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Zubareva VM, Lapashina AS, Shugaeva TE, Litvin AV, Feniouk BA. Rotary Ion-Translocating ATPases/ATP Synthases: Diversity, Similarities, and Differences. BIOCHEMISTRY (MOSCOW) 2021; 85:1613-1630. [PMID: 33705299 DOI: 10.1134/s0006297920120135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ion-translocating ATPases and ATP synthases (F-, V-, A-type ATPases, and several P-type ATPases and ABC-transporters) catalyze ATP hydrolysis or ATP synthesis coupled with the ion transport across the membrane. F-, V-, and A-ATPases are protein nanomachines that combine transmembrane transport of protons or sodium ions with ATP synthesis/hydrolysis by means of a rotary mechanism. These enzymes are composed of two multisubunit subcomplexes that rotate relative to each other during catalysis. Rotary ATPases phosphorylate/dephosphorylate nucleotides directly, without the generation of phosphorylated protein intermediates. F-type ATPases are found in chloroplasts, mitochondria, most eubacteria, and in few archaea. V-type ATPases are eukaryotic enzymes present in a variety of cellular membranes, including the plasma membrane, vacuoles, late endosomes, and trans-Golgi cisternae. A-type ATPases are found in archaea and some eubacteria. F- and A-ATPases have two main functions: ATP synthesis powered by the proton motive force (pmf) or, in some prokaryotes, sodium-motive force (smf) and generation of the pmf or smf at the expense of ATP hydrolysis. In prokaryotes, both functions may be vitally important, depending on the environment and the presence of other enzymes capable of pmf or smf generation. In eukaryotes, the primary and the most crucial function of F-ATPases is ATP synthesis. Eukaryotic V-ATPases function exclusively as ATP-dependent proton pumps that generate pmf necessary for the transmembrane transport of ions and metabolites and are vitally important for pH regulation. This review describes the diversity of rotary ion-translocating ATPases from different organisms and compares the structural, functional, and regulatory features of these enzymes.
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Affiliation(s)
- V M Zubareva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A S Lapashina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - T E Shugaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A V Litvin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Almasi S, El Hiani Y. Exploring the Therapeutic Potential of Membrane Transport Proteins: Focus on Cancer and Chemoresistance. Cancers (Basel) 2020; 12:cancers12061624. [PMID: 32575381 PMCID: PMC7353007 DOI: 10.3390/cancers12061624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Improving the therapeutic efficacy of conventional anticancer drugs represents the best hope for cancer treatment. However, the shortage of druggable targets and the increasing development of anticancer drug resistance remain significant problems. Recently, membrane transport proteins have emerged as novel therapeutic targets for cancer treatment. These proteins are essential for a plethora of cell functions ranging from cell homeostasis to clinical drug toxicity. Furthermore, their association with carcinogenesis and chemoresistance has opened new vistas for pharmacology-based cancer research. This review provides a comprehensive update of our current knowledge on the functional expression profile of membrane transport proteins in cancer and chemoresistant tumours that may form the basis for new cancer treatment strategies.
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Affiliation(s)
- Shekoufeh Almasi
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON KIH 8M5, Canada;
| | - Yassine El Hiani
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Correspondence:
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Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit. Int J Mol Sci 2019; 20:ijms20174186. [PMID: 31461845 PMCID: PMC6747279 DOI: 10.3390/ijms20174186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022] Open
Abstract
Traditionally, X-ray crystallography and NMR spectroscopy represent major workhorses of structural biologists, with the lion share of protein structures reported in protein data bank (PDB) being generated by these powerful techniques. Despite their wide utilization in protein structure determination, these two techniques have logical limitations, with X-ray crystallography being unsuitable for the analysis of highly dynamic structures and with NMR spectroscopy being restricted to the analysis of relatively small proteins. In recent years, we have witnessed an explosive development of the techniques based on Cryo-electron microscopy (Cryo-EM) for structural characterization of biological molecules. In fact, single-particle Cryo-EM is a special niche as it is a technique of choice for the structural analysis of large, structurally heterogeneous, and dynamic complexes. Here, sub-nanometer atomic resolution can be achieved (i.e., resolution below 10 Å) via single-particle imaging of non-crystalline specimens, with accurate 3D reconstruction being generated based on the computational averaging of multiple 2D projection images of the same particle that was frozen rapidly in solution. We provide here a brief overview of single-particle Cryo-EM and show how Cryo-EM has revolutionized structural investigations of membrane proteins. We also show that the presence of intrinsically disordered or flexible regions in a target protein represents one of the major limitations of this promising technique.
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Jain A, Holthuis JCM. Membrane contact sites, ancient and central hubs of cellular lipid logistics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1450-1458. [PMID: 28554771 DOI: 10.1016/j.bbamcr.2017.05.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 12/26/2022]
Abstract
Membrane contact sites (MCSs) are regions where two organelles are closely apposed to facilitate molecular communication and promote a functional integration of compartmentalized cellular processes. There is growing evidence that MCSs play key roles in controlling intracellular lipid flows and distributions. Strikingly, even organelles connected by vesicular trafficking exchange lipids en bulk via lipid transfer proteins that operate at MCSs. Herein, we describe how MCSs developed into central hubs of lipid logistics during the evolution of eukaryotic cells. We then focus on how modern eukaryotes exploit MCSs to help solve a major logistical problem, namely to preserve the unique lipid mixtures of their early and late secretory organelles in the face of extensive vesicular trafficking. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.
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Affiliation(s)
- Amrita Jain
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Joost C M Holthuis
- Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany; Membrane Biochemistry & Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands.
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Gould SB, Garg SG, Martin WF. Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System. Trends Microbiol 2016; 24:525-534. [PMID: 27040918 DOI: 10.1016/j.tim.2016.03.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/21/2022]
Abstract
Eukaryotes possess an elaborate endomembrane system with endoplasmic reticulum, nucleus, Golgi, lysosomes, peroxisomes, autophagosomes, and dynamic vesicle traffic. Theories addressing the evolutionary origin of eukaryotic endomembranes have overlooked the outer membrane vesicles (OMVs) that bacteria, archaea, and mitochondria secrete into their surroundings. We propose that the eukaryotic endomembrane system originated from bacterial OMVs released by the mitochondrial ancestor within the cytosol of its archaeal host at eukaryote origin. Confined within the host's cytosol, OMVs accumulated naturally, fusing either with each other or with the host's plasma membrane. This matched the host's archaeal secretory pathway for cotranslational protein insertion with outward bound mitochondrial-derived vesicles consisting of bacterial lipids, forging a primordial, secretory endoplasmic reticulum as the cornerstone of the eukaryotic endomembrane system. VIDEO ABSTRACT.
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Affiliation(s)
- Sven B Gould
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
| | - Sriram G Garg
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
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Balakrishna AM, Manimekalai MSS, Grüber G. Protein-protein interactions within the ensemble, eukaryotic V-ATPase, and its concerted interactions with cellular machineries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:84-93. [PMID: 26033199 DOI: 10.1016/j.pbiomolbio.2015.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/27/2022]
Abstract
The V1VO-ATPase (V-ATPase) is the important proton-pump in eukaryotic cells, responsible for pH-homeostasis, pH-sensing and amino acid sensing, and therefore essential for cell growths and metabolism. ATP-cleavage in the catalytic A3B3-hexamer of V1 has to be communicated via several so-called central and peripheral stalk units to the proton-pumping VO-part, which is membrane-embedded. A unique feature of V1VO-ATPase regulation is its reversible disassembly of the V1 and VO domain. Actin provides a network to hold the V1 in proximity to the VO, enabling effective V1VO-assembly to occur. Besides binding to actin, the 14-subunit V-ATPase interacts with multi-subunit machineries to form cellular sensors, which regulate the pH in cellular compartments or amino acid signaling in lysosomes. Here we describe a variety of subunit-subunit interactions within the V-ATPase enzyme during catalysis and its protein-protein assembling with key cellular machineries, essential for cellular function.
