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IMPROvER: the Integral Membrane Protein Stability Selector. Sci Rep 2020; 10:15165. [PMID: 32938971 PMCID: PMC7495477 DOI: 10.1038/s41598-020-71744-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 08/04/2020] [Indexed: 01/20/2023] Open
Abstract
Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of \documentclass[12pt]{minimal}
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\begin{document}$$\upalpha$$\end{document}α-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.
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Primo C, Pizzio GA, Yang J, Gaxiola RA, Scholz-Starke J, Hirschi KD. Plant proton pumping pyrophosphatase: the potential for its pyrophosphate synthesis activity to modulate plant growth. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:989-996. [PMID: 31081197 DOI: 10.1111/plb.13007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/09/2019] [Indexed: 05/25/2023]
Abstract
Cellular pyrophosphate (PPi) homeostasis is vital for normal plant growth and development. Plant proton-pumping pyrophosphatases (H+ -PPases) are enzymes with different tissue-specific functions related to the regulation of PPi homeostasis. Enhanced expression of plant H+ -PPases increases biomass and yield in different crop species. Here, we emphasise emerging studies utilising heterologous expression in yeast and plant vacuole electrophysiology approaches, as well as phylogenetic relationships and structural analysis, to showcase that the H+ -PPases possess a PPi synthesis function. We postulate this synthase activity contributes to modulating and promoting plant growth both in H+ -PPase-engineered crops and in wild-type plants. We propose a model where the PPi synthase activity of H+ -PPases maintains the PPi pool when cells adopt PPi-dependent glycolysis during high energy demands and/or low oxygen environments. We conclude by proposing experiments to further investigate the H+ -PPase-mediated PPi synthase role in plant growth.
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Affiliation(s)
- C Primo
- Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - G A Pizzio
- Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - J Yang
- Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - R A Gaxiola
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - J Scholz-Starke
- Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy
| | - K D Hirschi
- Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
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Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation. J Mol Biol 2019; 431:1619-1632. [PMID: 30878480 DOI: 10.1016/j.jmb.2019.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/26/2019] [Accepted: 03/03/2019] [Indexed: 12/25/2022]
Abstract
Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H+ and/or Na+) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH+-PPase), the VrH+-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion pore diameters along the translocation pathway of three VrH+-PPases complexes (Pi-, 2Pi- and imidodiphosphate-bound states) present a unique wave-like profile, with different pore diameters at the hydrophobic gate and exit channel, indicating that the ligands induced pore size alterations. The 2Pi-bound state with the largest pore diameter might mimic the hydrophobic gate open. In mutant structures, ordered waters detected at the hydrophobic gate among VrH+-PPase imply the possibility of solvation, and numerous waters at the exit channel might signify an open channel. A salt-bridge, E225-R562 is at the way out of the exit channel of VrH+-PPase; E225A mutant makes the interaction eliminated and reveals a decreased pumping ability. E225-R562 might act as a latch to regulate proton release. A water wire from the ion gate (R-D-K-E) through the hydrophobic gate and into the exit channel may reflect the path of proton transfer.
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Strauss J, Wilkinson C, Vidilaseris K, Harborne SPD, Goldman A. A Simple Strategy to Determine the Dependence of Membrane-Bound Pyrophosphatases on K + as a Cofactor. Methods Enzymol 2018; 607:131-156. [PMID: 30149856 DOI: 10.1016/bs.mie.2018.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Membrane-bound pyrophosphatases (mPPases) couple pyrophosphate hydrolysis to H+ and/or Na+ pumping across membranes and are found in all domains of life except for multicellular animals including humans. They are important for development and stress resistance in plants. Furthermore, mPPases play a role in virulence of human pathogens that cause severe diseases such as malaria and African sleeping sickness. Sequence analysis, functional studies, and recently solved crystal structures have contributed to the understanding of the mPPase catalytic cycle. However, several key mechanistic features remain unknown. During evolution, several subgroups of mPPases differing in their pumping specificity and cofactor dependency arose. mPPases are classified into one of five subgroups, usually by sequence analysis. However, classification based solely on sequence has been inaccurate in several instances due to our limited understanding of the molecular mechanism of mPPases. Thus, pumping specificity and cofactor dependency of mPPases require experimental confirmation. Here, we describe a simple method for the determination of K+ dependency in mPPases using a hydrolytic activity assay. By coupling these dependency studies with site-directed mutagenesis, we have begun to build a better understanding of the molecular mechanisms of mPPases. We optimized the assay for thermostable mPPases that are commonly used as model systems in our lab, but the method is equally applicable to mesophilic mPPases with minor modifications.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Craig Wilkinson
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Keni Vidilaseris
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Steven P D Harborne
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom.
