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Murali R, Pace LA, Sanford RA, Ward LM, Lynes MM, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proc Natl Acad Sci U S A 2024; 121:e2316422121. [PMID: 38900790 PMCID: PMC11214002 DOI: 10.1073/pnas.2316422121] [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: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/22/2024] Open
Abstract
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV89154
| | - Laura A. Pace
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- meliora.bio, Salt Lake City, UT84103
| | - Robert A. Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - L. M. Ward
- Department of Geosciences, Smith College, Northampton, MA01063
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Mackenzie M. Lynes
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Usha F. Lingappa
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
| | - James Hemp
- meliora.bio, Salt Lake City, UT84103
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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2
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Hon-Nami K, Hijikata A, Yura K, Bessho Y. Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus. J GEN APPL MICROBIOL 2023; 69:68-78. [PMID: 37394433 DOI: 10.2323/jgam.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the results of surveying genes with the heme c motif, CxxCH, in a genome database comprising four strains of Thermus thermophilus, including strain HB8, and the confirmation of 19 c-type cytochromes among 27 selected genes. We analyzed the 19 genes, including the expression of four, by a bioinformatics approach to elucidate their individual attributes. One of the approaches included an analysis based on the secondary structure alignment pattern between the heme c motif and the 6th ligand. The predicted structures revealed many cyt c domains with fewer β-strands, such as mitochondrial cyt c, in addition to the β-strand unique to Thermus inserted in cyt c domains, as in T. thermophilus cyt c552 and caa3 cyt c oxidase subunit IIc. The surveyed thermophiles harbor potential proteins with a variety of cyt c folds. The gene analyses led to the development of an index for the classification of cyt c domains. Based on these results, we propose names for T. thermophilus genes harboring the cyt c fold.
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Affiliation(s)
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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3
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Bhadra M, Albert T, Franke A, Josef V, Ivanović-Burmazović I, Swart M, Moënne-Loccoz P, Karlin KD. Reductive Coupling of Nitric Oxide by Cu(I): Stepwise Formation of Mono- and Dinitrosyl Species En Route to a Cupric Hyponitrite Intermediate. J Am Chem Soc 2023; 145:2230-2242. [PMID: 36652374 PMCID: PMC10122266 DOI: 10.1021/jacs.2c09874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Transition-metal-mediated reductive coupling of nitric oxide (NO(g)) to nitrous oxide (N2O(g)) has significance across the fields of industrial chemistry, biochemistry, medicine, and environmental health. Herein, we elucidate a density functional theory (DFT)-supplemented mechanism of NO(g) reductive coupling at a copper-ion center, [(tmpa)CuI(MeCN)]+ (1) {tmpa = tris(2-pyridylmethyl)amine}. At -110 °C in EtOH (<-90 °C in MeOH), exposing 1 to NO(g) leads to a new binuclear hyponitrite intermediate [{(tmpa)CuII}2(μ-N2O22-)]2+ (2), exhibiting temperature-dependent irreversible isomerization to the previously characterized κ2-O,O'-trans-[(tmpa)2Cu2II(μ-N2O22-)]2+ (OOXray) complex. Complementary stopped-flow kinetic analysis of the reaction in MeOH reveals an initial mononitrosyl species [(tmpa)Cu(NO)]+ (1-(NO)) that binds a second NO molecule, forming a dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2). The decay of 1-(NO)2 requires an available starting complex 1 to form a dicopper-dinitrosyl species hypothesized to be [{(tmpa)Cu}2(μ-NO)2]2+ (D) bearing a diamond-core motif, en route to the formation of hyponitrite intermediate 2. In contrast, exposing 1 to NO(g) in 2-MeTHF/THF (v/v 4:1) at <-80 °C leads to the newly observed transient metastable dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2) prior to its disproportionation-mediated transformation to the nitrite product [(tmpa)CuII(NO2)]+. Our study furnishes a near-complete profile of NO(g) activation at a reduced Cu site with tripodal tetradentate ligation in two distinctly different solvents, aided by detailed spectroscopic characterization of metastable intermediates, including resonance Raman characterization of the new dinitrosyl and hyponitrite species detected.
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Affiliation(s)
- Mayukh Bhadra
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alicja Franke
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Verena Josef
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Marcel Swart
- IQCC & Departament de Química, Universitat de Girona, Campus Montilivi (Ciencies), 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Borisov VB, Forte E. Bioenergetics and Reactive Nitrogen Species in Bacteria. Int J Mol Sci 2022; 23:7321. [PMID: 35806323 PMCID: PMC9266656 DOI: 10.3390/ijms23137321] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
The production of reactive nitrogen species (RNS) by the innate immune system is part of the host's defense against invading pathogenic bacteria. In this review, we summarize recent studies on the molecular basis of the effects of nitric oxide and peroxynitrite on microbial respiration and energy conservation. We discuss possible molecular mechanisms underlying RNS resistance in bacteria mediated by unique respiratory oxygen reductases, the mycobacterial bcc-aa3 supercomplex, and bd-type cytochromes. A complete picture of the impact of RNS on microbial bioenergetics is not yet available. However, this research area is developing very rapidly, and the knowledge gained should help us develop new methods of treating infectious diseases.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy;
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5
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The Evolution of Nitric Oxide Function: From Reactivity in the Prebiotic Earth to Examples of Biological Roles and Therapeutic Applications. Antioxidants (Basel) 2022; 11:antiox11071222. [PMID: 35883712 PMCID: PMC9311577 DOI: 10.3390/antiox11071222] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/01/2022] Open
Abstract
Nitric oxide was once considered to be of marginal interest to the biological sciences and medicine; however, there is now wide recognition, but not yet a comprehensive understanding, of its functions and effects. NO is a reactive, toxic free radical with numerous biological targets, especially metal ions. However, NO and its reaction products also play key roles as reductant and oxidant in biological redox processes, in signal transduction, immunity and infection, as well as other roles. Consequently, it can be sensed, metabolized and modified in biological systems. Here, we present a brief overview of the chemistry and biology of NO—in particular, its origins in geological time and in contemporary biology, its toxic consequences and its critical biological functions. Given that NO, with its intrinsic reactivity, appeared in the early Earth’s atmosphere before the evolution of complex lifeforms, we speculate that the potential for toxicity preceded biological function. To examine this hypothesis, we consider the nature of non-biological and biological targets of NO, the evolution of biological mechanisms for NO detoxification, and how living organisms generate this multifunctional gas.