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Affiliation(s)
- Asha Manikkoth Balakrishna
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Malathy Sony Subramanian Manimekalai
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
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Mai YZ, Li YW, Li RJ, Li W, Huang XZ, Mo ZQ, Li AX. Proteomic analysis of differentially expressed proteins in the marine fish parasitic ciliate Cryptocaryon irritans. Vet Parasitol 2015; 211:1-11. [PMID: 25997646 DOI: 10.1016/j.vetpar.2015.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/26/2015] [Accepted: 05/07/2015] [Indexed: 12/24/2022]
Abstract
Cryptocaryoniasis is a severe disease of farmed marine fish caused by the parasitic ciliate Cryptocaryon irritans. This disease can lead to considerable economic loss, but studies on proteins linked to disease development and antigenic proteins for vaccine development have been relatively scarce to date. In this study, 53 protein spots with differential abundance, representing 12 proteins, were identified based on a pair-wise comparison among theronts, trophonts, and tomonts. Meanwhile, 33 protein spots that elicited serological responses in rabbits were identified, representing 9 proteins. In addition, 27 common antigenic protein spots reacted with grouper anti-sera, representing 10 proteins. Most of the identified proteins were involved in cytoskeletal and metabolic pathways. Among these proteins, actin and α-tubulin appeared in all three developmental stages with differences in molecular weights and isoelectric points; 4 proteins (vacuolar ATP synthase catalytic subunit α, mcm2-3-5 family protein, 26S proteasome subunit P45 family protein and dnaK protein) were highly expressed only in theronts; while protein kinase domain containing protein and heat shock protein 70 showed high levels of expression only in trophonts and tomonts, respectively. Moreover, actin was co-detected with 3 rabbit anti-sera while β-tubulin, V-type ATPase α subunit family protein, heat shock protein 70, mitochondrial-type hsp70, and dnaK proteins showed immunoreactivity with corresponding rabbit anti-sera in theronts, trophonts, and tomonts. Furthermore, β-tubulin, the metabolic-related protein enolase, NADH-ubiquinone oxidoreductase 75 kDa subunit, malate dehydrogenase, as well as polypyrimidine tract-binding protein, glutamine synthetase, protein kinase domain containing protein, TNFR/NGFR cysteine-rich region family protein, and vacuolar ATP synthase catalytic subunit α, were commonly detected by grouper anti-sera. Therefore, these findings could contribute to an understanding of the differences in gene expression and phenotypes among the different stages of parasitic infection, and might be considered as a source of candidate proteins for disease diagnosis and vaccine development.
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Affiliation(s)
- Yong-Zhan Mai
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yan-Wei Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Rui-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xia-Zi Huang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Ze-Quan Mo
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - An-Xing Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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Grüber G, Manimekalai MSS, Mayer F, Müller V. ATP synthases from archaea: the beauty of a molecular motor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:940-52. [PMID: 24650628 DOI: 10.1016/j.bbabio.2014.03.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 11/18/2022]
Abstract
Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class of ATP synthases distinct from the F1FO ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A1AO ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H(+), Na(+) or even H(+) and Na(+) using enzymes. The evolution of the H(+) binding site to a Na(+) binding site and its implications for the energy metabolism and physiology of the cell are discussed.
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Affiliation(s)
- Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
| | | | - Florian Mayer
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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Marshansky V, Rubinstein JL, Grüber G. Eukaryotic V-ATPase: novel structural findings and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:857-79. [PMID: 24508215 DOI: 10.1016/j.bbabio.2014.01.018] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 12/25/2013] [Accepted: 01/27/2014] [Indexed: 02/06/2023]
Abstract
The eukaryotic V-type adenosine triphosphatase (V-ATPase) is a multi-subunit membrane protein complex that is evolutionarily related to F-type adenosine triphosphate (ATP) synthases and A-ATP synthases. These ATPases/ATP synthases are functionally conserved and operate as rotary proton-pumping nano-motors, invented by Nature billions of years ago. In the first part of this review we will focus on recent structural findings of eukaryotic V-ATPases and discuss the role of different subunits in the function of the V-ATPase holocomplex. Despite structural and functional similarities between rotary ATPases, the eukaryotic V-ATPases are the most complex enzymes that have acquired some unconventional cellular functions during evolution. In particular, the novel roles of V-ATPases in the regulation of cellular receptors and their trafficking via endocytotic and exocytotic pathways were recently uncovered. In the second part of this review we will discuss these unique roles of V-ATPases in modulation of function of cellular receptors, involved in the development and progression of diseases such as cancer and diabetes as well as neurodegenerative and kidney disorders. Moreover, it was recently revealed that the V-ATPase itself functions as an evolutionarily conserved pH sensor and receptor for cytohesin-2/Arf-family GTP-binding proteins. Thus, in the third part of the review we will evaluate the structural basis for and functional insights into this novel concept, followed by the analysis of the potentially essential role of V-ATPase in the regulation of this signaling pathway in health and disease. Finally, future prospects for structural and functional studies of the eukaryotic V-ATPase will be discussed.
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Affiliation(s)
- Vladimir Marshansky
- Center for Systems Biology, Program in Membrane Biology, Division of Nephrology, Simches Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Kadmon Pharmaceuticals Corporation, Alexandria Center for Life Science, 450 East 29th Street, New York, NY 10016, USA.
| | - John L Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5G 1X8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Gerhard Grüber
- Nanyang Technological University, Division of Structural Biology and Biochemistry, School of Biological Sciences, Singapore 637551, Republic of Singapore; Bioinformatics Institute, A(⁎)STAR, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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Forterre P. The common ancestor of archaea and eukarya was not an archaeon. ARCHAEA (VANCOUVER, B.C.) 2013; 2013:372396. [PMID: 24348094 PMCID: PMC3855935 DOI: 10.1155/2013/372396] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/24/2013] [Indexed: 02/06/2023]
Abstract
It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
- Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France
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Muench SP, Scheres SHW, Huss M, Phillips C, Vitavska O, Wieczorek H, Trinick J, Harrison MA. Subunit positioning and stator filament stiffness in regulation and power transmission in the V1 motor of the Manduca sexta V-ATPase. J Mol Biol 2013; 426:286-300. [PMID: 24075871 PMCID: PMC3899036 DOI: 10.1016/j.jmb.2013.09.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/01/2022]
Abstract
The vacuolar H+-ATPase (V-ATPase) is an ATP-driven proton pump essential to the function of eukaryotic cells. Its cytoplasmic V1 domain is an ATPase, normally coupled to membrane-bound proton pump Vo via a rotary mechanism. How these asymmetric motors are coupled remains poorly understood. Low energy status can trigger release of V1 from the membrane and curtail ATP hydrolysis. To investigate the molecular basis for these processes, we have carried out cryo-electron microscopy three-dimensional reconstruction of deactivated V1 from Manduca sexta. In the resulting model, three peripheral stalks that are parts of the mechanical stator of the V-ATPase are clearly resolved as unsupported filaments in the same conformations as in the holoenzyme. They are likely therefore to have inherent stiffness consistent with a role as flexible rods in buffering elastic power transmission between the domains of the V-ATPase. Inactivated V1 adopted a homogeneous resting state with one open active site adjacent to the stator filament normally linked to the H subunit. Although present at 1:1 stoichiometry with V1, both recombinant subunit C reconstituted with V1 and its endogenous subunit H were poorly resolved in three-dimensional reconstructions, suggesting structural heterogeneity in the region at the base of V1 that could indicate positional variability. If the position of H can vary, existing mechanistic models of deactivation in which it binds to and locks the axle of the V-ATPase rotary motor would need to be re-evaluated. Dissociation of vacuolar H+-ATPase domains deactivates its V1 motor. V1 has one “open” catalytic site linked to the stator filament bound by subunit H. Movement of subunit H to prevent rotary catalysis is possible. Three stator filaments project from deactivated V1, indicating inherent stiffness. This work gives new insight into energetic coupling and control in V-ATPases.
