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Montgomery MG, Petri J, Spikes TE, Walker JE. Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis. Proc Natl Acad Sci U S A 2021; 118:e2111899118. [PMID: 34782468 PMCID: PMC8617483 DOI: 10.1073/pnas.2111899118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023] Open
Abstract
The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from Mycobacterium smegmatis This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.
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Affiliation(s)
- Martin G Montgomery
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Jessica Petri
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Tobias E Spikes
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - John E Walker
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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2
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Petri J, Nakatani Y, Montgomery MG, Ferguson SA, Aragão D, Leslie AGW, Heikal A, Walker JE, Cook GM. Structure of F 1-ATPase from the obligate anaerobe Fusobacterium nucleatum. Open Biol 2019; 9:190066. [PMID: 31238823 PMCID: PMC6597759 DOI: 10.1098/rsob.190066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F1-ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The βE-subunits in all three enzymes are in the conventional ‘open’ state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.
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Affiliation(s)
- Jessica Petri
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - Yoshio Nakatani
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Martin G Montgomery
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Scott A Ferguson
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand
| | - David Aragão
- 4 Australian Synchrotron , 800 Blackburn Road, Clayton, Victoria 3168 , Australia
| | - Andrew G W Leslie
- 5 Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Cambridge CB2 0QH , UK
| | - Adam Heikal
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - John E Walker
- 3 Medical Research Council Mitochondrial Biology Unit , Cambridge Biomedical Campus, Cambridge CB2 0XY , UK
| | - Gregory M Cook
- 1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.,2 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
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3
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Morales-Ríos E, Montgomery MG, Leslie AGW, García-Trejo JJ, Walker JE. Structure of a catalytic dimer of the α- and β-subunits of the F-ATPase from Paracoccus denitrificans at 2.3 Å resolution. Acta Crystallogr F Struct Biol Commun 2015; 71:1309-17. [PMID: 26457523 PMCID: PMC4601596 DOI: 10.1107/s2053230x15016076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/27/2015] [Indexed: 02/02/2023] Open
Abstract
The structures of F-ATPases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied. Paracoccus denitrificans is a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. The P. denitrificans F-ATPase is an example of a eubacterial F-ATPase that can carry out ATP synthesis only, whereas many others can catalyse both the synthesis and the hydrolysis of ATP. Inhibition of the ATP hydrolytic activity of the P. denitrificans F-ATPase involves the ζ inhibitor protein, an α-helical protein that binds to the catalytic F1 domain of the enzyme. This domain is a complex of three α-subunits and three β-subunits, and one copy of each of the γ-, δ- and ℇ-subunits. Attempts to crystallize the F1-ζ inhibitor complex yielded crystals of a subcomplex of the catalytic domain containing the α- and β-subunits only. Its structure was determined to 2.3 Å resolution and consists of a heterodimer of one α-subunit and one β-subunit. It has no bound nucleotides, and it corresponds to the `open' or `empty' catalytic interface found in other F-ATPases. The main significance of this structure is that it aids in the determination of the structure of the intact membrane-bound F-ATPase, which has been crystallized.
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Affiliation(s)
- Edgar Morales-Ríos
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Martin G. Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
| | - Andrew G. W. Leslie
- The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - José J. García-Trejo
- Departmento de Biología, Facultad Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, England
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Morales-Rios E, Watt IN, Zhang Q, Ding S, Fearnley IM, Montgomery MG, Wakelam MJO, Walker JE. Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans. Open Biol 2015; 5:150119. [PMID: 26423580 PMCID: PMC4593670 DOI: 10.1098/rsob.150119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The structures of F-ATPases have been determined predominantly with mitochondrial enzymes, but hitherto no F-ATPase has been crystallized intact. A high-resolution model of the bovine enzyme built up from separate sub-structures determined by X-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of ATP. Here the isolation, characterization and crystallization of an integral F-ATPase complex from the α-proteobacterium Paracoccus denitrificans are described. Unlike many eubacterial F-ATPases, which can both synthesize and hydrolyse ATP, the P. denitrificans enzyme can only carry out the synthetic reaction. The mechanism of inhibition of its ATP hydrolytic activity involves a ζ inhibitor protein, which binds to the catalytic F₁-domain of the enzyme. The complex that has been crystallized, and the crystals themselves, contain the nine core proteins of the complete F-ATPase complex plus the ζ inhibitor protein. The formation of crystals depends upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize. The experiments open the way to an atomic structure of an F-ATPase complex.
