1
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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 PMCID: PMC11189923 DOI: 10.1038/s41467-024-49628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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2
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Eldeeb MH, Camacho Lopez LJ, Fontanesi F. Mitochondrial respiratory supercomplexes of the yeast Saccharomyces cerevisiae. IUBMB Life 2024. [PMID: 38529880 DOI: 10.1002/iub.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
The functional and structural relationship among the individual components of the mitochondrial respiratory chain constitutes a central aspect of our understanding of aerobic catabolism. This interplay has been a subject of intense debate for over 50 years. It is well established that individual respiratory enzymes associate into higher-order structures known as respiratory supercomplexes, which represent the evolutionarily conserved organizing principle of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, supercomplexes are formed by a complex III homodimer flanked by one or two complex IV monomers, and their high-resolution structures have been recently elucidated. Despite the wealth of structural information, several proposed supercomplex functions remain speculative and our understanding of their physiological relevance is still limited. Recent advances in the field were made possible by the construction of yeast strains where the association of complex III and IV into supercomplexes is impeded, leading to diminished respiratory capacity and compromised cellular competitive fitness. Here, we discuss the experimental evidence and hypotheses relative to the functional roles of yeast respiratory supercomplexes. Moreover, we review the current models of yeast complex III and IV assembly in the context of supercomplex formation and highlight the data scattered throughout the literature suggesting the existence of cross talk between their biogenetic processes.
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Affiliation(s)
- Mazzen H Eldeeb
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Lizeth J Camacho Lopez
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
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3
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Shimada A, Tsukihara T, Yoshikawa S. Recent progress in experimental studies on the catalytic mechanism of cytochrome c oxidase. Front Chem 2023; 11:1108190. [PMID: 37214485 PMCID: PMC10194837 DOI: 10.3389/fchem.2023.1108190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Cytochrome c oxidase (CcO) reduces molecular oxygen (O2) to water, coupled with a proton pump from the N-side to the P-side, by receiving four electrons sequentially from the P-side to the O2-reduction site-including Fea3 and CuB-via the two low potential metal sites; CuA and Fea. The catalytic cycle includes six intermediates as follows, R (Fea3 2+, CuB 1+, Tyr244OH), A (Fea3 2+-O2, CuB 1+, Tyr244OH), Pm (Fea3 4+ = O2-, CuB 2+-OH-, Tyr244O•), F (Fea3 4+ = O2-, CuB 2+-OH-, Tyr244OH), O (Fea3 3+-OH-, CuB 2+-OH-, Tyr244OH), and E (Fea3 3+-OH-, CuB 1+-H2O, Tyr244OH). CcO has three proton conducting pathways, D, K, and H. The D and K pathways connect the N-side surface with the O2-reduction site, while the H-pathway is located across the protein from the N-side to the P-side. The proton pump is driven by electrostatic interactions between the protons to be pumped and the net positive charges created during the O2 reduction. Two different proton pump proposals, each including either the D-pathway or H-pathway as the proton pumping site, were proposed approximately 30 years ago and continue to be under serious debate. In our view, the progress in understanding the reaction mechanism of CcO has been critically rate-limited by the resolution of its X-ray crystallographic structure. The improvement of the resolutions of the oxidized/reduced bovine CcO up to 1.5/1.6 Å resolution in 2016 provided a breakthrough in the understanding of the reaction mechanism of CcO. In this review, experimental studies on the reaction mechanism of CcO before the appearance of the 1.5/1.6 Å resolution X-ray structures are summarized as a background description. Following the summary, we will review the recent (since 2016) experimental findings which have significantly improved our understanding of the reaction mechanism of CcO including: 1) redox coupled structural changes of bovine CcO; 2) X-ray structures of all six intermediates; 3) spectroscopic findings on the intermediate species including the Tyr244 radical in the Pm form, a peroxide-bound form between the A and Pm forms, and Fr, a one-electron reduced F-form; 4) time resolved X-ray structural changes during the photolysis of CO-bound fully reduced CcO using XFEL; 5) a simulation analysis for the Pm→Pr→F transition.