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Affiliation(s)
- Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Markus Huss
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - Clair Phillips
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Olga Vitavska
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - Helmut Wieczorek
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - John Trinick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael A Harrison
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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Nagamatsu Y, Takeda K, Kuranaga T, Numoto N, Miki K. Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus. J Mol Biol 2013; 425:2699-708. [PMID: 23639357 DOI: 10.1016/j.jmb.2013.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/21/2013] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
Abstract
V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases. Here, we report a complete model of the extra-membrane domain of the V-ATPase (V1-ATPase) of a thermophilic bacterium, Thermus thermophilus, consisting of three A subunits, three B subunits, one D subunit, and one F subunit. The X-ray structure at 3.9Å resolution provides detailed information about the interactions between A3B3 and DF subcomplexes as well as interactions among the respective subunits, which are defined by the properties of side chains. Asymmetry at the intersubunit interfaces was detected from the structural differences among the three AB pairs in the different reaction states, while the large interdomain motion in the catalytic A subunits was not observed unlike F1 from various species and V1 from Enterococcus hirae. Asymmetry is mainly realized by rigid-body rearrangements of the relative position between A and B subunits. This is consistent with the previous observations by the high-resolution electron microscopy for the whole V-ATPase complexes. Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits.
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Affiliation(s)
- Yumemi Nagamatsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Basak S, Lim J, Manimekalai MSS, Balakrishna AM, Grüber G. Crystal and NMR structures give insights into the role and dynamics of subunit F of the eukaryotic V-ATPase from Saccharomyces cerevisiae. J Biol Chem 2013; 288:11930-9. [PMID: 23476018 DOI: 10.1074/jbc.m113.461533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subunit F of V-ATPases is proposed to undergo structural alterations during catalysis and reversible dissociation from the V1VO complex. Recently, we determined the low resolution structure of F from Saccharomyces cerevisiae V-ATPase, showing an N-terminal egg shape, connected to a C-terminal hook-like segment via a linker region. To understand the mechanistic role of subunit F of S. cerevisiae V-ATPase, composed of 118 amino acids, the crystal structure of the major part of F, F(1-94), was solved at 2.3 Å resolution. The structural features were confirmed by solution NMR spectroscopy using the entire F subunit. The eukaryotic F subunit consists of the N-terminal F(1-94) domain with four-parallel β-strands, which are intermittently surrounded by four α-helices, and the C terminus, including the α5-helix encompassing residues 103 to 113. Two loops (26)GQITPETQEK(35) and (60)ERDDI(64) are described to be essential in mechanistic processes of the V-ATPase enzyme. The (26)GQITPETQEK(35) loop becomes exposed when fitted into the recently determined EM structure of the yeast V1VO-ATPase. A mechanism is proposed in which the (26)GQITPETQEK(35) loop of subunit F and the flexible C-terminal domain of subunit H move in proximity, leading to an inhibitory effect of ATPase activity in V1. Subunits D and F are demonstrated to interact with subunit d. Together with NMR dynamics, the role of subunit F has been discussed in the light of its interactions in the processes of reversible disassembly and ATP hydrolysis of V-ATPases by transmitting movements of subunit d and H of the VO and V1 sector, respectively.
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Affiliation(s)
- Sandip Basak
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
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14
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Kulkarni H, Göring HHH, Curran JE, Diego V, Dyer TD, Cole S, Walder KR, Collier GR, Blangero J, Carless MA. Genetic basis for the increased expression of vacuolar H+ translocating ATPase genes upon imatinib treatment in human lymphoblastoid cells. Cancer Chemother Pharmacol 2013; 71:1095-100. [PMID: 23420437 DOI: 10.1007/s00280-013-2110-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 02/05/2013] [Indexed: 12/01/2022]
Abstract
PURPOSE The role of v-ATPases in cancer biology is being increasingly recognized. Yeast studies indicate that the tyrosine kinase inhibitor imatinib may interact with the v-ATPase genes and alter the course of cancer progression. Data from humans in this regard are lacking. METHODS We constructed 55 lymphoblastoid cell lines from pedigreed, cancer-free human subjects and treated them with IC20 concentration of imatinib mesylate. Using these cell lines, we (i) estimated the heritability and differential expression of 19 genes encoding several subunits of the v-ATPase protein in response to imatinib treatment; (ii) estimated the genetic similarity among these genes; and (iii) conducted a high-density scan to find cis-regulating genetic variation associated with differential expression of these genes. RESULTS We found that the imatinib response of the genes encoding v-ATPase subunits is significantly heritable and can be clustered to identify novel drug targets in imatinib therapy. Further, five of these genes were significantly cis-regulated and together represented nearly half-log fold change in response to imatinib (p = 0.0107) that was homogenous (p = 0.2598). CONCLUSIONS Our results proffer support to the growing view that personalized regimens using proton pump inhibitors or v-ATPase inhibitors may improve outcomes of imatinib therapy in various cancers.
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Affiliation(s)
- Hemant Kulkarni
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
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15
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Hosokawa H, Dip PV, Merkulova M, Bakulina A, Zhuang Z, Khatri A, Jian X, Keating SM, Bueler SA, Rubinstein JL, Randazzo PA, Ausiello DA, Grüber G, Marshansky V. The N termini of a-subunit isoforms are involved in signaling between vacuolar H+-ATPase (V-ATPase) and cytohesin-2. J Biol Chem 2013; 288:5896-913. [PMID: 23288846 DOI: 10.1074/jbc.m112.409169] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previously, we reported an acidification-dependent interaction of the endosomal vacuolar H(+)-ATPase (V-ATPase) with cytohesin-2, a GDP/GTP exchange factor (GEF), suggesting that it functions as a pH-sensing receptor. Here, we have studied the molecular mechanism of signaling between the V-ATPase, cytohesin-2, and Arf GTP-binding proteins. We found that part of the N-terminal cytosolic tail of the V-ATPase a2-subunit (a2N), corresponding to its first 17 amino acids (a2N(1-17)), potently modulates the enzymatic GDP/GTP exchange activity of cytohesin-2. Moreover, this peptide strongly inhibits GEF activity via direct interaction with the Sec7 domain of cytohesin-2. The structure of a2N(1-17) and its amino acids Phe(5), Met(10), and Gln(14) involved in interaction with Sec7 domain were determined by NMR spectroscopy analysis. In silico docking experiments revealed that part of the V-ATPase formed by its a2N(1-17) epitope competes with the switch 2 region of Arf1 and Arf6 for binding to the Sec7 domain of cytohesin-2. The amino acid sequence alignment and GEF activity studies also uncovered the conserved character of signaling between all four (a1-a4) a-subunit isoforms of mammalian V-ATPase and cytohesin-2. Moreover, the conserved character of this phenomenon was also confirmed in experiments showing binding of mammalian cytohesin-2 to the intact yeast V-ATPase holo-complex. Thus, here we have uncovered an evolutionarily conserved function of the V-ATPase as a novel cytohesin-signaling receptor.