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Affiliation(s)
- Edgar Morales-Rios
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ian N. Watt
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Shujing Ding
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ian M. Fearnley
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Martin G. Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,e-mail:
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Lee J, Ding S, Walpole TB, Holding AN, Montgomery MG, Fearnley IM, Walker JE. Organization of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking. J Biol Chem 2015; 290:13308-20. [PMID: 25851905 PMCID: PMC4505582 DOI: 10.1074/jbc.m115.645283] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 12/21/2022] Open
Abstract
The F-ATPase in bovine mitochondria is a membrane-bound complex of about 30 subunits of 18 different kinds. Currently, ∼85% of its structure is known. The enzyme has a membrane extrinsic catalytic domain, and a membrane intrinsic domain where the turning of the enzyme's rotor is generated from the transmembrane proton-motive force. The domains are linked by central and peripheral stalks. The central stalk and a hydrophobic ring of c-subunits in the membrane domain constitute the enzyme's rotor. The external surface of the catalytic domain and membrane subunit a are linked by the peripheral stalk, holding them static relative to the rotor. The membrane domain contains six additional subunits named ATP8, e, f, g, DAPIT (diabetes-associated protein in insulin-sensitive tissues), and 6.8PL (6.8-kDa proteolipid), each with a single predicted transmembrane α-helix, but their orientation and topography are unknown. Mutations in ATP8 uncouple the enzyme and interfere with its assembly, but its roles and the roles of the other five subunits are largely unknown. We have reacted accessible amino groups in the enzyme with bifunctional cross-linking agents and identified the linked residues. Cross-links involving the supernumerary subunits, where the structures are not known, show that the C terminus of ATP8 extends ∼70 Å from the membrane into the peripheral stalk and that the N termini of the other supernumerary subunits are on the same side of the membrane, probably in the mitochondrial matrix. These experiments contribute significantly toward building up a complete structural picture of the F-ATPase.
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Affiliation(s)
- Jennifer Lee
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
| | - ShuJing Ding
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
| | - Thomas B Walpole
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
| | - Andrew N Holding
- The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin G Montgomery
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
| | - Ian M Fearnley
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
| | - John E Walker
- From the The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom and
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Zhou A, Rohou A, Schep DG, Bason JV, Montgomery MG, Walker JE, Grigorieff N, Rubinstein JL. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. eLife 2015; 4:e10180. [PMID: 26439008 PMCID: PMC4718723 DOI: 10.7554/elife.10180] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/05/2015] [Indexed: 02/02/2023] Open
Abstract
Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.