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6
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Chen J, Xie P, Huang Y, Gao H. Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide. Int J Mol Sci 2022; 23:979. [PMID: 35055165 PMCID: PMC8780969 DOI: 10.3390/ijms23020979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Affiliation(s)
| | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (J.C.); (P.X.); (Y.H.)
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7
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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8
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Blomberg MRA. The importance of exact exchange-A methodological investigation of NO reduction in heme-copper oxidases. J Chem Phys 2021; 154:055103. [PMID: 33557557 DOI: 10.1063/5.0035634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Significant improvements of the density functional theory (DFT) methodology during the past few decades have made DFT calculations a powerful tool in studies of enzymatic reaction mechanisms. For metalloenzymes, however, there are still concerns about the reliability in the DFT-results. Therefore, a systematic study is performed where the fraction of exact exchange in a hybrid DFT functional is used as a parameter. By varying this parameter, a set of different but related functionals are obtained. The various functionals are applied to one of the reactions occurring in the enzyme family heme-copper oxidases, the reduction of nitric oxide (NO) to nitrous oxide (N2O) and water. The results show that, even though certain parts of the calculated energetics exhibit large variations, the qualitative pictures of the reaction mechanisms are quite stable. Furthermore, it is found that the functional with 15% exact exchange (B3LYP*) gives the best agreement with experimental data for the particular reactions studied. An important aspect of the procedure used is that the computational results are carefully combined with a few more general experimental data to obtain a complete description of the entire catalytic cycle of the reactions studied.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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9
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Affiliation(s)
- Sven T. Stripp
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195 Berlin, Germany
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10
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Borisov VB, Siletsky SA, Nastasi MR, Forte E. ROS Defense Systems and Terminal Oxidases in Bacteria. Antioxidants (Basel) 2021; 10:antiox10060839. [PMID: 34073980 PMCID: PMC8225038 DOI: 10.3390/antiox10060839] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) comprise the superoxide anion (O2•−), hydrogen peroxide (H2O2), hydroxyl radical (•OH), and singlet oxygen (1O2). ROS can damage a variety of macromolecules, including DNA, RNA, proteins, and lipids, and compromise cell viability. To prevent or reduce ROS-induced oxidative stress, bacteria utilize different ROS defense mechanisms, of which ROS scavenging enzymes, such as superoxide dismutases, catalases, and peroxidases, are the best characterized. Recently, evidence has been accumulating that some of the terminal oxidases in bacterial respiratory chains may also play a protective role against ROS. The present review covers this role of terminal oxidases in light of recent findings.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
- Correspondence: (V.B.B.); (E.F.)
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
| | - Martina R. Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
- Correspondence: (V.B.B.); (E.F.)
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11
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Blomberg MRA. Activation of O 2 and NO in heme-copper oxidases - mechanistic insights from computational modelling. Chem Soc Rev 2021; 49:7301-7330. [PMID: 33006348 DOI: 10.1039/d0cs00877j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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12
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Sun C, Yang L, Ortuño MA, Wright AM, Chen T, Head AR, López N, Dincă M. Spectroscopic Evidence of Hyponitrite Radical Intermediate in NO Disproportionation at a MOF-Supported Mononuclear Copper Site. Angew Chem Int Ed Engl 2021; 60:7845-7850. [PMID: 33645907 DOI: 10.1002/anie.202015359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/11/2022]
Abstract
Dianionic hyponitrite (N2 O2 2- ) is often proposed, based on model complexes, as the key intermediate in reductive coupling of nitric oxide to nitrous oxide at the bimetallic active sites of heme-copper oxidases and nitric oxide reductases. In this work, we examine the gas-solid reaction of nitric oxide with the metal-organic framework CuI -ZrTpmC* with a suite of in situ spectroscopies and density functional theory simulations, and identify an unusual chelating N2 O2 .- intermediate. These results highlight the advantage provided by site-isolation in metal-organic frameworks (MOFs) for studying important reaction intermediates, and provide a mechanistic scenario compatible with the proposed one-electron couple in these enzymes.