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Affiliation(s)
- Hiroyuki Hosokawa
- Center for Systems Biology, Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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16
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Relevance of the conserved histidine and asparagine residues in the phosphate-binding loop of the nucleotide binding subunit B of A₁A₀ ATP synthases. J Struct Biol 2012; 180:509-18. [PMID: 23063756 DOI: 10.1016/j.jsb.2012.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/28/2012] [Accepted: 10/01/2012] [Indexed: 11/21/2022]
Abstract
The nucleotide binding sites in A-ATP synthases are located at the interfaces of subunit A and B, which is proposed to play a regulatory role. Differential binding of MgATP and -ADP to subunit B has been described, which does not exist in the related α and B subunits of F-ATP synthases and V-ATPases, respectively. The conserved phosphate loop residues, histidine and asparagine, of the A-ATP synthase subunit B have been proposed to be essential for γ-phosphate interaction. To investigate the role of these conserved P-loop residues in nucleotide-binding, subunit B residues H156 and N157 of the Methanosarcina mazei Gö1 A-ATP synthase were separately substituted with alanine. In addition, N157 was mutated to threonine, because it is the corresponding amino acid in the P-loop of F-ATP synthase subunit α. The structures of the subunit B mutants H156A, N157A/T were solved up to a resolution of 1.75 and 1.7 Å. The binding constants for MgATP and -ADP were determined, demonstrating that the H156A and N157A mutants have a preference to the nucleotide over the wild type and N157T proteins. Importantly, the ability to distinguish MgATP or -ADP was lost, demonstrating that the histidine and asparagine residues are crucial for nucleotide differentiation in subunit B. The structures reveal that the enhanced binding of the alanine mutants is attributed to the increased accessibility of the nucleotide binding cavity, explaining that the structural arrangement of the conserved H156 and N157 define the nucleotide-binding characteristics of the regulatory subunit B of A-ATP synthases.
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17
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Mayer F, Leone V, Langer JD, Faraldo-Gómez JD, Müller V. A c subunit with four transmembrane helices and one ion (Na+)-binding site in an archaeal ATP synthase: implications for c ring function and structure. J Biol Chem 2012; 287:39327-37. [PMID: 23007388 DOI: 10.1074/jbc.m112.411223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ion-driven membrane rotors of ATP synthases consist of multiple copies of subunit c, forming a closed ring. Subunit c typically comprises two transmembrane helices, and the c ring features an ion-binding site in between each pair of adjacent subunits. Here, we use experimental and computational methods to study the structure and specificity of an archaeal c subunit more akin to those of V-type ATPases, namely that from Pyrococcus furiosus. The c subunit was purified by chloroform/methanol extraction and determined to be 15.8 kDa with four predicted transmembrane helices. However, labeling with DCCD as well as Na(+)-DCCD competition experiments revealed only one binding site for DCCD and Na(+), indicating that the mature c subunit of this A(1)A(O) ATP synthase is indeed of the V-type. A structural model generated computationally revealed one Na(+)-binding site within each of the c subunits, mediated by a conserved glutamate side chain alongside other coordinating groups. An intriguing second glutamate located in-between adjacent c subunits was ruled out as a functional Na(+)-binding site. Molecular dynamics simulations indicate that the c ring of P. furiosus is highly Na(+)-specific under in vivo conditions, comparable with the Na(+)-dependent V(1)V(O) ATPase from Enterococcus hirae. Interestingly, the same holds true for the c ring from the methanogenic archaeon Methanobrevibacter ruminantium, whose c subunits also feature a V-type architecture but carry two Na(+)-binding sites instead. These findings are discussed in light of their physiological relevance and with respect to the mode of ion coupling in A(1)A(O) ATP synthases.
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Affiliation(s)
- Florian Mayer
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany
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18
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Basak S, Balakrishna AM, Manimekalai MSS, Grüber G. Crystallization and preliminary X-ray crystallographic analysis of subunit F (F(1-94)), an essential coupling subunit of the eukaryotic V(1)V(O)-ATPase from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1055-9. [PMID: 22949193 PMCID: PMC3433196 DOI: 10.1107/s1744309112032526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/17/2012] [Indexed: 11/10/2022]
Abstract
V-ATPases are very complex multi-subunit enzymes which function as proton-pumping rotary nanomotors. The rotary and coupling subunit F (F(1-94)) was crystallized by the hanging-drop vapour-diffusion method. The native crystals diffracted to a resolution of 2.64 Å and belonged to space group C222(1), with unit-cell parameters a = 47.21, b = 160.26, c = 102.49 Å. The selenomethionyl form of the F(1-94) I69M mutant diffracted to a resolution of 2.3 Å and belonged to space group C222(1), with unit-cell parameters a = 47.22, b = 160.83, c = 102.74 Å. Initial phasing and model building suggested the presence of four molecules in the asymmetric unit.
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Affiliation(s)
- Sandip Basak
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Asha Manikkoth Balakrishna
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Balakrishna AM, Hunke C, Grüber G. The Structure of Subunit E of the Pyrococcus horikoshii OT3 A-ATP Synthase Gives Insight into the Elasticity of the Peripheral Stalk. J Mol Biol 2012; 420:155-63. [DOI: 10.1016/j.jmb.2012.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/04/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
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20
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Bhargava A, Voronov I, Wang Y, Glogauer M, Kartner N, Manolson MF. Osteopetrosis mutation R444L causes endoplasmic reticulum retention and misprocessing of vacuolar H+-ATPase a3 subunit. J Biol Chem 2012; 287:26829-39. [PMID: 22685294 DOI: 10.1074/jbc.m112.345702] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Osteopetrosis is a genetic bone disease characterized by increased bone density and fragility. The R444L missense mutation in the human V-ATPase a3 subunit (TCIRG1) is one of several known mutations in a3 and other proteins that can cause this disease. The autosomal recessive R444L mutation results in a particularly malignant form of infantile osteopetrosis that is lethal in infancy, or early childhood. We have studied this mutation using the pMSCV retroviral vector system to integrate the cDNA construct for green fluorescent protein (GFP)-fused a3(R445L) mutant protein into the RAW 264.7 mouse osteoclast differentiation model. In comparison with wild-type a3, the mutant glycoprotein localized to the ER instead of lysosomes and its oligosaccharide moiety was misprocessed, suggesting inability of the core-glycosylated glycoprotein to traffic to the Golgi. Reduced steady-state expression of the mutant protein, in comparison with wild type, suggested that the former was being degraded, likely through the endoplasmic reticulum-associated degradation pathway. In differentiated osteoclasts, a3(R445L) was found to degrade at an increased rate over the course of osteoclastogenesis. Limited proteolysis studies suggested that the R445L mutation alters mouse a3 protein conformation. Together, these data suggest that Arg-445 plays a role in protein folding, or stability, and that infantile malignant osteopetrosis caused by the R444L mutation in the human V-ATPase a3 subunit is another member of the growing class of protein folding diseases. This may have implications for early-intervention treatment, using protein rescue strategies.