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Affiliation(s)
- Anna Zhou
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada
| | - Alexis Rohou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Daniel G Schep
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada
| | - John V Bason
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom
| | | | - John E Walker
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom, (JEW)
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States, (NG)
| | - John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada,Department of Biochemistry, The University of Toronto, Ontario, Canada, (JLR)
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Bason JV, Montgomery MG, Leslie AGW, Walker JE. Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase. Proc Natl Acad Sci U S A 2014; 111:11305-10. [PMID: 25049402 PMCID: PMC4128166 DOI: 10.1073/pnas.1411560111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF1. Bovine IF1 has 84 amino acids, and its N-terminal inhibitory region is intrinsically disordered. In a known structure of bovine F1-ATPase inhibited with residues 1-60 of IF1, the inhibitory region from residues 1-50 is mainly α-helical and buried deeply at the α(DP)β(DP)-catalytic interface, where it forms extensive interactions with five of the nine subunits of F1-ATPase but mainly with the β(DP)-subunit. As described here, on the basis of two structures of inhibited complexes formed in the presence of large molar excesses of residues 1-60 of IF1 and of a version of IF1 with the mutation K39A, it appears that the intrinsically disordered inhibitory region interacts first with the αEβE-catalytic interface, the most open of the three catalytic interfaces, where the available interactions with the enzyme allow it to form an α-helix from residues 31-49. Then, in response to the hydrolysis of an ATP molecule and the associated partial closure of the interface to the αTPβTP state, the extent of the folded α-helical region of IF1 increases to residues 23-50 as more interactions with the enzyme become possible. Finally, in response to the hydrolysis of a second ATP molecule and a concomitant 120° rotation of the γ-subunit, the interface closes further to the α(DP)β(DP)-state, allowing more interactions to form between the enzyme and IF1. The structure of IF1 now extends to its maximally folded state found in the previously observed inhibited complex.
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Affiliation(s)
- John V Bason
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and
| | - Martin G Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and
| | - Andrew G W Leslie
- The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - John E Walker
- The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and
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Runswick MJ, Bason JV, Montgomery MG, Robinson GC, Fearnley IM, Walker JE. The affinity purification and characterization of ATP synthase complexes from mitochondria. Open Biol 2013; 3:120160. [PMID: 23407638 PMCID: PMC3603449 DOI: 10.1098/rsob.120160] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/21/2013] [Indexed: 01/30/2023] Open
Abstract
The mitochondrial F₁-ATPase inhibitor protein, IF₁, inhibits the hydrolytic, but not the synthetic activity of the F-ATP synthase, and requires the hydrolysis of ATP to form the inhibited complex. In this complex, the α-helical inhibitory region of the bound IF₁ occupies a deep cleft in one of the three catalytic interfaces of the enzyme. Its N-terminal region penetrates into the central aqueous cavity of the enzyme and interacts with the γ-subunit in the enzyme's rotor. The intricacy of forming this complex and the binding mode of the inhibitor endow IF₁ with high specificity. This property has been exploited in the development of a highly selective affinity procedure for purifying the intact F-ATP synthase complex from mitochondria in a single chromatographic step by using inhibitor proteins with a C-terminal affinity tag. The inhibited complex was recovered with residues 1-60 of bovine IF₁ with a C-terminal green fluorescent protein followed by a His-tag, and the active enzyme with the same inhibitor with a C-terminal glutathione-S-transferase domain. The wide applicability of the procedure has been demonstrated by purifying the enzyme complex from bovine, ovine, porcine and yeast mitochondria. The subunit compositions of these complexes have been characterized. The catalytic properties of the bovine enzyme have been studied in detail. Its hydrolytic activity is sensitive to inhibition by oligomycin, and the enzyme is capable of synthesizing ATP in vesicles in which the proton-motive force is generated from light by bacteriorhodopsin. The coupled enzyme has been compared by limited trypsinolysis with uncoupled enzyme prepared by affinity chromatography. In the uncoupled enzyme, subunits of the enzyme's stator are degraded more rapidly than in the coupled enzyme, indicating that uncoupling involves significant structural changes in the stator region.