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Affiliation(s)
- Atsuhiro Shimada
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Tomitake Tsukihara
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Shinya Yoshikawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
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4
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Guo Y, Karimullina E, Emde T, Otwinowski Z, Borek D, Savchenko A. Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli. Protein Sci 2023; 32:e4616. [PMID: 36880269 PMCID: PMC10037687 DOI: 10.1002/pro.4616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
The E. coli cytochrome bo3 ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts - the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 Å and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yirui Guo
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Ligo Analytics, 2207 Chunk Ct, Dallas, Texas, United States
| | - Elina Karimullina
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Tabitha Emde
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, US
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, Illinois, USA
- Centers for Research on Structural Biology of Infectious Diseases (CSBID), Chicago, Illinois, USA
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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5
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Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun 2022; 13:7591. [PMID: 36481732 PMCID: PMC9731990 DOI: 10.1038/s41467-022-34771-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.
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Affiliation(s)
- Yuya Nishida
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Sachiko Yanagisawa
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Rikuri Morita
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Hideki Shigematsu
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan ,grid.410592.b0000 0001 2170 091XPresent Address: Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8; Sayo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hitomi Yuki
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Satoshi Ogasawara
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Ken Shimuta
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan ,grid.410795.e0000 0001 2220 1880Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Iwamoto
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Chisa Nakabayashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Waka Matsumura
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hisakazu Kato
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | | | - Takemasa Nagao
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Tasneem Qaqorh
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yusuke Takahashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Satoru Yamazaki
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Katsumasa Kamiya
- grid.419709.20000 0004 0371 3508Center for Basic Education Integrated Learning, Kanagawa Institute of Technology, Atsugi, Kanagawa Japan
| | - Ryuhei Harada
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Nobuhiro Mizuno
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Hideyuki Takahashi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Ishii
- grid.265050.40000 0000 9290 9879Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Takashi Kumasaka
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Takeshi Murata
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Kazumasa Muramoto
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Takehiko Tosha
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan
| | - Yoshitsugu Shiro
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Teruki Honma
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Yasuteru Shigeta
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Minoru Kubo
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Seiji Takashima
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yasunori Shintani
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
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6
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Gopalasingam CC, Hasnain SS. Frontiers in metalloprotein crystallography and cryogenic electron microscopy. Curr Opin Struct Biol 2022; 75:102420. [PMID: 35841747 DOI: 10.1016/j.sbi.2022.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022]
Abstract
Metalloproteins comprise at least a third of all proteins that utilize redox properties of transition metals on their own or as parts of cofactors. The development of third generation storage ring sources and X-ray free-electron lasers with femtosecond pulses in the first decade of the 21st century has transformed metalloprotein crystallography. In the past decade, cryogenic-electron microscopy single-particle analysis, which does not require crystallization of biological samples has been extensively utilized, particularly for membrane-bound metalloprotein systems. Here, we explore recent frontiers in metalloprotein crystallography and cryogenic electron microscopy, organized for convenience under three metalloprotein-centered biological cycles, focusing on contributions from each technique, their synergy and the ability to preserve metals' redox states when subjected to a particular probe.
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Affiliation(s)
- Chai C Gopalasingam
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK; Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan. https://twitter.com/@Chai_Gopal
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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7
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Zhou L, Maldonado M, Padavannil A, Guo F, Letts JA. Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism. Science 2022; 376:831-839. [PMID: 35357889 PMCID: PMC9169680 DOI: 10.1126/science.abn7747] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII2 (Tt-SC I+III2) and a structure of Tt-CIV2. Tt-SC I+III2 (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV2 is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM83-TIM133-like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism.
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Affiliation(s)
- Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - María Maldonado
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fei Guo
- BIOEM Facility, University of California, Davis, CA 95616, USA
| | - James A. Letts
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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8
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Vogt S, Ramzan R, Grossman LI, Singh KK, Ferguson-Miller S, Yoshikawa S, Lee I, Hüttemann M. Mitochondrial respiration is controlled by Allostery, Subunit Composition and Phosphorylation Sites of Cytochrome c Oxidase: A trailblazer's tale - Bernhard Kadenbach. Mitochondrion 2021; 60:228-233. [PMID: 34481964 DOI: 10.1016/j.mito.2021.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022]
Abstract
In memoriam of Bernhard Kadenbach: Although the main focus of his research was the structure, function, and regulation of mitochondrial cytochrome c oxidase (CytOx), he earlier studied the mitochondrial phosphate carrier and found an essential role of cardiolipin. Later, he discovered tissue-specific and developmental-specific protein isoforms of CytOx. Defective activity of CytOx is found with increasing age in human muscle and neuronal cells resulting in mitochondrial diseases. Kadenbach proposed a theory on the cause of oxidative stress, aging, and associated diseases stating that allosteric feedback inhibition of CytOx at high mitochondrial ATP/ADP ratios is essential for healthy living while stress-induced reversible dephosphorylation of CytOx results in the formation of excessive reactive oxygen species that trigger degenerative diseases. This article summarizes the main discoveries of Kadenbach related to mammalian CytOx and discusses their implications for human disease.