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Affiliation(s)
- Ajay Bhargava
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
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21
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Dip PV, Saw WG, Roessle M, Marshansky V, Grüber G. Solution structure of subunit a, a 104-363, of the Saccharomyces cerevisiae V-ATPase and the importance of its C-terminus in structure formation. J Bioenerg Biomembr 2012; 44:341-50. [DOI: 10.1007/s10863-012-9442-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 04/19/2012] [Indexed: 11/30/2022]
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22
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Kane PM. Targeting reversible disassembly as a mechanism of controlling V-ATPase activity. Curr Protein Pept Sci 2012; 13:117-23. [PMID: 22044153 PMCID: PMC3536023 DOI: 10.2174/138920312800493142] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/05/2011] [Accepted: 08/06/2011] [Indexed: 11/22/2022]
Abstract
Vacuolar proton-translocating ATPases (V-ATPases) are highly conserved proton pumps consisting of a peripheral membrane subcomplex called V1, which contains the sites of ATP hydrolysis, attached to an integral membrane subcomplex called Vo, which encompasses the proton pore. V-ATPase regulation by reversible dissociation, characterized by release of assembled V1 sectors into the cytosol and inhibition of both ATPase and proton transport activities, was first identified in tobacco hornworm and yeast. It has since become clear that modulation of V-ATPase assembly level is also a regulatory mechanism in mammalian cells. In this review, the implications of reversible disassembly for V-ATPase structure are discussed, along with insights into underlying subunit-subunit interactions provided by recent structural work. Although initial experiments focused on glucose deprivation as a trigger for disassembly, it is now clear that V-ATPase assembly can be regulated by other extracellular conditions. Consistent with a complex, integrated response to extracellular signals, a number of different regulatory proteins, including RAVE/rabconnectin, aldolase and other glycolytic enzymes, and protein kinase A have been suggested to control V-ATPase assembly and disassembly. It is likely that multiple signaling pathways dictate the ultimate level of assembly and activity. Tissue-specific V-ATPase inhibition is a potential therapy for osteoporosis and cancer; the possibility of exploiting reversible disassembly in design of novel V-ATPase inhibitors is discussed.
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Affiliation(s)
- Patricia M Kane
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY 13210, USA.
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23
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Raghunathan D, Gayen S, Kumar A, Hunke C, Grüber G, Verma CS. Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Gö1. J Bioenerg Biomembr 2012; 44:213-24. [PMID: 22350011 DOI: 10.1007/s10863-012-9410-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/08/2012] [Indexed: 10/28/2022]
Abstract
The interaction of the nucleotide-binding subunit B with subunit F is essential in coupling of ion pumping and ATP synthesis in A(1)A(O) ATP synthases. Here we provide structural and thermodynamic insights on the nucleotide binding to the surface of subunits B and F of Methanosarcina mazei Gö1 A(1)A(O) ATP synthase, which initiated migration to its final binding pocket via two transitional intermediates on the surface of subunit B. NMR- and fluorescence spectroscopy as well as ITC data combined with molecular dynamics simulations of the nucleotide bound subunit B and nucleotide bound B-F complex in explicit solvent, suggests that subunit F is critical for the migration to and eventual occupancy of the final binding site by the nucleotide of subunit B. Rotation of the C-terminus and conformational changes in subunit B are initiated upon binding with subunit F causing a perturbation that leads to the migration of ATP from the transition site 1 through an intermediate transition site 2 to the final binding site 3. This mechanism is elucidated on the basis of change in binding affinity for the nucleotide at the specific sites on subunit B upon complexation with subunit F. The change in enthalpy is further explained based on the fluctuating local environment around the binding sites.
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24
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Tadwal VS, Manimekalai MSS, Grüber G. Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1485-91. [PMID: 22139149 PMCID: PMC3232122 DOI: 10.1107/s1744309111039595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
A reporter tryptophan residue was individually introduced by site-directed mutagenesis into the adenine-binding pocket of the catalytic subunit A (F427W and F508W mutants) of the motor protein A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3. The crystal structures of the F427W and F508W mutant proteins were determined to 2.5 and 2.6 Å resolution, respectively. The tryptophan substitution caused the fluorescence signal to increase by 28% (F427W) and 33% (F508W), with a shift from 333 nm in the wild-type protein to 339 nm in the mutant proteins. Tryptophan emission spectra showed binding of Mg-ATP to the F427W mutant with a K(d) of 8.5 µM. In contrast, no significant binding of nucleotide could be observed for the F508W mutant. A closer inspection of the crystal structure of the F427W mutant showed that the adenine-binding pocket had widened by 0.7 Å (to 8.70 Å) in comparison to the wild-type subunit A (8.07 Å) owing to tryptophan substitution, as a result of which it was able to bind ATP. In contrast, the adenine-binding pocket had narrowed in the F508W mutant. The two mutants presented demonstrate that the exact volume of the adenine ribose binding pocket is essential for nucleotide binding and even minor narrowing makes it unfit for nucleotide binding. In addition, structural and fluorescence data confirmed the viability of the fluorescently active mutant F427W, which had ideal tryptophan spectra for future structure-based time-resolved dynamic measurements of the catalytic subunit A of the ATP-synthesizing enzyme A-ATP synthase.
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25
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Rishikesan S, Grüber G. Structural elements of the C-terminal domain of subunit E (E₁₃₃₋₂₂₂) from the Saccharomyces cerevisiae V₁V₀ ATPase determined by solution NMR spectroscopy. J Bioenerg Biomembr 2011; 43:447-55. [PMID: 21826517 DOI: 10.1007/s10863-011-9379-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/15/2011] [Indexed: 01/08/2023]
Abstract
Subunit E of the vacuolar ATPase (V-ATPase) contains an N-terminal extended α helix (Rishikesan et al. J Bioenerg Biomembr 43:187-193, 2011) and a globular C-terminal part that is predicted to consist of a mixture of α-helices and β-sheets (Grüber et al. Biochem Biophys Res Comm 298:383-391, 2002). Here we describe the production, purification and 2D structure of the C-terminal segment E₁₃₃₋₂₂₂ of subunit E from Saccharamyces cerevisiae V-ATPase in solution based on the secondary structure calculation from NMR spectroscopy studies. E₁₃₃₋₂₂₂ consists of four β-strands, formed by the amino acids from K136-V139, E170-V173, G186-V189, D195-E198 and two α-helices, composed of the residues from R144-A164 and T202-I218. The sheets and helices are arranged as β1:α1:β2:β3:β4:α2, which are connected by flexible loop regions. These new structural details of subunit E are discussed in the light of the structural arrangements of this subunit inside the V₁- and V₁V₀ ATPase.
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Affiliation(s)
- Sankaranarayanan Rishikesan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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26
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Hunke C, Antosch M, Müller V, Grüber G. Binding of subunit E into the A-B interface of the A(1)A(O) ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2111-8. [PMID: 21669184 DOI: 10.1016/j.bbamem.2011.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 11/17/2022]
Abstract
Two of the distinct diversities of the engines A(1)A(O) ATP synthase and F(1)F(O) ATP synthase are the existence of two peripheral stalks and the 24kDa stalk subunit E inside the A(1)A(O) ATP synthase. Crystallographic structures of subunit E have been determined recently, but the epitope(s) and the strength to which this subunit does bind in the enzyme complex are still a puzzle. Using the recombinant A(3)B(3)D complex and the major subunits A and B of the methanogenic A(1)A(O) ATP synthase in combination with fluorescence correlation spectroscopy (FCS) we demonstrate, that the stalk subunit E does bind to the catalytic headpiece formed by the A(3)B(3) hexamer with an affinity (K(d)) of 6.1±0.2μM. FCS experiments with single A and B, respectively, demonstrated unequivocally that subunit E binds stronger to subunit B (K(d)=18.9±3.7μM) than to the catalytic A subunit (K(d)=53.1±4.4). Based on the crystallographic structures of the three subunits A, B and E available, the arrangement of the peripheral stalk subunit E in the A-B interface has been modeled, shining light into the A-B-E assembly of this enzyme.
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Affiliation(s)
- Cornelia Hunke
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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27
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Abstract
Since their discovery in the early 1980s, viruses that infect the third domain of life, the Archaea, have captivated our attention because of their virions' unusual morphologies and proteins, which lack homologues in extant databases. Moreover, the life cycles of these viruses have unusual features, as revealed by the recent discovery of a novel virus egress mechanism that involves the formation of specific pyramidal structures on the host cell surface. The available data elucidate the particular nature of the archaeal virosphere and shed light on questions concerning the origin and evolution of viruses and cells. In this review, we summarize the current knowledge of archeoviruses, their interaction with hosts and plasmids and their role in the evolution of life.