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Affiliation(s)
| | | | | | | | | | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
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Robinson GC, Bason JV, Montgomery MG, Fearnley IM, Mueller DM, Leslie AGW, Walker JE. The structure of F₁-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF₁. Open Biol 2013; 3:120164. [PMID: 23407639 PMCID: PMC3603450 DOI: 10.1098/rsob.120164] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/21/2013] [Indexed: 11/29/2022] Open
Abstract
The structure of F₁-ATPase from Saccharomyces cerevisiae inhibited by the yeast IF₁ has been determined at 2.5 Å resolution. The inhibitory region of IF₁ from residues 1 to 36 is entrapped between the C-terminal domains of the α(DP)- and β(DP)-subunits in one of the three catalytic interfaces of the enzyme. Although the structure of the inhibited complex is similar to that of the bovine-inhibited complex, there are significant differences between the structures of the inhibitors and their detailed interactions with F₁-ATPase. However, the most significant difference is in the nucleotide occupancy of the catalytic β(E)-subunits. The nucleotide binding site in β(E)-subunit in the yeast complex contains an ADP molecule without an accompanying magnesium ion, whereas it is unoccupied in the bovine complex. Thus, the structure provides further evidence of sequential product release, with the phosphate and the magnesium ion released before the ADP molecule.
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Affiliation(s)
- Graham C. Robinson
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - John V. Bason
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Martin G. Montgomery
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Ian M. Fearnley
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - David M. Mueller
- Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Andrew G. W. Leslie
- The Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - John E. Walker
- The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
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Montgomery MG, Coker AR, Taylor IA, Wood SP. Assembly of a 20-nm protein cage by Escherichia coli 2-hydroxypentadienoic acid hydratase. J Mol Biol 2010; 396:1379-91. [PMID: 20053352 DOI: 10.1016/j.jmb.2009.12.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/21/2009] [Accepted: 12/26/2009] [Indexed: 10/20/2022]
Abstract
The pentameric Escherichia coli enzyme 2-hydroxypentadienoic acid hydratase assembles to form a 20-nm-diameter particle comprising 60 protein subunits, arranged with 532 symmetry when crystallised at low pH in the presence of phosphate or sulphate ions. The particles form rapidly and are stable in solution during gel filtration at low pH. They are probably formed through trimers of pentamers, which are stabilised by the interaction of two phosphate ions with residues of the N-terminal domains of subunits at the 3-fold axis. Once the particles are formed at high concentrations of phosphate (or sulphate), they remain stable in solution at 20-fold lower concentrations of the anion. Guest molecules can be trapped within the hollow protein shell during assembly. The C-termini of the subunits are freely accessible on the surface of the protein cage and thus are ideal sites for addition of affinity tags or other modifications. These particles offer a convenient model system for studying the assembly of large symmetrical structures and a novel protein nanoparticle for encapsulation and cargo delivery.
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Affiliation(s)
- M G Montgomery
- Division of Medicine, UCL Medical School, Centre for Amyloidosis and Acute Phase Proteins, London NW3 2PF, UK.
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Gledhill JR, Montgomery MG, Leslie AGW, Walker JE. How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria. Proc Natl Acad Sci U S A 2007; 104:15671-6. [PMID: 17895376 PMCID: PMC1994141 DOI: 10.1073/pnas.0707326104] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Indexed: 11/18/2022] Open
Abstract
The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues 8-50 consists of an extended structure from residues 8-13, followed by two alpha-helices from residues 14-18 and residues 21-50 linked by a turn. The binding site in the beta(DP)-alpha(DP) catalytic interface is complex with contributions from five different subunits of F(1)-ATPase. The longer helix extends from the external surface of F(1) via a deep groove made from helices and loops in the C-terminal domains of subunits beta(DP), alpha(DP), beta(TP), and alpha(TP) to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the gamma-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the alpha(E) subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F(1) forms via the open conformation of the beta(E) subunit. Then, as two ATP molecules are hydrolyzed, the beta(E)-alpha(E) interface converts to the beta(DP)-alpha(DP) interface via the beta(TP)-alpha(TP) interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit beta(DP). The inhibition probably arises by IF(1) imposing the structure and properties of the beta(TP)-alpha(TP) interface on the beta(DP)-alpha(DP) interface, thereby preventing it from hydrolyzing the bound ATP.