| | - Adrian Goldman
- Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Hsu YD, Huang YF, Pan YJ, Huang LK, Liao YY, Lin WH, Liu TY, Lee CH, Pan RL. Regulation of H +-pyrophosphatase by 14-3-3 Proteins from Arabidopsis thaliana. J Membr Biol 2018; 251:263-276. [PMID: 29453559 DOI: 10.1007/s00232-018-0020-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/10/2018] [Indexed: 12/29/2022]
Abstract
Plant vacuolar H+-transporting inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) is a crucial enzyme that exists on the tonoplast to maintain pH homeostasis across the vacuolar membrane. This enzyme generates proton gradient between cytosol and vacuolar lumen by hydrolysis of a metabolic byproduct, pyrophosphate (PP i ). The regulation of V-PPase at protein level has drawn attentions of many workers for decades, but its mechanism is still unclear. In this work, we show that AVP1, the V-PPase from Arabidopsis thaliana, is a target protein for regulatory 14-3-3 proteins at the vacuolar membrane, and all twelve 14-3-3 isoforms were analyzed for their association with AVP1. In the presence of 14-3-3ν, -µ, -ο, and -ι, both enzymatic activities and its associated proton pumping of AVP1 were increased. Among these 14-3-3 proteins, 14-3-3 µ shows the highest stimulation on coupling efficiency. Furthermore, 14-3-3ν, -µ, -ο, and -ι exerted protection of AVP1 against the inhibition of suicidal substrate PP i at high concentration. Moreover, the thermal profile revealed the presence of 14-3-3ο improves the structural stability of AVP1 against high temperature deterioration. Additionally, the 14-3-3 proteins mitigate the inhibition of Na+ to AVP1. Besides, the binding sites/motifs of AVP1 were identified for each 14-3-3 protein. Taken together, a working model was proposed to elucidate the association of 14-3-3 proteins with AVP1 for stimulation of its enzymatic activity.
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Affiliation(s)
- Yu-Di Hsu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Yu-Fen Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Yih-Jiuan Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Li-Kun Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Ya-Yun Liao
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Wei-Hua Lin
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China
| | - Ching-Hung Lee
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China.
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan, Republic of China.
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Regmi KC, Pizzio GA, Gaxiola RA. Structural basis for the reversibility of proton pyrophosphatase. PLANT SIGNALING & BEHAVIOR 2016; 11:e1231294. [PMID: 27611445 PMCID: PMC5257167 DOI: 10.1080/15592324.2016.1231294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Proton Pyrophosphatase (H+-PPase) is an evolutionarily conserved enzyme regarded as a bona fide vacuolar marker. However, H+-PPase also localizes at the plasma membrane of the phloem, where, evidence suggests that it functions as a Pyrophosphate Synthase and participates in phloem loading and photosynthate partitioning. We believe that this pyrophosphate synthesising function of H+-PPase is fundamentally rooted to its molecular structure, and here we postulate, on the basis of published crystal structures of membrane-bound pyrophosphatases, a plausible mechanism of pyrophosphate synthesis.
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Affiliation(s)
- Kamesh C. Regmi
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Gaston A. Pizzio
- Center for Research in Agricultural Genomics, Cerdanyola del Vallès, Barcelona, Spain
| | - Roberto A. Gaxiola
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- CONTACT Roberto A. Gaxiola
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Role of H(+)-pyrophosphatase activity in the regulation of intracellular pH in a scuticociliate parasite of turbot: Physiological effects. Exp Parasitol 2016; 169:59-68. [PMID: 27480055 DOI: 10.1016/j.exppara.2016.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 06/04/2016] [Accepted: 07/28/2016] [Indexed: 11/21/2022]
Abstract
The scuticociliatosis is a very serious disease that affects the cultured turbot, and whose causal agent is the anphizoic and marine euryhaline ciliate Philasterides dicentrarchi. Several protozoans possess acidic organelles that contain high concentrations of pyrophosphate (PPi), Ca(2+) and other elements with essential roles in vesicular trafficking, pH homeostasis and osmoregulation. P. dicentrarchi possesses a pyrophosphatase (H(+)-PPase) that pumps H(+) through the membranes of vacuolar and alveolar sacs. These compartments share common features with the acidocalcisomes described in other parasitic protozoa (e.g. acid content and Ca(2+) storage). We evaluated the effects of Ca(2+) and ATP on H (+)-PPase activity in this ciliate and analyzed their role in maintaining intracellular pH homeostasis and osmoregulation, by the addition of PPi and inorganic molecules that affect osmolarity. Addition of PPi led to acidification of the intracellular compartments, while the addition of ATP, CaCl2 and bisphosphonates analogous of PPi and Ca(2+) metabolism regulators led to alkalinization and a decrease in H(+)-PPase expression in trophozoites. Addition of NaCl led to proton release, intracellular Ca(2+) accumulation and downregulation of H(+)-PPase expression. We conclude that the regulation of the acidification of intracellular compartments may be essential for maintaining the intracellular pH homeostasis necessary for survival of ciliates and their adaptation to salt stress, which they will presumably face during the endoparasitic phase, in which the salinity levels are lower than in their natural environment.