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Affiliation(s)
- Mery Pina
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Paris, France
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28
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Manimekalai MSS, Kumar A, Jeyakanthan J, Grüber G. The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase. J Mol Biol 2011; 408:736-54. [PMID: 21396943 DOI: 10.1016/j.jmb.2011.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 11/18/2022]
Abstract
Archaeal A-ATP synthases catalyze the formation of the energy currency ATP. The chemical mechanisms of ATP synthesis in A-ATP synthases are unknown. We have determined the crystal structure of a transition-like state of the vanadate-bound form of catalytic subunit A (A(Vi)) of the A-ATP synthase from Pyrococcus horikoshii OT3. Two orthovanadate molecules were observed in the A(Vi) structure, one of which interacts with the phosphate binding loop through residue S238. The second vanadate is positioned in the transient binding site, implicating for the first time the pathway for phosphate entry to the catalytic site. Moreover, since residues K240 and T241 are proposed to be essential for catalysis, the mutant structures of K240A and T241A were also determined. The results demonstrate the importance of these two residues for transition-state stabilization. The structures presented shed light on the diversity of catalytic mechanisms used by the biological motors A- and F-ATP synthases and eukaryotic V-ATPases.
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29
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Rishikesan S, Thaker YR, Grüber G. NMR solution structure of subunit E (fragment E1–69) of the Saccharomyces cerevisiae V1VO ATPase. J Bioenerg Biomembr 2011; 43:187-93. [DOI: 10.1007/s10863-011-9342-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
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30
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Schumacher K, Krebs M. The V-ATPase: small cargo, large effects. CURRENT OPINION IN PLANT BIOLOGY 2010; 13:724-30. [PMID: 20801076 DOI: 10.1016/j.pbi.2010.07.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/30/2010] [Indexed: 05/18/2023]
Abstract
About 30 years ago seminal reports of anion-sensitive proton-pumping activity associated with microsomal membranes initiated research on the plant vacuolar-type H(+)-ATPase (V-ATPase, VHA). Since, it has been firmly established that these complex molecular machines are essential for what can be defined as cellular logistics. In a eukaryotic cell, the flow of goods between compartments is achieved either by protein-mediated membrane transport or via vesicular trafficking. Over the past years, it has become increasingly clear that V-ATPases do not only energize secondary active transport but are also important regulators of membrane trafficking.
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Affiliation(s)
- Karin Schumacher
- Heidelberg Institute for Plant Sciences (HIP), Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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31
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Basak S, Gayen S, Thaker YR, Manimekalai MSS, Roessle M, Hunke C, Grüber G. Solution structure of subunit F (Vma7p) of the eukaryotic V(1)V(O) ATPase from Saccharomyces cerevisiae derived from SAXS and NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:360-8. [PMID: 20840841 DOI: 10.1016/j.bbamem.2010.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 11/26/2022]
Abstract
Vacuolar ATPases use the energy derived from ATP hydrolysis, catalyzed in the A(3)B(3) sector of the V(1) ATPase to pump protons via the membrane-embedded V(O) sector. The energy coupling between the two sectors occurs via the so-called central stalk, to which subunit F does belong. Here we present the first low resolution structure of recombinant subunit F (Vma7p) of a eukaryotic V-ATPase from Saccharomyces cerevisiae, analyzed by small angle X-ray scattering (SAXS). The protein is divided into a 5.5nm long egg-like shaped region, connected via a 1.5nm linker to a hook-like segment at one end. Circular dichroism spectroscopy revealed that subunit F comprises of 43% α-helix, 32% β-sheet and a 25% random coil arrangement. To determine the localization of the N- and C-termini in the protein, the C-terminal truncated form of F, F(1-94) was produced and analyzed by SAXS. Comparison of the F(1-94) shape with the one of subunit F showed the missing hook-like region in F(1-94), supported by the decreased D(max) value of F(1-94) (7.0nm), and indicating that the hook-like region consists of the C-terminal residues. The NMR solution structure of the C-terminal peptide, F(90-116), was solved, displaying an α-helical region between residues 103 and 113. The F(90-116) solution structure fitted well in the hook-like region of subunit F. Finally, the arrangement of subunit F within the V(1) ATPase is discussed.
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Affiliation(s)
- Sandip Basak
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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32
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van Niftrik L, van Helden M, Kirchen S, van Donselaar EG, Harhangi HR, Webb RI, Fuerst JA, Op den Camp HJM, Jetten MSM, Strous M. Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium 'Candidatus Kuenenia stuttgartiensis'. Mol Microbiol 2010; 77:701-15. [PMID: 20545867 PMCID: PMC2936114 DOI: 10.1111/j.1365-2958.2010.07242.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2010] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are divided into three compartments by bilayer membranes (from out- to inside): paryphoplasm, riboplasm and anammoxosome. It is proposed that the anammox reaction is performed by proteins located in the anammoxosome and on its membrane giving rise to a proton-motive-force and subsequent ATP synthesis by membrane-bound ATPases. To test this hypothesis, we investigated the location of membrane-bound ATPases in the anammox bacterium 'Candidatus Kuenenia stuttgartiensis'. Four ATPase gene clusters were identified in the K. stuttgartiensis genome: one typical F-ATPase, two atypical F-ATPases and a prokaryotic V-ATPase. K. stuttgartiensis transcriptomic and proteomic analysis and immunoblotting using antisera directed at catalytic subunits of the ATPase gene clusters indicated that only the typical F-ATPase gene cluster most likely encoded a functional ATPase under these cultivation conditions. Immunogold localization showed that the typical F-ATPase was predominantly located on both the outermost and anammoxosome membrane and to a lesser extent on the middle membrane. This is consistent with the anammox physiology model, and confirms the status of the outermost cell membrane as cytoplasmic membrane. The occurrence of ATPase in the anammoxosome membrane suggests that anammox bacteria have evolved a prokaryotic organelle; a membrane-bounded compartment with a specific cellular function: energy metabolism.
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Affiliation(s)
- Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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33
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The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding. J Mol Biol 2010; 401:892-905. [PMID: 20615420 DOI: 10.1016/j.jmb.2010.06.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/29/2010] [Accepted: 06/30/2010] [Indexed: 11/24/2022]
Abstract
The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3. Both the structures show unique, altered conformations for the P-loop. Comparison with the previously solved wild type and P-loop mutant S238A structures of subunit A showed that the P-loop conformation for these two novel mutants occupy intermediate positions, with the wild type fully arched and the well-relaxed S238A mutant structures taking the extreme positions. Even though the deviation is similar for both mutants, the curvature of the P-loop faces the opposite direction. Deviations in the GER-loop, lying above the P-loop, are similar for both mutants, but in F236A, it moves towards the P-loop by around 2 A. The curvature of the loop region V392-V410, located directly behind the P-loop, moves close by 3.6 A towards the P-loop in the F236A structure and away by 2.5 A in the P235A structure. Two major deviations were observed in the P235A mutant, which are not identified in any of the subunit A structures analyzed so far, one being a wide movement of the N-terminal loop region (R90-P110) making a rotation of 80 degrees and the other being rigid-body rotation of the C-terminal helices from Q520-A588 by around 4 degrees upwards. Taken together, the data presented demonstrate the concerted effects of the critical residues P235A, F236, and S238 in the unique P-loop conformation of the A-ATP synthases.