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Affiliation(s)
- Jonathan R. Gledhill
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
| | - Martin G. Montgomery
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - John E. Walker
- *Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom; and
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Gledhill JR, Montgomery MG, Leslie AGW, Walker JE. Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols. Proc Natl Acad Sci U S A 2007; 104:13632-7. [PMID: 17698806 PMCID: PMC1948022 DOI: 10.1073/pnas.0706290104] [Citation(s) in RCA: 275] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Indexed: 12/31/2022] Open
Abstract
The structures of F(1)-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-A resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three alpha- and three beta-subunits beneath the "crown" of beta-strands in their N-terminal domains. This region of F(1)-ATPase forms a bearing to allow the rotation of the tip of the gamma-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the gamma-subunit and the beta(TP) subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the gamma-subunit and either the beta(DP) or the beta(E) subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the gamma-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.
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Affiliation(s)
- Jonathan R. Gledhill
- *Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom; and
| | - Martin G. Montgomery
- *Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - John E. Walker
- *Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom; and
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Carbajo RJ, Kellas FA, Yang JC, Runswick MJ, Montgomery MG, Walker JE, Neuhaus D. How the N-terminal Domain of the OSCP Subunit of Bovine F1Fo-ATP Synthase Interacts with the N-terminal Region of an Alpha Subunit. J Mol Biol 2007; 368:310-8. [PMID: 17355883 DOI: 10.1016/j.jmb.2007.02.059] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 02/13/2007] [Accepted: 02/15/2007] [Indexed: 11/23/2022]
Abstract
The peripheral stalk of ATP synthase acts as a stator holding the alpha(3)beta(3) catalytic subcomplex and the membrane subunit a against the torque of the rotating central stalk and attached c ring. In bovine mitochondria, the N-terminal domain of the oligomycin sensitivity conferral protein (OSCP-NT; residues 1-120) anchors one end of the peripheral stalk to the N-terminal tails of one or more alpha subunits of the F(1) subcomplex. Here, we present an NMR characterisation of the interaction between OSCP-NT and a peptide corresponding to residues 1-25 of the alpha-subunit of bovine F(1)-ATPase. The interaction site contains adjoining hydrophobic surfaces of helices 1 and 5 of OSCP-NT binding to hydrophobic side-chains of the alpha-peptide.
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14
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Abstract
The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase determined at 1.95A resolution with crystals grown under the same conditions but in the presence of azide. The two structures are extremely similar, but they differ in the nucleotides that are bound to the catalytic site in the beta(DP)-subunit. In the present structure, the nucleotide binding sites in the beta(DP)- and beta(TP)-subunits are both occupied by AMP-PNP, whereas in the earlier structure, the beta(TP) site was occupied by AMP-PNP and the beta(DP) site by ADP, where its binding is enhanced by a bound azide ion. Also, the conformation of the side chain of the catalytically important residue, alphaArg-373 differs in the beta(DP)- and beta(TP)-subunits. Thus, the structure with bound azide represents the ADP inhibited state of the enzyme, and the new structure represents a ground state intermediate in the active catalytic cycle of ATP hydrolysis.
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Affiliation(s)
- Matthew W Bowler
- The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge, UK
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15
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Bowler MW, Montgomery MG, Leslie AGW, Walker JE. Reproducible improvements in order and diffraction limit of crystals of bovine mitochondrial F(1)-ATPase by controlled dehydration. Acta Crystallogr D Biol Crystallogr 2006; 62:991-5. [PMID: 16929099 DOI: 10.1107/s0907444906020877] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 06/01/2006] [Indexed: 11/10/2022]
Abstract
Orthorhombic crystals of bovine F(1)-ATPase have been subjected to controlled dehydration. A decrease in the relative humidity surrounding the crystals to 90% reproducibly reduced their unit-cell volume by 22% (950,000 Angstrom(3)) and improved the diffraction limit and mosaic spread of the crystals significantly. These dehydrated crystals diffracted X-rays to 1.8 Angstrom resolution at a synchrotron source, the best diffraction limit yet attained with these crystals, although radiation damage limited the resolution of a complete data set to 1.95 Angstrom.