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Affiliation(s)
- Chenyue Sun
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Luming Yang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Manuel A Ortuño
- Institute of Chemical Research of Catalonia, The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Ashley M Wright
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Tianyang Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Ashley R Head
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Núria López
- Institute of Chemical Research of Catalonia, The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Mircea Dincă
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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13
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Sun C, Yang L, Ortuño MA, Wright AM, Chen T, Head AR, López N, Dincă M. Spectroscopic Evidence of Hyponitrite Radical Intermediate in NO Disproportionation at a MOF‐Supported Mononuclear Copper Site. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chenyue Sun
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Luming Yang
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Manuel A. Ortuño
- Institute of Chemical Research of Catalonia The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - Ashley M. Wright
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Tianyang Chen
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Ashley R. Head
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
| | - Núria López
- Institute of Chemical Research of Catalonia The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - Mircea Dincă
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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14
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Nitric Oxide Does Not Inhibit but Is Metabolized by the Cytochrome bcc- aa3 Supercomplex. Int J Mol Sci 2020; 21:ijms21228521. [PMID: 33198276 PMCID: PMC7697965 DOI: 10.3390/ijms21228521] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Nitric oxide (NO) is a well-known active site ligand and inhibitor of respiratory terminal oxidases. Here, we investigated the interaction of NO with a purified chimeric bcc-aa3 supercomplex composed of Mycobacterium tuberculosis cytochrome bcc and Mycobacterium smegmatisaa3-type terminal oxidase. Strikingly, we found that the enzyme in turnover with O2 and reductants is resistant to inhibition by the ligand, being able to metabolize NO at 25 °C with an apparent turnover number as high as ≈303 mol NO (mol enzyme)−1 min−1 at 30 µM NO. The rate of NO consumption proved to be proportional to that of O2 consumption, with 2.65 ± 0.19 molecules of NO being consumed per O2 molecule by the mycobacterial bcc-aa3. The enzyme was found to metabolize the ligand even under anaerobic reducing conditions with a turnover number of 2.8 ± 0.5 mol NO (mol enzyme)−1 min−1 at 25 °C and 8.4 µM NO. These results suggest a protective role of mycobacterial bcc-aa3 supercomplexes against NO stress.
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16
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Blomberg MRA. Role of the Two Metals in the Active Sites of Heme Copper Oxidases-A Study of NO Reduction in cbb3 Cytochrome c Oxidase. Inorg Chem 2020; 59:11542-11553. [PMID: 32799475 DOI: 10.1021/acs.inorgchem.0c01351] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The superfamily of heme copper oxidases reduces molecular oxygen or nitric oxide, and the active sites comprise a high-spin heme group (a3 or b3) and a non-heme metal (CuB or FeB). The cbb3 C family of cytochrome c oxidases, with the high-spin heme b3 and CuB in the active site, is a subfamily of the heme copper oxidases that can reduce both molecular oxygen, which is the main substrate, and nitric oxide. The mechanism for NO reduction in cbb3 oxidase is studied here using hybrid density functional theory and compared to other cytochrome c oxidases (A and B families), with a high-spin heme a3 and CuB in the active site, and to cytochrome c dependent NO reductase, with a high-spin heme b3 and a non-heme FeB in the active site. It is found that the reaction mechanism and the detailed reaction energetics of the cbb3 oxidases are not similar to those of cytochrome c dependent NO reductase, which has the same type of high-spin heme group but a different non-heme metal. This is in contrast to earlier expectations. Instead, the NO reduction mechanism in cbb3 oxidases is very similar to that in the other cytochrome c oxidases, with the same non-heme metal, CuB, and is independent of the type of high-spin heme group. The conclusion is that the type of non-heme metal (CuB or FeB) in the active site of the heme copper oxidases is more important for the reaction mechanisms than the type of high-spin heme, at least for the NO reduction reaction. The reason is that the proton-coupled reduction potentials of the active site cofactors determine the energetics for the NO reduction reaction, and they depend to a larger extent on the non-heme metal. Observed differences in NO reduction reactivity among the various cytochrome c oxidases may be explained by differences outside the BNC, affecting the rate of proton transfer, rather than in the BNC itself.
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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18
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Integral caa 3-Cytochrome c Oxidase from Thermus thermophilus: Purification and Crystallization. Methods Mol Biol 2020. [PMID: 31342419 DOI: 10.1007/978-1-4939-9678-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cytochrome c oxidase is a respiratory enzyme catalyzing the energy-conserving reduction of molecular oxygen to water-a fundamental biological process of cell respiration. The first crystal structures of the type A cytochrome c oxidases, bovine heart and Paracoccus denitrificans cytochrome c oxidases, were published in 1995 and contributed immensely to the understanding of the enzyme's mechanism of action. The senior author's research focus was directed toward understanding the structure and function of the type B cytochrome c oxidases, ba3-oxidase and type A2 caa3-oxidase, both from the extreme thermophilic bacterium Thermus thermophilus. While the ba3-oxidase structure was published in 2000 and functional characterization is well-documented in the literature, we recently successfully solved the structure of the caa3-nature made enzyme-substrate complex. This chapter is dedicated to the purification and crystallization process of caa3-cytochrome c oxidase.
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19
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Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth. mSystems 2020; 5:5/1/e00562-19. [PMID: 31937676 PMCID: PMC6967387 DOI: 10.1128/msystems.00562-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions. Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria. IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.