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34
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The NMR solution structure of subunit G (G(61)(-)(101)) of the eukaryotic V1VO ATPase from Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1961-8. [PMID: 20599533 DOI: 10.1016/j.bbamem.2010.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 11/20/2022]
Abstract
Subunit G is an essential stalk subunit of the eukaryotic proton pump V(1)V(O) ATPase. Previously the structure of the N-terminal region, G(1)(-)(59), of the 13kDa subunit G was solved at higher resolution. Here solution NMR was performed to determine the structure of the recombinant C-terminal region (G(61)(-)(101)) of subunit G of the Saccharomyces cerevisiae V(1)V(O) ATPase. The protein forms an extended alpha-helix between residues 64 and 100, whereby the first five- and the last residues of G(61)(-)(101) are flexible. The surface charge distribution of G(61)(-)(101) reveals an amphiphilic character at the C-terminus due to positive and negative charge distribution at one side and a hydrophobic surface on the opposite side of the structure. The hydrophobic surface pattern is mainly formed by alanine residues. The alanine residues 72, 74 and 81 were exchanged by a single cysteine in the entire subunit G. Cysteines at positions 72 and 81 showed disulfide formation. In contrast, no crosslink could be formed for the mutant Ala74Cys. Together with the recently determined NMR solution structure of G(1)(-)(59), the presented solution structure of G(61)(-)(101) enabled us to present a first structural model of the entire subunit G of the S. cerevisiae V(1)V(O) ATPase.
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35
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Crystal and solution structure of the C-terminal part of the Methanocaldococcus jannaschii A1AO ATP synthase subunit E revealed by X-ray diffraction and small-angle X-ray scattering. J Bioenerg Biomembr 2010; 42:311-20. [DOI: 10.1007/s10863-010-9298-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 05/23/2010] [Indexed: 10/19/2022]
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36
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Raghunathan D, Gayen S, Grüber G, Verma CS. Crosstalk along the Stalk: Dynamics of the Interaction of Subunits B and F in the A1AO ATP Synthase of Methanosarcina mazei Gö1. Biochemistry 2010; 49:4181-90. [DOI: 10.1021/bi9021236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Shovanlal Gayen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Gerhard Grüber
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chandra S. Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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37
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Balakrishna AM, Hunke C, Grüber G. Purification and crystallization of the entire recombinant subunit E of the energy producer A(1)A(o) ATP synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:324-6. [PMID: 20208172 DOI: 10.1107/s1744309110001016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 01/08/2010] [Indexed: 11/10/2022]
Abstract
A(1)A(o) ATP synthases are the major energy producers in archaea. Subunit E of the stator domain of the ATP synthase from Pyrococcus horikoshii OT3 was cloned, expressed and purified to homogeneity. The monodispersed protein was crystallized by vapour diffusion. A complete diffraction data set was collected to 3.3 A resolution with 99.4% completeness using a synchrotron-radiation source. The crystals belonged to space group I4, with unit-cell parameters a = 112.51, b = 112.51, c = 96.25 A, and contained three molecules in the asymmetric unit.
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Affiliation(s)
- Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
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38
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Merkulova M, Bakulina A, Thaker YR, Grüber G, Marshansky V. Specific motifs of the V-ATPase a2-subunit isoform interact with catalytic and regulatory domains of ARNO. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1398-409. [PMID: 20153292 DOI: 10.1016/j.bbabio.2010.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 01/11/2010] [Accepted: 02/08/2010] [Indexed: 11/19/2022]
Abstract
We have previously shown that the V-ATPase a2-subunit isoform interacts specifically, and in an intra-endosomal acidification-dependent manner, with the Arf-GEF ARNO. In the present study, we examined the molecular mechanism of this interaction using synthetic peptides and purified recombinant proteins in protein-association assays. In these experiments, we revealed the involvement of multiple sites on the N-terminus of the V-ATPase a2-subunit (a2N) in the association with ARNO. While six a2N-derived peptides interact with wild-type ARNO, only two of them (named a2N-01 and a2N-03) bind to its catalytic Sec7-domain. However, of these, only the a2N-01 peptide (MGSLFRSESMCLAQLFL) showed specificity towards the Sec7-domain compared to other domains of the ARNO protein. Surface plasmon resonance kinetic analysis revealed a very strong binding affinity between this a2N-01 peptide and the Sec7-domain of ARNO, with dissociation constant KD=3.44x10(-7) M, similar to the KD=3.13x10(-7) M binding affinity between wild-type a2N and the full-length ARNO protein. In further pull-down experiments, we also revealed the involvement of multiple sites on ARNO itself in the association with a2N. However, while its catalytic Sec7-domain has the strongest interaction, the PH-, and PB-domains show much weaker binding to a2N. Interestingly, an interaction of the a2N to a peptide corresponding to ARNO's PB-domain was abolished by phosphorylation of ARNO residue Ser392. The 3D-structures of the non-phosphorylated and phosphorylated peptides were resolved by NMR spectroscopy, and we have identified rearrangements resulting from Ser392 phosphorylation. Homology modeling suggests that these alterations may modulate the access of the a2N to its interaction pocket on ARNO that is formed by the Sec7 and PB-domains. Overall, our data indicate that the interaction between the a2-subunit of V-ATPase and ARNO is a complex process involving various binding sites on both proteins. Importantly, the binding affinity between the a2-subunit and ARNO is in the same range as those previously reported for the intramolecular association of subunits within V-ATPase complex itself, indicating an important cell biological role for the interaction between the V-ATPase and small GTPase regulatory proteins.
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Affiliation(s)
- Maria Merkulova
- Center for Systems Biology, Program in Membrane Biology and Division of Nephrology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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39
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Abstract
In reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class.
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40
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Chardwiriyapreecha S, Inoue T, Sugimoto N, Sekito T, Yamato I, Murata T, Homma M, Kakinuma Y. Tributyltin sensitivity of vacuolar-type Na(+)-transporting ATPase from Enterococcus hirae. J Toxicol Sci 2010; 34:575-9. [PMID: 19797867 DOI: 10.2131/jts.34.575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tributyltin chloride (TBT), an environmental pollutant, is toxic to a variety of eukaryotic and prokaryotic organisms. Some members of F-ATP synthase (F-ATPase)/vacuolar type ATPase (V-ATPase) superfamily have been identified as the molecular target of this compound. TBT inhibited the activities of H(+)-transporting or Na(+)-transporting F-ATPase as well as H(+)-transporting V-ATPase originated from various organisms. However, the sensitivity to TBT of Na(+)-transporting V-ATPase has not been investigated. We examined the effect of TBT on Na(+)-transporting V-ATPase from an eubacterium Enterococus hirae. The ATP hydrolytic activity of E. hirae V-ATPase in purified form as well as in membrane-bound form was little inhibited by less than 10 microM TBT; IC50 for TBT inhibition of purified enzyme was estimated to be about 35 microM. Active sodium transport by E. hirae cells, indicating the in vivo activity of this V-ATPase, was not inhibited by 20 microM TBT. By contrast, IC50 of H(+)-transporting V-ATPase of the vacuolar membrane vesicles from Saccharomyces cerevisiae was about 0.2 microM. E. hirae V-ATPase is thus extremely less sensitive to TBT.
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41
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Hunke C, Tadwal VS, Manimekalai MSS, Roessle M, Grüber G. The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A1AO ATP synthase. J Bioenerg Biomembr 2010; 42:1-10. [PMID: 20082212 DOI: 10.1007/s10863-009-9266-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/10/2009] [Indexed: 11/24/2022]
Abstract
Subunit alpha of the Escherichia coli F(1)F(O) ATP synthase has been produced, and its low-resolution structure has been determined. The monodispersity of alpha allowed the studies of nucleotide-binding and inhibitory effect of 4-Chloro-7-nitrobenzofurazan (NBD-Cl) to ATP/ADP-binding. Binding constants (K ( d )) of 1.6 microM of bound MgATP-ATTO-647N and 2.9 microM of MgADP-ATTO-647N have been determined from fluorescence correlation spectroscopy data. A concentration of 51 microM and 55 microM of NBD-Cl dropped the MgATP-ATTO-647N and MgADP-ATTO-647N binding capacity to 50% (IC(50)), respectively. In contrast, no effect was observed in the presence of N,N'-dicyclohexylcarbodiimide. As subunit alpha is the homologue of subunit B of the A(1)A(O) ATP synthase, the interaction of NBD-Cl with B of the A-ATP synthase from Methanosarcina mazei Gö1 has also been shown. The data reveal a reduction of nucleotide-binding of B due to NBD-Cl, resulting in IC(50) values of 41 microM and 42 microM for MgATP-ATTO-647N and MgADP-ATTO-647N, respectively.