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Affiliation(s)
- Matthew W Bowler
- The Medical Research Council Dunn Human Nutrition Unit, Cambridge, England
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16
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Abstract
In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.
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Affiliation(s)
- Matthew W. Bowler
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Martin G. Montgomery
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Andrew G. W. Leslie
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - John E. Walker
- *Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom; and
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17
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Carbajo RJ, Kellas FA, Runswick MJ, Montgomery MG, Walker JE, Neuhaus D. Structure of the F1-binding domain of the stator of bovine F1Fo-ATPase and how it binds an alpha-subunit. J Mol Biol 2005; 351:824-38. [PMID: 16045926 DOI: 10.1016/j.jmb.2005.06.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 06/03/2005] [Accepted: 06/07/2005] [Indexed: 11/17/2022]
Abstract
The peripheral stalk of ATP synthase holds the alpha3beta3 catalytic subcomplex stationary against the torque of the rotating central stalk. In bovine mitochondria, the N-terminal domain of the oligomycin sensitivity conferral protein (OSCP-NT; residues 1-120) anchors one end of the peripheral stalk to the N-terminal tails of one or more alpha-subunits of the F1 subcomplex. Here we present the solution structure of OSCP-NT and an NMR titration study of its interaction with peptides representing N-terminal tails of F1 alpha-subunits. The structure comprises a bundle of six alpha-helices, and its interaction site contains adjoining hydrophobic surfaces of helices 1 and 5; residues in the region 1-8 of the alpha-subunit are essential for the interaction. The OSCP-NT is similar to the N-terminal domain of the delta-subunit from Escherichia coli ATP synthase (delta-NT), except that their surface charges differ (basic and acidic, respectively). As the charges of the adjacent crown regions in their alpha3beta3 complexes are similar, the OSCP-NT and delta-NT probably do not contact the crowns extensively. The N-terminal tails of alpha-subunit tails are probably alpha-helical, and so this interface, which is essential for the rotary mechanism of the enzyme, appears to consist of helix-helix interactions.
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Dunn G, Montgomery MG, Mohammed F, Coker A, Cooper JB, Robertson T, Garcia JL, Bugg TDH, Wood SP. The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism. J Mol Biol 2004; 346:253-65. [PMID: 15663942 DOI: 10.1016/j.jmb.2004.11.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 11/12/2004] [Accepted: 11/15/2004] [Indexed: 11/26/2022]
Abstract
2-Hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase (MhpC) is a 62 kDa homodimeric enzyme of the phenylpropionate degradation pathway of Escherichia coli. The 2.1 A resolution X-ray structure of the native enzyme determined from orthorhombic crystals confirms that it is a member of the alpha/beta hydrolase fold family, comprising eight beta-strands interconnected by loops and helices. The 2.8 A resolution structure of the enzyme co-crystallised with the non-hydrolysable substrate analogue 2,6-diketo-nona-1,9-dioic acid (DKNDA) confirms the location of the active site in a buried channel including Ser110, His263 and Asp235, postulated contributors to a serine protease-like catalytic triad in homologous enzymes. It appears that the ligand binds in two separate orientations. In the first, the C6 keto group of the inhibitor forms a hemi-ketal adduct with the Ser110 side-chain, the C9 carboxylate group interacts, via the intermediacy of a water molecule, with Arg188 at one end of the active site, while the C1 carboxylate group of the inhibitor comes close to His114 at the other end. In the second orientation, the C1 carboxylate group binds at the Arg188 end of the active site and the C9 carboxylate group at the His114 end. These arrangements implicated His114 or His263 as plausible contributors to catalysis of the initial enol/keto tautomerisation of the substrate but lack of conservation of His114 amongst related enzymes and mutagenesis results suggest that His263 is the residue involved. Variability in the quality of the electron density for the inhibitor amongst the eight molecules of the crystal asymmetric unit appears to correlate with alternative positions for the side-chain of His114. This might arise from half-site occupation of the dimeric enzyme and reflect the apparent dissociation of approximately 50% of the keto intermediate from the enzyme during the catalytic cycle.