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20
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Szundi I, Funatogawa C, Soulimane T, Einarsdóttir Ó. The Reactions of O 2 and NO with Mixed-Valence ba 3 Cytochrome c Oxidase from Thermus thermophilus. Biophys J 2019; 118:386-395. [PMID: 31870538 DOI: 10.1016/j.bpj.2019.11.3390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Earlier CO flow-flash experiments on the fully reduced Thermus thermophilus ba3 (Tt ba3) cytochrome oxidase revealed that O2 binding was slowed down by a factor of 10 in the presence of CO (Szundi et al., 2010, PNAS 107, 21010-21015). The goal of the current study is to explore whether the long apparent lifetime (∼50 ms) of the CuB+-CO complex generated upon photolysis of the CO-bound mixed-valence Tt ba3 (Koutsoupakis et al., 2019, Acc. Chem. Res. 52, 1380-1390) affects O2 and NO binding and the ability of CuB to act as an electron donor during O-O bond splitting. The CO recombination, NO binding, and the reaction of mixed-valence Tt ba3 with O2 were investigated by time-resolved optical absorption spectroscopy using the CO flow-flash approach and photolabile O2 and NO carriers. No electron backflow was detected after photolysis of the mixed-valence CO-bound Tt ba3. The rate of O2 and NO binding was two times slower than in the fully reduced enzyme in the presence of CO and 20 times slower than in the absence of CO. The purported long-lived CuB+-CO complex did not prevent O-O bond splitting and the resulting PM formation, which was significantly faster (5-10 times) than in the bovine heart enzyme. We propose that O2 binding to heme a3 in Tt ba3 causes CO to dissociate from CuB+ in a concerted manner through steric and/or electronic effects, thus allowing CuB+ to act as an electron donor in the mixed-valence enzyme. The significantly faster O2 binding and O-O bond cleavage in Tt ba3 compared to analogous steps in the aa3 oxidases could reflect evolutionary adaptation of the enzyme to the microaerobic conditions of the T. thermophilus HB8 species.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Chie Funatogawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Tewfik Soulimane
- Deparment of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ólőf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California.
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21
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Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans. Sci Rep 2019; 9:17234. [PMID: 31754148 PMCID: PMC6872814 DOI: 10.1038/s41598-019-53553-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/29/2019] [Indexed: 12/25/2022] Open
Abstract
Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd1 nitrite reductase (cd1NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd1NiR, presumably because cd1NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd1NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd1NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd1NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.
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22
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Mandal SK, Adhikari R, Sharma A, Chandravanshi M, Gogoi P, Kanaujia SP. Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8. Metallomics 2019; 11:597-612. [DOI: 10.1039/c8mt00374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquisition of different metal ions by metal uptake ABC transporters of Thermus thermophilus HB8 for accomplishing its various cellular functions.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Rahi Adhikari
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Anjaney Sharma
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
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23
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Sabuncu S, Reed JH, Lu Y, Moënne-Loccoz P. Nitric Oxide Reductase Activity in Heme-Nonheme Binuclear Engineered Myoglobins through a One-Electron Reduction Cycle. J Am Chem Soc 2018; 140:17389-17393. [PMID: 30512937 DOI: 10.1021/jacs.8b11037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
FeBMbs are structural and functional models of native bacterial nitric oxide reductases (NORs) generated through engineering of myoglobin. These biosynthetic models replicate the heme-nonheme diiron site of NORs and allow substitutions of metal centers and heme cofactors. Here, we provide evidence for multiple NOR turnover in monoformyl-heme-containing FeBMb1 proteins loaded with FeII, CoII, or ZnII metal ions at the FeB site (FeII/CoII/ZnII-FeBMb1(MF-heme)). FTIR detection of the ν(NNO) band of N2O at 2231 cm-1 provides a direct quantitative measurement of the product in solution. A maximum number of turnover is observed with FeII-FeBMb1(MF-heme), but the NOR activity is retained when the FeB site is loaded with ZnII. These data support the viability of a one-electron semireduced pathway for the reduction of NO at binuclear centers in reducing conditions.
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Affiliation(s)
- Sinan Sabuncu
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
| | - Julian H Reed
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
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24
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Blomberg MRA, Ädelroth P. Mechanisms for enzymatic reduction of nitric oxide to nitrous oxide - A comparison between nitric oxide reductase and cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1223-1234. [PMID: 30248312 DOI: 10.1016/j.bbabio.2018.09.368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022]
Abstract
Cytochrome c oxidases (CcO) reduce O2 to H2O in the respiratory chain of mitochondria and many aerobic bacteria. In addition, some species of CcO can also reduce NO to N2O and water while others cannot. Here, the mechanism for NO-reduction in CcO is investigated using quantum mechanical calculations. Comparison is made to the corresponding reaction in a "true" cytochrome c-dependent NO reductase (cNOR). The calculations show that in cNOR, where the reduction potentials are low, the toxic NO molecules are rapidly reduced, while the higher reduction potentials in CcO lead to a slower or even impossible reaction, consistent with experimental observations. In both enzymes the reaction is initiated by addition of two NO molecules to the reduced active site, forming a hyponitrite intermediate. In cNOR, N2O can then be formed using only the active-site electrons. In contrast, in CcO, one proton-coupled reduction step most likely has to occur before N2O can be formed, and furthermore, proton transfer is most likely rate-limiting. This can explain why different CcO species with the same heme a3-Cu active site differ with respect to NO reduction efficiency, since they have a varying number and/or properties of proton channels. Finally, the calculations also indicate that a conserved active site valine plays a role in reducing the rate of NO reduction in CcO.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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25
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:712-724. [PMID: 29883591 DOI: 10.1016/j.bbabio.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/05/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O2 reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze an intermediate step of denitrification by reducing nitric oxide (NO) to nitrous oxide (N2O). They are structurally similar to heme‑copper oxygen reductases (HCOs), which reduce O2 to water. The experimentally observed apparent bimolecular rate constant of NO delivery to the deeply buried catalytic site of NORs was previously reported to approach the diffusion-controlled limit (108-109 M-1 s-1). Using the crystal structure of cytochrome-c dependent NOR (cNOR) from Pseudomonas aeruginosa, we employed several protocols of molecular dynamics (MD) simulation, which include flooding simulations of NO molecules, implicit ligand sampling and umbrella sampling simulations, to elucidate how NO in solution accesses the catalytic site of this cNOR. The results show that NO partitions into the membrane, enters the enzyme from the lipid bilayer and diffuses to the catalytic site via a hydrophobic tunnel that is resolved in the crystal structures. This is similar to what has been found for O2 diffusion through the closely related O2 reductases. The apparent second order rate constant approximated using the simulation data is ~5 × 108 M-1 s-1, which is optimized by the dynamics of the amino acid side chains lining in the tunnel. It is concluded that both NO and O2 reductases utilize well defined hydrophobic tunnels to assure that substrate diffusion to the buried catalytic sites is not rate limiting under physiological conditions.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