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Affiliation(s)
- Cornelia Hunke
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Republic of Singapore
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42
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Gayen S, Grüber G. Disulfide linkage in the coiled-coil domain of subunit H of A1AO ATP synthase from Methanocaldococcus jannaschii and the NMR structure of the C-terminal segment H(85-104). FEBS Lett 2009; 584:713-8. [PMID: 20026332 DOI: 10.1016/j.febslet.2009.12.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/15/2009] [Accepted: 12/15/2009] [Indexed: 10/20/2022]
Abstract
The C-terminal residues 98-104 are important for structure stability of subunit H of A(1)A(O) ATP synthases as well as its interaction with subunit A. Here we determined the structure of the segment H(85-104) of H from Methanocaldococcus jannaschii, showing a helix between residues Lys90 to Glu100 and flexible tails at both ends. The helix-helix arrangement in the C-terminus was investigated by exchange of hydrophobic residues to single cysteine in mutants of the entire subunit H (H(I93C), H(L96C) and H(L98C)). Together with the surface charge distribution of H(85-104), these results shine light into the A-H assembly of this enzyme.
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Affiliation(s)
- Shovanlal Gayen
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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43
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Kumar A, Manimekalai MSS, Balakrishna AM, Jeyakanthan J, Grüber G. Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution. J Mol Biol 2009; 396:301-20. [PMID: 19944110 DOI: 10.1016/j.jmb.2009.11.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/12/2009] [Accepted: 11/17/2009] [Indexed: 11/17/2022]
Abstract
The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the A(E) form, the phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.
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Affiliation(s)
- Anil Kumar
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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44
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Numoto N, Hasegawa Y, Takeda K, Miki K. Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase. EMBO Rep 2009; 10:1228-34. [PMID: 19779483 DOI: 10.1038/embor.2009.202] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 11/09/2022] Open
Abstract
V-type ATPases (V-ATPases) are categorized as rotary ATP synthase/ATPase complexes. The V-ATPases are distinct from F-ATPases in terms of their rotation scheme, architecture and subunit composition. However, there is no detailed structural information on V-ATPases despite the abundant biochemical and biophysical research. Here, we report a crystallographic study of V1-ATPase, from Thermus thermophilus, which is a soluble component consisting of A, B, D and F subunits. The structure at 4.5 A resolution reveals inter-subunit interactions and nucleotide binding. In particular, the structure of the central stalk composed of D and F subunits was shown to be characteristic of V1-ATPases. Small conformational changes of respective subunits and significant rearrangement of the quaternary structure observed in the three AB pairs were related to the interaction with the straight central stalk. The rotation mechanism is discussed based on a structural comparison between V1-ATPases and F1-ATPases.
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Affiliation(s)
- Nobutaka Numoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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45
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Gayen S, Balakrishna AM, Grüber G. NMR solution structure of the N-terminal domain of subunit E (E1–52) of A1AO ATP synthase from Methanocaldococcus jannaschii. J Bioenerg Biomembr 2009; 41:343-8. [DOI: 10.1007/s10863-009-9237-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/20/2009] [Indexed: 12/01/2022]
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46
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Biuković G, Gayen S, Pervushin K, Grüber G. Domain features of the peripheral stalk subunit H of the methanogenic A1AO ATP synthase and the NMR solution structure of H(1-47). Biophys J 2009; 97:286-94. [PMID: 19580766 PMCID: PMC2711374 DOI: 10.1016/j.bpj.2009.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 04/09/2009] [Accepted: 04/16/2009] [Indexed: 11/25/2022] Open
Abstract
A series of truncated forms of subunit H were generated to establish the domain features of that protein. Circular dichroism analysis demonstrated that H is divided at least into a C-terminal coiled-coil domain within residues 54-104, and an N-terminal domain formed by adjacent alpha-helices. With a cysteine at the C-terminus of each of the truncated proteins (H(1-47), H(1-54), H(1-59), H(1-61), H(1-67), H(1-69), H(1-71), H(1-78), H(1-80), H(1-91), and H(47-105)), the residues involved in formation of the coiled-coil interface were determined. Proteins H(1-54), H(1-61), H(1-69), and H(1-80) showed strong cross-link formation, which was weaker in H(1-47), H(1-59), H(1-71), and H(1-91). A shift in disulfide formation between cysteines at positions 71 and 80 reflected an interruption in the periodicity of hydrophobic residues in the region 71AEKILEETEKE81. To understand how the N-terminal domain of H is formed, we determined for the first time, to our knowledge, the solution NMR structure of H(1-47), which revealed an alpha-helix between residues 15-42 and a flexible N-terminal stretch. The alpha-helix includes a kink that would bring the two helices of the C-terminus into the coiled-coil arrangement. H(1-47) revealed a strip of alanines involved in dimerization, which were tested by exchange to single cysteines in subunit H mutants.
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Key Words
- cd, circular dichroism
- dss, 2, 2-dimethyl-2-silapentane-5-sulphonate
- dtt, dithiothreitol
- edta, ethylenediaminetetraacetic acid
- hsqc, heteronuclear single quantum coherence
- iptg, isopropyl-β-d-thio-galactoside
- nmr, nuclear magnetic resonance
- noe, nuclear overhauser effect
- noesy, noe spectroscopy
- nta, nitrilotriacetic acid
- page, polyacrylamide gel electrophoresis
- pcr, polymerase chain reaction
- pfg, pulsed field gradient
- saxs, small-angle x-ray scattering
- r1, longitudinal relaxation time
- r2, transverse relaxation time
- rmsd, root mean-square deviation
- sds, sodium dodecyl sulfate
- tocsy, total correlation spectroscopy
- tris, tris-(hydroxymethyl)aminomethane
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Affiliation(s)
| | | | | | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore
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47
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Assembly of subunit d (Vma6p) and G (Vma10p) and the NMR solution structure of subunit G (G(1-59)) of the Saccharomyces cerevisiae V(1)V(O) ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:242-51. [PMID: 19344662 DOI: 10.1016/j.bbabio.2009.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 01/12/2009] [Accepted: 01/13/2009] [Indexed: 11/21/2022]
Abstract
Understanding the structural traits of subunit G is essential, as it is needed for V(1)V(O) assembly and function. Here solution NMR of the recombinant N- (G(1-59)) and C-terminal segment (G(61-114)) of subunit G, has been performed in the absence and presence of subunit d of the yeast V-ATPase. The data show that G does bind to subunit d via its N-terminal part, G(1-59) only. The residues of G(1-59) involved in d binding are Gly7 to Lys34. The structure of G(1-59) has been solved, revealing an alpha-helix between residues 10 and 56, whereby the first nine- and the last three residues of G(1-59) are flexible. The surface charge distribution of G(1-59) reveals an amphiphilic character at the N-terminus due to positive and negative charge distribution at one side and a hydrophobic surface on the opposite side of the structure. The C-terminus exhibits a strip of negative residues. The data imply that G(1-59)-d assembly is accomplished by hydrophobic interactions and salt-bridges of the polar residues. Based on the recently determined NMR structure of segment E(18-38) of subunit E of yeast V-ATPase and the presently solved structure of G(1-59), both proteins have been docked and binding epitopes have been analyzed.
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