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Hsu SH, Lo YY, Liu TH, Pan YJ, Huang YT, Sun YJ, Hung CC, Tseng FG, Yang CW, Pan RL. Substrate-induced changes in domain interaction of vacuolar H⁺-pyrophosphatase. J Biol Chem 2015; 290:1197-209. [PMID: 25451931 DOI: 10.1074/jbc.m114.568139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Single molecule atomic force microscopy (smAFM) was employed to unfold transmembrane domain interactions of a unique vacuolar H(+)-pyrophosphatase (EC 3.6.1.1) from Vigna radiata. H(+)-Pyrophosphatase is a membrane-embedded homodimeric protein containing a single type of polypeptide and links PPi hydrolysis to proton translocation. Each subunit consists of 16 transmembrane domains with both ends facing the lumen side. In this investigation, H(+)-pyrophosphatase was reconstituted into the lipid bilayer in the same orientation for efficient fishing out of the membrane by smAFM. The reconstituted H(+)-pyrophosphatase in the lipid bilayer showed an authentically dimeric structure, and the size of each monomer was ∼4 nm in length, ∼2 nm in width, and ∼1 nm in protrusion height. Upon extracting the H(+)-pyrophosphatase out of the membrane, force-distance curves containing 10 peaks were obtained and assigned to distinct domains. In the presence of pyrophosphate, phosphate, and imidodiphosphate, the numbers of interaction curves were altered to 7, 8, and 10, respectively, concomitantly with significant modification in force strength. The substrate-binding residues were further replaced to verify these domain changes upon substrate binding. A working model is accordingly proposed to show the interactions between transmembrane domains of H(+)-pyrophosphatase in the presence and absence of substrate and its analog.
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Affiliation(s)
- Shen-Hsing Hsu
- From the Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33333
| | - Yueh-Yu Lo
- From the Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33333
| | - Tseng-Huang Liu
- the Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, and
| | - Yih-Jiuan Pan
- the Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, and
| | - Yun-Tzu Huang
- the Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, and
| | - Yuh-Ju Sun
- the Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, and
| | - Cheng-Chieh Hung
- From the Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33333
| | - Fan-Gang Tseng
- Department of Engineering and System Science, College of Nuclear Science, National Tsing Hua University, Hsin Chu 30013, Taiwan
| | - Chih-Wei Yang
- From the Department of Nephrology, Kidney Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33333,
| | - Rong-Long Pan
- the Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, and
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9
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Proton/sodium pumping pyrophosphatases: the last of the primary ion pumps. Curr Opin Struct Biol 2014; 27:38-47. [DOI: 10.1016/j.sbi.2014.03.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/18/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
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10
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Asaoka M, Segami S, Maeshima M. Identification of the critical residues for the function of vacuolar H+-pyrophosphatase by mutational analysis based on the 3D structure. ACTA ACUST UNITED AC 2014; 156:333-44. [DOI: 10.1093/jb/mvu046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Lee CH, Chen YW, Huang YT, Pan YJ, Lee CH, Lin SM, Huang LK, Lo YY, Huang YF, Hsu YD, Yen SC, Hwang JK, Pan RL. Functional Investigation of Transmembrane Helix 3 in H+-Translocating Pyrophosphatase. J Membr Biol 2013; 246:959-66. [DOI: 10.1007/s00232-013-9599-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/24/2013] [Indexed: 10/26/2022]
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12
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Huang YT, Liu TH, Lin SM, Chen YW, Pan YJ, Lee CH, Sun YJ, Tseng FG, Pan RL. Squeezing at entrance of proton transport pathway in proton-translocating pyrophosphatase upon substrate binding. J Biol Chem 2013; 288:19312-20. [PMID: 23720778 DOI: 10.1074/jbc.m113.469353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homodimeric proton-translocating pyrophosphatase (H(+)-PPase; EC 3.6.1.1) is indispensable for many organisms in maintaining organellar pH homeostasis. This unique proton pump couples the hydrolysis of PPi to proton translocation across the membrane. H(+)-PPase consists of 14-16 relatively hydrophobic transmembrane domains presumably for proton translocation and hydrophilic loops primarily embedding a catalytic site. Several highly conserved polar residues located at or near the entrance of the transport pathway in H(+)-PPase are essential for proton pumping activity. In this investigation single molecule FRET was employed to dissect the action at the pathway entrance in homodimeric Clostridium tetani H(+)-PPase upon ligand binding. The presence of the substrate analog, imidodiphosphate mediated two sites at the pathway entrance moving toward each other. Moreover, single molecule FRET analyses after the mutation at the first proton-carrying residue (Arg-169) demonstrated that conformational changes at the entrance are conceivably essential for the initial step of H(+)-PPase proton translocation. A working model is accordingly proposed to illustrate the squeeze at the entrance of the transport pathway in H(+)-PPase upon substrate binding.