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Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proc Natl Acad Sci U S A 2018; 115:6195-6200. [PMID: 29802230 DOI: 10.1073/pnas.1720298115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite high structural homology between NO reductases (NORs) and heme-copper oxidases (HCOs), factors governing their reaction specificity remain to be understood. Using a myoglobin-based model of NOR (FeBMb) and tuning its heme redox potentials (E°') to cover the native NOR range, through manipulating hydrogen bonding to the proximal histidine ligand and replacing heme b with monoformyl (MF-) or diformyl (DF-) hemes, we herein demonstrate that the E°' holds the key to reactivity differences between NOR and HCO. Detailed electrochemical, kinetic, and vibrational spectroscopic studies, in tandem with density functional theory calculations, demonstrate a strong influence of heme E°' on NO reduction. Decreasing E°' from +148 to -130 mV significantly impacts electronic properties of the NOR mimics, resulting in 180- and 633-fold enhancements in NO association and heme-nitrosyl decay rates, respectively. Our results indicate that NORs exhibit finely tuned E°' that maximizes their enzymatic efficiency and helps achieve a balance between opposite factors: fast NO binding and decay of dinitrosyl species facilitated by low E°' and fast electron transfer facilitated by high E°'. Only when E°' is optimally tuned in FeBMb(MF-heme) for NO binding, heme-nitrosyl decay, and electron transfer does the protein achieve multiple (>35) turnovers, previously not achieved by synthetic or enzyme-based NOR models. This also explains a long-standing question in bioenergetics of selective cross-reactivity in HCOs. Only HCOs with heme E°' in a similar range as NORs (between -59 and 200 mV) exhibit NOR reactivity. Thus, our work demonstrates efficient tuning of E°' in various metalloproteins for their optimal functionality.
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27
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Nitric Oxide and Mitochondrial Function in Neurological Diseases. Neuroscience 2018; 376:48-71. [DOI: 10.1016/j.neuroscience.2018.02.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/20/2018] [Accepted: 02/09/2018] [Indexed: 12/17/2022]
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28
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Insights into the recognition and electron transfer steps in nitric oxide reductase from Marinobacter hydrocarbonoclasticus. J Inorg Biochem 2017; 177:402-411. [DOI: 10.1016/j.jinorgbio.2017.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/04/2017] [Accepted: 09/02/2017] [Indexed: 11/23/2022]
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29
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Santana MM, Gonzalez JM, Cruz C. Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis. Front Microbiol 2017; 8:1947. [PMID: 29067010 PMCID: PMC5641340 DOI: 10.3389/fmicb.2017.01947] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.
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Affiliation(s)
- Margarida M Santana
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Cristina Cruz
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Siletsky SA, Belevich I, Belevich NP, Soulimane T, Wikström M. Time-resolved generation of membrane potential by ba 3 cytochrome c oxidase from Thermus thermophilus coupled to single electron injection into the O and O H states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:915-926. [PMID: 28807731 DOI: 10.1016/j.bbabio.2017.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
Abstract
Two electrogenic phases with characteristic times of ~14μs and ~290μs are resolved in the kinetics of membrane potential generation coupled to single-electron reduction of the oxidized "relaxed" O state of ba3 oxidase from T. thermophilus (O→E transition). The rapid phase reflects electron redistribution between CuA and heme b. The slow phase includes electron redistribution from both CuA and heme b to heme a3, and electrogenic proton transfer coupled to reduction of heme a3. The distance of proton translocation corresponds to uptake of a proton from the inner water phase into the binuclear center where heme a3 is reduced, but there is no proton pumping and no reduction of CuB. Single-electron reduction of the oxidized "unrelaxed" state (OH→EH transition) is accompanied by electrogenic reduction of the heme b/heme a3 pair by CuA in a "fast" phase (~22μs) and transfer of protons in "middle" and "slow" electrogenic phases (~0.185ms and ~0.78ms) coupled to electron redistribution from the heme b/heme a3 pair to the CuB site. The "middle" and "slow" electrogenic phases seem to be associated with transfer of protons to the proton-loading site (PLS) of the proton pump, but when all injected electrons reach CuB the electronic charge appears to be compensated by back-leakage of the protons from the PLS into the binuclear site. Thus proton pumping occurs only to the extent of ~0.1 H+/e-, probably due to the formed membrane potential in the experiment.
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Affiliation(s)
- Sergey A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Nikolai P Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Research Institute, University of Limerick, Ireland
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
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Abstract
Cytochrome bd is a unique prokaryotic respiratory terminal oxidase that does not belong to the extensively investigated family of haem-copper oxidases (HCOs). The enzyme catalyses the four-electron reduction of O2 to 2H2O, using quinols as physiological reducing substrates. The reaction is electrogenic and cytochrome bd therefore sustains bacterial energy metabolism by contributing to maintain the transmembrane proton motive force required for ATP synthesis. As compared to HCOs, cytochrome bd displays several distinctive features in terms of (i) metal composition (it lacks Cu and harbours a d-type haem in addition to two haems b), (ii) overall three-dimensional structure, that only recently has been solved, and arrangement of the redox cofactors, (iii) lesser energetic efficiency (it is not a proton pump), (iv) higher O2 affinity, (v) higher resistance to inhibitors such as cyanide, nitric oxide (NO) and hydrogen sulphide (H2S) and (vi) ability to efficiently metabolize potentially toxic reactive oxygen and nitrogen species like hydrogen peroxide (H2O2) and peroxynitrite (ONOO-). Compelling evidence suggests that, beyond its bioenergetic role, cytochrome bd plays multiple functions in bacterial physiology and affords protection against oxidative and nitrosative stress. Relevant to human pathophysiology, thanks to its peculiar properties, the enzyme has been shown to promote virulence in several bacterial pathogens, being currently recognized as a target for the development of new antibiotics. This review aims to give an update on our current understanding of bd-type oxidases with a focus on their reactivity with gaseous ligands and its potential impact on bacterial physiology and human pathophysiology.