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Affiliation(s)
- G Dunn
- Department of Biomolecular Science, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, UK
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19
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Kagawa R, Montgomery MG, Braig K, Leslie AGW, Walker JE. The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride. EMBO J 2004; 23:2734-44. [PMID: 15229653 PMCID: PMC514953 DOI: 10.1038/sj.emboj.7600293] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 06/02/2004] [Indexed: 11/09/2022] Open
Abstract
The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift in the guanidinium of alphaArg373, the conformations of catalytic side chains are very similar in both sites. However, the ordered water molecule that carries out nucleophilic attack on the gamma-phosphate of ATP during hydrolysis is 2.6 angstroms from the beryllium in the beta(DP) subunit and 3.8 angstroms away in the beta(TP) subunit, strongly indicating that the beta(DP) subunit is the catalytically active conformation. In the structure of F1-ATPase with five bound ADP molecules (three in alpha-subunits, one each in the beta(TP) and beta(DP) subunits), which has also been determined, the conformation of alphaArg373 suggests that it senses the presence (or absence) of the gamma-phosphate of ATP. Two catalytic schemes are discussed concerning the various structures of bovine F1-ATPase.
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Affiliation(s)
- Reiko Kagawa
- The Medical Research Council Dunn Human Nutrition Unit, Cambridge, UK
| | | | - Kerstin Braig
- The Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew G W Leslie
- The Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. Tel.: +44 1223 248011; Fax: +44 1223 213556; E-mail:
| | - John E Walker
- The Medical Research Council Dunn Human Nutrition Unit, Cambridge, UK
- The Medical Research Council Dunn Human Nutrition Unit, Welcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK. Tel.: +44 1223 252701; Fax: +44 1223 252705; E-mail:
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Cabezón E, Montgomery MG, Leslie AGW, Walker JE. The structure of bovine F1-ATPase in complex with its regulatory protein IF1. Nat Struct Mol Biol 2003; 10:744-50. [PMID: 12923572 DOI: 10.1038/nsb966] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Accepted: 07/22/2003] [Indexed: 11/09/2022]
Abstract
In mitochondria, the hydrolytic activity of ATP synthase is prevented by an inhibitor protein, IF1. The active bovine protein (84 amino acids) is an alpha-helical dimer with monomers associated via an antiparallel alpha-helical coiled coil composed of residues 49-81. The N-terminal inhibitory sequences in the active dimer bind to two F1-ATPases in the presence of ATP. In the crystal structure of the F1-IF1 complex at 2.8 A resolution, residues 1-37 of IF1 bind in the alpha(DP)-beta(DP) interface of F1-ATPase, and also contact the central gamma subunit. The inhibitor opens the catalytic interface between the alpha(DP) and beta(DP) subunits relative to previous structures. The presence of ATP in the catalytic site of the beta(DP) subunit implies that the inhibited state represents a pre-hydrolysis step on the catalytic pathway of the enzyme.
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Affiliation(s)
- Elena Cabezón
- The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK
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Gibbons C, Montgomery MG, Leslie AG, Walker JE. The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution. Nat Struct Biol 2000; 7:1055-61. [PMID: 11062563 DOI: 10.1038/80981] [Citation(s) in RCA: 357] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In other crystals of F(1)-ATPase, the protrusion was disordered, but with crystals of F(1)-ATPase inhibited with dicyclohexylcarbodiimide, the complete structure was revealed. The delta and epsilon subunits interact with a Rossmann fold in the gamma subunit, forming a foot. In ATP synthase, this foot interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (alpha beta)(3) domain.