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Affiliation(s)
- Yun-Tzu Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu 30013, Taiwan
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Kellosalo J, Kajander T, Kogan K, Pokharel K, Goldman A. The structure and catalytic cycle of a sodium-pumping pyrophosphatase. Science 2012; 337:473-6. [PMID: 22837527 DOI: 10.1126/science.1222505] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Membrane-integral pyrophosphatases (M-PPases) are crucial for the survival of plants, bacteria, and protozoan parasites. They couple pyrophosphate hydrolysis or synthesis to Na(+) or H(+) pumping. The 2.6-angstrom structure of Thermotoga maritima M-PPase in the resting state reveals a previously unknown solution for ion pumping. The hydrolytic center, 20 angstroms above the membrane, is coupled to the gate formed by the conserved Asp(243), Glu(246), and Lys(707) by an unusual "coupling funnel" of six α helices. Comparison with our 4.0-angstrom resolution structure of the product complex suggests that helix 12 slides down upon substrate binding to open the gate by a simple binding-change mechanism. Below the gate, four helices form the exit channel. Superimposing helices 3 to 6, 9 to 12, and 13 to 16 suggests that M-PPases arose through gene triplication.
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Affiliation(s)
- Juho Kellosalo
- Structural Biology and Biophysics Program, Institute of Biotechnology, Post Office Box 65, University of Helsinki, FIN-00014, Finland
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14
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Crystal structure of a membrane-embedded H+-translocating pyrophosphatase. Nature 2012; 484:399-403. [PMID: 22456709 DOI: 10.1038/nature10963] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 02/17/2012] [Indexed: 11/08/2022]
Abstract
H(+)-translocating pyrophosphatases (H(+)-PPases) are active proton transporters that establish a proton gradient across the endomembrane by means of pyrophosphate (PP(i)) hydrolysis. H(+)-PPases are found primarily as homodimers in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes. The three-dimensional structure and detailed mechanisms underlying the enzymatic and proton translocation reactions of H(+)-PPases are unclear. Here we report the crystal structure of a Vigna radiata H(+)-PPase (VrH(+)-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 Å resolution. Each VrH(+)-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices. IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg(2+) ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PP(i) hydrolysis, and H(+) is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. We propose a working model of the mechanism for the coupling between proton pumping and PP(i) hydrolysis by H(+)-PPases.
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Luoto HH, Belogurov GA, Baykov AA, Lahti R, Malinen AM. Na+-translocating membrane pyrophosphatases are widespread in the microbial world and evolutionarily precede H+-translocating pyrophosphatases. J Biol Chem 2011; 286:21633-42. [PMID: 21527638 DOI: 10.1074/jbc.m111.244483] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane pyrophosphatases (PPases), divided into K(+)-dependent and K(+)-independent subfamilies, were believed to pump H(+) across cell membranes until a recent demonstration that some K(+)-dependent PPases function as Na(+) pumps. Here, we have expressed seven evolutionarily important putative PPases in Escherichia coli and estimated their hydrolytic, Na(+) transport, and H(+) transport activities as well as their K(+) and Na(+) requirements in inner membrane vesicles. Four of these enzymes (from Anaerostipes caccae, Chlorobium limicola, Clostridium tetani, and Desulfuromonas acetoxidans) were identified as K(+)-dependent Na(+) transporters. Phylogenetic analysis led to the identification of a monophyletic clade comprising characterized and predicted Na(+)-transporting PPases (Na(+)-PPases) within the K(+)-dependent subfamily. H(+)-transporting PPases (H(+)-PPases) are more heterogeneous and form at least three independent clades in both subfamilies. These results suggest that rather than being a curious rarity, Na(+)-PPases predominantly constitute the K(+)-dependent subfamily. Furthermore, Na(+)-PPases possibly preceded H(+)-PPases in evolution, and transition from Na(+) to H(+) transport may have occurred in several independent enzyme lineages. Site-directed mutagenesis studies facilitated the identification of a specific Glu residue that appears to be central in the transport mechanism. This residue is located in the cytoplasm-membrane interface of transmembrane helix 6 in Na(+)-PPases but shifted to within the membrane or helix 5 in H(+)-PPases. These results contribute to the prediction of the transport specificity and K(+) dependence for a particular membrane PPase sequence based on its position in the phylogenetic tree, identity of residues in the K(+) dependence signature, and position of the membrane-located Glu residue.
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Affiliation(s)
- Heidi H Luoto
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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