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Bhagi-Damodaran A, Petrik I, Lu Y. Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities. Isr J Chem 2016; 56:773-790. [PMID: 27994254 PMCID: PMC5161413 DOI: 10.1002/ijch.201600033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In biology, a heme-Cu center in heme-copper oxidases (HCOs) is used to catalyze the four-electron reduction of oxygen to water, while a heme-nonheme diiron center in nitric oxide reductases (NORs) is employed to catalyze the two-electron reduction of nitric oxide to nitrous oxide. Although much progress has been made in biochemical and biophysical studies of HCOs and NORs, structural features responsible for similarities and differences within the two enzymatic systems remain to be understood. Here, we discuss the progress made in the design and characterization of myoglobin-based enzyme models of HCOs and NORs. In particular, we focus on use of these models to understand the structure-function relations between HCOs and NORs, including the role of nonheme metals, conserved amino acids in the active site, heme types and hydrogen-bonding network in tuning enzymatic activities and total turnovers. Insights gained from these studies are summarized and future directions are proposed.
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Affiliation(s)
| | - Igor Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
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Lo FC, Hsieh CC, Maestre-Reyna M, Chen CY, Ko TP, Horng YC, Lai YC, Chiang YW, Chou CM, Chiang CH, Huang WN, Lin YH, Bohle DS, Liaw WF. Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO. Chemistry 2016; 22:9768-76. [DOI: 10.1002/chem.201600990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Feng-Chun Lo
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chang-Chih Hsieh
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | | | - Chin-Yu Chen
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry; Academia Sinica; Taipei Taiwan
| | - Yih-Chern Horng
- Department of Chemistry; National Changhua University of Education; Changhua Taiwan
| | - Yei-Chen Lai
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
| | - Chih-Mao Chou
- Department of Life Sciences; National Central University; Taoyuan Taiwan
| | | | - Wei-Ning Huang
- Department of Biotechnology; Yuanpei University; Hsinchu Taiwan
| | - Yi-Hung Lin
- National Synchrotron Radiation Research Center Hsinchu; Taiwan
| | - D. Scott Bohle
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal QC H3A2K6 Canada
| | - Wen-Feng Liaw
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
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Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. J Biol Inorg Chem 2016; 21:39-52. [PMID: 26767750 DOI: 10.1007/s00775-015-1329-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/28/2015] [Indexed: 12/27/2022]
Abstract
Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal.
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Lyons JA, Hilbers F, Caffrey M. Structure and Function of Bacterial Cytochrome c Oxidases. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Loullis A, Pinakoulaki E. Probing the nitrite and nitric oxide reductase activity of cbb3 oxidase: resonance Raman detection of a six-coordinate ferrous heme-nitrosyl species in the binuclear b3/CuB center. Chem Commun (Camb) 2015; 51:17398-401. [PMID: 26465875 DOI: 10.1039/c5cc06802a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this work we report the first spectroscopic evidence demonstrating that cbb3 oxidase catalyzes the reduction of nitrite to nitrous oxide under reducing anaerobic conditions. The reaction proceeds through the formation of a ferrous six-coordinate heme b3-nitrosyl species that has been characterized by resonance Raman spectroscopy.
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Affiliation(s)
- Andreas Loullis
- University of Cyprus, Department of Chemistry, PO Box 20537, 1678 Nicosia, Cyprus.
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37
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Chakraborty S, Reed J, Sage JT, Branagan NC, Petrik ID, Miner KD, Hu MY, Zhao J, Alp EE, Lu Y. Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies. Inorg Chem 2015; 54:9317-29. [PMID: 26274098 PMCID: PMC4677664 DOI: 10.1021/acs.inorgchem.5b01105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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This Forum Article focuses on recent
advances in structural and spectroscopic studies of biosynthetic models
of nitric oxide reductases (NORs). NORs are complex metalloenzymes
found in the denitrification pathway of Earth’s nitrogen cycle
where they catalyze the proton-dependent two-electron reduction of
nitric oxide (NO) to nitrous oxide (N2O). While much progress
has been made in biochemical and biophysical studies of native NORs
and their variants, a clear mechanistic understanding of this important
metalloenzyme related to its function is still elusive. We report
herein UV–vis and nuclear resonance vibrational spectroscopy
(NRVS) studies of mononitrosylated intermediates of the NOR reaction
of a biosynthetic model. The ability to selectively substitute metals
at either heme or nonheme metal sites allows the introduction of independent 57Fe probe atoms at either site, as well as allowing the preparation
of analogues of stable reaction intermediates by replacing either
metal with a redox inactive metal. Together with previous structural
and spectroscopic results, we summarize insights gained from studying
these biosynthetic models toward understanding structural features
responsible for the NOR activity and its mechanism. The outlook on
NOR modeling is also discussed, with an emphasis on the design of
models capable of catalytic turnovers designed based on close mimics
of the secondary coordination sphere of native NORs. New insights into nitric oxide reductases (NORs) are obtained. Using
nuclear resonance vibrational spectroscopy, we probe both iron atoms
in mononitrosylated intermediates of the NOR reaction in a biosynthetic
protein model that reveal new insights into the structural and electronic
features responsible for the NOR activity and its likely mechanism.