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Affiliation(s)
- Sebastian Vogt
- Department of Heart Surgery, Campus Marburg, University Hospital of Giessen and Marburg, D-35043 Marburg, Germany; Cardiovascular Research Laboratory, Biochemical-Pharmacological Center, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany.
| | - Rabia Ramzan
- Department of Heart Surgery, Campus Marburg, University Hospital of Giessen and Marburg, D-35043 Marburg, Germany; Cardiovascular Research Laboratory, Biochemical-Pharmacological Center, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Keshav K Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, South Korea
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA.
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9
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Shinzawa-Itoh K, Muramoto K. Biochemical and crystallographic studies of monomeric and dimeric bovine cytochrome c oxidase. Biophys Physicobiol 2021; 18:186-195. [PMID: 34513548 PMCID: PMC8390318 DOI: 10.2142/biophysico.bppb-v18.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
Cytochrome c oxidase (CcO), a terminal oxidase in the respiratory chain, catalyzes the reduction of O2 to water coupled with the proton pump across the membrane. Mitochondrial CcO exists in monomeric and dimeric forms, and as a monomer as part of the respiratory supercomplex, although the enzymatic reaction proceeds in the CcO monomer. Recent biochemical and crystallographic studies of monomeric and dimeric CcOs have revealed functional and structural differences among them. In solubilized mitochondrial membrane, the monomeric form is dominant, and a small amount of dimer is observed. The activity of the monomeric CcO is higher than that of the dimer, suggesting that the monomer is the active form. In the structure of monomeric CcO, a hydrogen bond network of water molecules is formed at the entrance of the proton transfer K-pathway, and in dimeric CcO, this network is altered by a cholate molecule binding between monomers. The specific binding of the cholate molecule at the dimer interface suggests that the binding of physiological ligands similar in size or shape to cholate could also trigger dimer formation as a physiological standby form. Because the dimer interface also contains weak interactions of nonspecifically bound lipid molecules, hydrophobic interactions between the transmembrane helices, and a Met-Met interaction between the extramembrane regions, these interactions could support the stabilization of the standby form. Structural analyses also suggest that hydrophobic interactions of cardiolipins bound to the trans-membrane surface of CcO are involved in forming the supercomplex.
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Affiliation(s)
- Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Muramoto
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
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Ramzan R, Napiwotzki J, Weber P, Kadenbach B, Vogt S. Cholate Disrupts Regulatory Functions of Cytochrome c Oxidase. Cells 2021; 10:1579. [PMID: 34201437 PMCID: PMC8303988 DOI: 10.3390/cells10071579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c oxidase (CytOx), the oxygen-accepting and rate-limiting enzyme of mitochondrial respiration, binds with 10 molecules of ADP, 7 of which are exchanged by ATP at high ATP/ADP-ratios. These bound ATP and ADP can be exchanged by cholate, which is generally used for the purification of CytOx. Many crystal structures of isolated CytOx were performed with the enzyme isolated from mitochondria using sodium cholate as a detergent. Cholate, however, dimerizes the enzyme isolated in non-ionic detergents and induces a structural change as evident from a spectral change. Consequently, it turns off the "allosteric ATP-inhibition of CytOx", which is reversibly switched on under relaxed conditions via cAMP-dependent phosphorylation and keeps the membrane potential and ROS formation in mitochondria at low levels. This cholate effect gives an insight into the structural-functional relationship of the enzyme with respect to ATP inhibition and its role in mitochondrial respiration and energy production.
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Affiliation(s)
- Rabia Ramzan
- Biochemical-Pharmacological Center, Cardiovascular Research Laboratory, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany; (R.R.); (P.W.)
- Department of Heart Surgery, University Hospital of Giessen and Marburg, D-35043 Campus Marburg, Germany
| | | | - Petra Weber
- Biochemical-Pharmacological Center, Cardiovascular Research Laboratory, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany; (R.R.); (P.W.)
| | | | - Sebastian Vogt
- Biochemical-Pharmacological Center, Cardiovascular Research Laboratory, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany; (R.R.); (P.W.)
- Department of Heart Surgery, University Hospital of Giessen and Marburg, D-35043 Campus Marburg, Germany
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