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Affiliation(s)
- C Gibbons
- The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK
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22
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Abstract
BACKGROUND The globular domain of the membrane-associated F(1)F(o)-ATP synthase complex can be detached intact as a water-soluble fragment known as F(1)-ATPase. It consists of five different subunits, alpha, beta, gamma, delta and epsilon, assembled with the stoichiometry 3:3:1:1:1. In the crystal structure of bovine F(1)-ATPase determined previously at 2.8 A resolution, the three catalytic beta subunits and the three noncatalytic alpha subunits are arranged alternately around a central alpha-helical coiled coil in the gamma subunit. In the crystals, the catalytic sites have different nucleotide occupancies. One contains the triphosphate form of the nucleotide, the second contains the diphosphate, and the third is unoccupied. Fluoroaluminate complexes have been shown to mimic the transition state in several ATP and GTP hydrolases. In order to understand more about its catalytic mechanism, F(1)-ATPase was inhibited with Mg(2+)ADP and aluminium fluoride and the structure of the inhibited complex was determined by X-ray crystallography. RESULTS The structure of bovine F(1)-ATPase inhibited with Mg(2+)ADP and aluminium fluoride determined at 2.5 A resolution differs little from the original structure with bound AMP-PNP and ADP. The nucleotide occupancies of the alpha and beta subunits are unchanged except that both aluminium trifluoride and Mg(2+)ADP are bound in the nucleotide-binding site of the beta(DP) subunit. The presence of aluminium fluoride is accompanied by only minor adjustments in the surrounding protein. CONCLUSIONS The structure appears to mimic a possible transition state. The coordination of the aluminofluoride group has many features in common with other aluminofluoride-NTP hydrolase complexes. Apparently, once nucleotide is bound to the catalytic beta subunit, no additional major structural changes are required for catalysis to occur.
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Affiliation(s)
- K Braig
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs Universität Freiburg, Freiburg in Breisgau, D-79104, Germany
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van Raaij MJ, Orriss GL, Montgomery MG, Runswick MJ, Fearnley IM, Skehel JM, Walker JE. The ATPase inhibitor protein from bovine heart mitochondria: the minimal inhibitory sequence. Biochemistry 1996; 35:15618-25. [PMID: 8961923 DOI: 10.1021/bi960628f] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The mitochondrial ATPase inhibitor subunit is a basic protein of 84 amino acids that helps to regulate the activity of F1F0-ATPase. In order to obtain structural information on the mechanism of inhibition, the bovine inhibitor subunit has been expressed in Escherichia coli and purified in high yield. The recombinant protein has a similar inhibitory activity to the inhibitor subunit isolated from bovine mitochondria. Progressive N-terminal and C-terminal deletion mutants of the inhibitor subunit have been produced either by overexpression and purification, or by chemical synthesis. By assaying the truncated proteins for inhibitory activity, the minimal inhibitory sequence of the inhibitor subunit has been defined as consisting of residues 14-47. The immediately adjacent sequences 10-13 and 48-56 help to stabilize the complex between F1F0-ATPase and the inhibitor protein, and residues 1-9 and 57-84 appear to be dispensable. At physiological pH values, the inhibitor subunit is mainly alpha-helical and forms monodisperse aggregates in solution. Smaller inhibitory fragments of the inhibitor protein, such as residues 10-50, seem to have a mainly random coil structure in solution, but they can adopt the correct inhibitory conformation when they from a complex with the ATPase. However, these latter fragments are mainly monomeric in solution, suggesting that the aggregation of the inhibitor subunit in solution may be due to intermolecular alpha-helical coiled-coil formation via the C-terminal region. The noninhibitory peptides consisting of residues 10-40 and 23-84 of the inhibitor protein can bind to F1F0-ATPase, and interfere with inhibition by the intact inhibitor subunit. The noninhibitory fragments of the inhibitor protein consisting of residues 22-46 and 44-84 do not compete with the inhibitor subunit for its binding site on F1F0-ATPase.
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