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Affiliation(s)
| | | | - J Timothy Sage
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Nicole C Branagan
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | | | | | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
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Ducluzeau AL, Schoepp-Cothenet B, van Lis R, Baymann F, Russell MJ, Nitschke W. The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective. J R Soc Interface 2015; 11:20140196. [PMID: 24968694 DOI: 10.1098/rsif.2014.0196] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O2-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O2 in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O2-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O2-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O2 reductases, alias the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O2 levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O2-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O2 reductases (SoxB or B and cbb3 or C) as arising independently from NO-reducing precursor enzymes.
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Affiliation(s)
- Anne-Lise Ducluzeau
- Beadle Center, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln, NE 68588-0660, USA
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, Marseille Cedex 20 13402, France
| | - Robert van Lis
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, Marseille Cedex 20 13402, France
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, Marseille Cedex 20 13402, France
| | - Michael J Russell
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099, USA
| | - Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, Marseille Cedex 20 13402, France
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Koutsoupakis C, Soulimane T, Varotsis C. Photobiochemical production of carbon monoxide by Thermus thermophilus ba3 -cytochrome c oxidase. Chemistry 2015; 21:4958-61. [PMID: 25689606 DOI: 10.1002/chem.201406239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 11/08/2022]
Abstract
We report the photobiochemical production of carbon monoxide by a terminal ba3 -cytochrome c oxidase from T. thermophilus HB8. FTIR and time-resolved step-scan FTIR spectroscopies were combined to probe this process and also monitor the concomitant binding of the produced gas to other intact ba3 molecules forming the ba3 -CO complex. The activation of this mechanism by ba3 -oxidase under visible excitation raises the question as to whether such a mechanism is physiologically relevant to the extreme environment in which it operates.
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Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos (Cyprus)
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40
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Nicolaides A, Soulimane T, Varotsis C. Detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba3-oxidoreductase. Phys Chem Chem Phys 2015; 17:8113-9. [DOI: 10.1039/c5cp00043b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we report FTIR data on the detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba3-oxidoreductase.
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Affiliation(s)
- Antonis Nicolaides
- Department of Environmental Science and Technology
- Cyprus University of Technology
- 3603 Lemesos
- Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department and Materials & Surface Science Institute
- University of Limerick
- Limerick
- Ireland
| | - Constantinos Varotsis
- Department of Environmental Science and Technology
- Cyprus University of Technology
- 3603 Lemesos
- Cyprus
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41
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Ohta T, Soulimane T, Kitagawa T, Varotsis C. Nitric oxide activation by caa3 oxidoreductase from Thermus thermophilus. Phys Chem Chem Phys 2015; 17:10894-8. [DOI: 10.1039/c5cp01013f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present UV-Raman evidence for the formation of the hyponitrite (HO–NN–O−) species in the binuclear heme a3 Fe–CuB center (νN–N = 1330 cm−1) of caa3 heme-copper oxidoreductase from Thermus thermophilus.
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Affiliation(s)
- Takehiro Ohta
- Graduate School of Life Science
- University of Hyogo
- Hyogo 678-1297
- Japan
| | - Tewfik Soulimane
- Chemical & Environmental Sciences Department and Materials & Surface Science Institute
- University of Limerick
- Limerick
- Ireland
| | - Teizo Kitagawa
- Graduate School of Life Science
- University of Hyogo
- Hyogo 678-1297
- Japan
| | - Constantinos Varotsis
- Cyprus University of Technology
- Department of Environmental Science and Technology
- 3603 Lemesos
- Cyprus
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Reimann J, Jetten MSM, Keltjens JT. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane. Met Ions Life Sci 2015; 15:257-313. [PMID: 25707470 DOI: 10.1007/978-3-319-12415-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.
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Affiliation(s)
- Joachim Reimann
- Department of Microbiology, Institute of Wetland and Water Research (IWWR), Radboud University of Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands,
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43
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Loullis A, Noor MR, Soulimane T, Pinakoulaki E. The structure of a ferrous heme-nitro species in the binuclear heme a3/CuB center of ba3-cytochrome c oxidase as determined by resonance Raman spectroscopy. Chem Commun (Camb) 2014; 51:286-9. [PMID: 25406996 DOI: 10.1039/c4cc08019j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Members of the cytochrome c oxidase family exhibit nitrite reductase activity. In this work, we have characterized a ferrous heme a3-nitro species in ba3-oxidase by resonance Raman spectroscopy. This provides the first evidence for the structure of a nitrite-bound species in the binuclear heme/copper center of cytochrome c oxidases.
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Affiliation(s)
- Andreas Loullis
- Department of Chemistry, University of Cyprus, PO Box 20537, 1678, Nicosia, Cyprus.
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44
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Sharma V, Wikström M. A structural and functional perspective on the evolution of the heme-copper oxidases. FEBS Lett 2014; 588:3787-92. [PMID: 25261254 DOI: 10.1016/j.febslet.2014.09.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 11/15/2022]
Abstract
The heme-copper oxidases (HCOs) catalyze the reduction of O2 to water, and couple the free energy to proton pumping across the membrane. HCOs are divided into three sub-classes, A, B and C, whose order of emergence in evolution has been controversial. Here we have analyzed recent structural and functional data on HCOs and their homologues, the nitric oxide reductases (NORs). We suggest that the C-type oxidases are ancient enzymes that emerged from the NORs. In contrast, the A-type oxidases are the most advanced from both structural and functional viewpoints, which we interpret as evidence for having evolved later.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland.
