked increment during the last three years in the number of crystal structures of P-type ATPases has greatly improved our understanding of the similarities and differences of pumps with different ion specificities, since the structures of the Ca2+-ATPase, the Na+,K+-ATPase and the H+-ATPase can now be compared directly. Mechanisms for ion gating, charge neutralization and backflow prevention are starting to emerge from comparative structural analysis; and in combination with functional studies of mutated pumps this provides a framework for speculating on how the ions are bound and released as well as on how specificity is achieved.
Collapse
|
26
|
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
|
27
|
Clausen JD, Andersen JP. Glutamate 90 at the luminal ion gate of sarcoplasmic reticulum Ca2+-ATPase is critical for Ca(2+) binding on both sides of the membrane. J Biol Chem 2010; 285:20780-92. [PMID: 20421308 DOI: 10.1074/jbc.m110.116459] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The roles of Ser(72), Glu(90), and Lys(297) at the luminal ends of transmembrane helices M1, M2, and M4 of sarcoplasmic reticulum Ca(2+)-ATPase were examined by transient and steady-state kinetic analysis of mutants. The dependence on the luminal Ca(2+) concentration of phosphorylation by P(i) ("Ca(2+) gradient-dependent E2P formation") showed a reduction of the apparent affinity for luminal Ca(2+) in mutants with alanine or leucine replacement of Glu(90), whereas arginine replacement of Glu(90) or Ser(72) allowed E2P formation from P(i) even at luminal Ca(2+) concentrations much too small to support phosphorylation in wild type. The latter mutants further displayed a blocked dephosphorylation of E2P and an increased rate of conversion of the ADP-sensitive E1P phosphoenzyme intermediate to ADP-insensitive E2P as well as insensitivity of the E2.BeF(3)(-) complex to luminal Ca(2+). Altogether, these findings, supported by structural modeling, indicate that the E2P intermediate is stabilized in the mutants with arginine replacement of Glu(90) or Ser(72), because the positive charge of the arginine side chain mimics Ca(2+) occupying a luminally exposed low affinity Ca(2+) site of E2P, thus identifying an essential locus (a "leaving site") on the luminal Ca(2+) exit pathway. Mutants with alanine or leucine replacement of Glu(90) further displayed a marked slowing of the Ca(2+) binding transition as well as slowing of the dissociation of Ca(2+) from Ca(2)E1 back toward the cytoplasm, thus demonstrating that Glu(90) is also critical for the function of the cytoplasmically exposed Ca(2+) sites on the opposite side of the membrane relative to where Glu(90) is located.
Collapse
Affiliation(s)
- Johannes D Clausen
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Department of Physiology and Biophysics, Aarhus University, DK-8000 Aarhus C, Denmark
| | | |
Collapse
|
28
|
Abe K, Tani K, Fujiyoshi Y. Structural and functional characterization of H+,K+-ATPase with bound fluorinated phosphate analogs. J Struct Biol 2010; 170:60-8. [DOI: 10.1016/j.jsb.2009.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/02/2009] [Accepted: 12/08/2009] [Indexed: 11/26/2022]
|
29
|
Suzuki H, Yamasaki K, Daiho T, Danko S. [Mechanism of ca(2+) pump as revealed by mutations, development of stable analogs of phosphorylated intermediates, and their structural analyses]. YAKUGAKU ZASSHI 2010; 130:179-89. [PMID: 20118641 DOI: 10.1248/yakushi.130.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sarco(endo)plasmic reticulum Ca(2+)-ATPase is a representative member of P-type cation transporting ATPases and catalyzes Ca(2+) transport coupled with ATP hydrolysis. The ATPase possesses three cytoplasmic domains (N, P, and A) and ten transmembrane helices (M1-M10). Ca(2+) binding at the transport sites in the transmembrane domain activates the ATPase and then the catalytic aspartate is auto-phosphorylated to form the phosphorylated intermediate (EP). Structural and functional studies have shown that, during the isomerization of EP in the Ca(2+) transport cycle, large motions of the three cytoplasmic domains take place, which then rearranges the transmembrane helices thereby destroying the Ca(2+) binding sites, opening the lumenal gate, and thus releasing the Ca(2+) into lumen. Stable structural analogues for the Ca(2+)-occluded and -released states of phosphorylated intermediates and for the transition and product states of the phosphorylation and dephosphorylation reactions were developed for biochemical and atomic-level structural studies to reveal the coupled changes in the catalytic and transport sites. Mutation studies identified the residues and structural regions essential for the structural changes and Ca(2+) transport function. Genetic dysfunction of Ca(2+)-ATPase causes various isoform-specific diseases. In this manuscript, recent understanding of the Ca-ATPase will be reviewed.
Collapse
Affiliation(s)
- Hiroshi Suzuki
- Department of Biochemistry, Asahikawa Medical College, Hokkaido, Japan.
| | | | | | | |
Collapse
|