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
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Einarsdóttir O, McDonald W, Funatogawa C, Szundi I, Woodruff WH, Dyer RB. The pathway of O₂to the active site in heme-copper oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:109-18. [PMID: 24998308 DOI: 10.1016/j.bbabio.2014.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/24/2014] [Indexed: 11/16/2022]
Abstract
The route of O₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (CO). Time-resolved and stationary infrared experiments in our laboratories of the fully reduced CO-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of CO pressure, have provided strong support for CO binding to CuB⁺ on the pathway to and from the high-spin heme. The presence of CO on CuB⁺ suggests that O₂binding may be compromised in CO flow-flash experiments. Time-resolved optical absorption studies show that the rate of O₂and NO binding in the bovine enzyme (1 × 10⁸M⁻¹s⁻¹) is unaffected by the presence of CO, which is consistent with the rapid dissociation (t½ = 1.5μs) of CO from CuB⁺. In contrast, in Thermus thermophilus (Tt) cytochrome ba3 the O₂and NO binding to heme a3 slows by an order of magnitude in the presence of CO (from 1 × 10⁹ to 1 × 10⁸M⁻¹s⁻¹), but is still considerably faster (~10μs at 1atm O₂) than the CO off-rate from CuB in the absence of O₂(milliseconds). These results show that traditional CO flow-flash experiments do not give accurate results for the physiological binding of O₂and NO in Tt ba3, namely, in the absence of CO. They also raise the question whether in CO flow-flash experiments on Tt ba3 the presence of CO on CuB⁺ impedes the binding of O₂to CuB⁺ or, if O₂does not bind to CuB⁺ prior to heme a3, whether the CuB⁺-CO complex sterically restricts access of O₂to the heme. Both possibilities are discussed, and we argue that O₂binds directly to heme a3 in Tt ba3, causing CO to dissociate from CuB⁺ in a concerted manner through steric and/or electronic effects. This would allow CuB⁺ to function as an electron donor during the fast (5μs) breaking of the OO bond. These results suggest that the binding of CO to CuB⁺ on the path to and from heme a3 may not be applicable to O₂and NO in all heme-copper oxidases. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Olöf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
| | - William McDonald
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Chie Funatogawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | | | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1178-87. [PMID: 24486503 DOI: 10.1016/j.bbabio.2014.01.016] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/25/2014] [Accepted: 01/27/2014] [Indexed: 12/28/2022]
Abstract
Cytochrome bd is a prokaryotic respiratory quinol:O2 oxidoreductase, phylogenetically unrelated to the extensively studied heme-copper oxidases (HCOs). The enzyme contributes to energy conservation by generating a proton motive force, though working with a lower energetic efficiency as compared to HCOs. Relevant to patho-physiology, members of the bd-family were shown to promote virulence in some pathogenic bacteria, which makes these enzymes of interest also as potential drug targets. Beyond its role in cell bioenergetics, cytochrome bd accomplishes several additional physiological functions, being apparently implicated in the response of the bacterial cell to a number of stress conditions. Compelling experimental evidence suggests that the enzyme enhances bacterial tolerance to oxidative and nitrosative stress conditions, owing to its unusually high nitric oxide (NO) dissociation rate and a notable catalase activity; the latter has been recently documented in one of the two bd-type oxidases of Escherichia coli. Current knowledge on cytochrome bd and its reactivity with O2, NO and H2O2 is summarized in this review in the light of the hypothesis that the preferential (over HCOs) expression of cytochrome bd in pathogenic bacteria may represent a strategy to evade the host immune attack based on production of NO and reactive oxygen species (ROS). This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Biochemical and biophysical characterization of the two isoforms of cbb3-type cytochrome c oxidase from Pseudomonas stutzeri. J Bacteriol 2013; 196:472-82. [PMID: 24214947 DOI: 10.1128/jb.01072-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cbb3-type cytochrome c oxidases (cbb3-CcOs) are members of the heme-copper oxidase superfamily that couple the reduction of oxygen to translocation of protons across the membrane. The cbb3-CcOs are present only in bacteria and play a primary role in microaerobic respiration, being essential for nitrogen-fixing endosymbionts and for some human pathogens. As frequently observed in Pseudomonads, Pseudomonas stutzeri contains two independent ccoNO(Q)P operons encoding the two cbb3 isoforms, Cbb3-1 and Cbb3-2. While the crystal structure of Cbb3-1 from P. stutzeri was determined recently and cbb3-CcOs from other organisms were characterized functionally, less emphasis has been placed on the isoform-specific differences between the cbb3-CcOs. In this work, both isoforms were homologously expressed in P. stutzeri strains from which the genomic version of the respective operon was deleted. We purified both cbb3 isoforms separately by affinity chromatography and increased the yield of Cbb3-2 to a similar level as Cbb3-1 by replacing its native promoter. Mass spectrometry, UV-visible (UV-Vis) spectroscopy, differential scanning calorimetry, as well as oxygen reductase and catalase activity measurements were employed to characterize both cbb3 isoforms. Differences were found concerning the thermal stability and the presence of subunit CcoQ. However, no significant differences between the two isoforms were observed otherwise. Interestingly, a surprisingly high turnover of at least 2,000 electrons s(-1) and a high Michaelis-Menten constant (Km ~ 3.6 mM) using ascorbate-N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride (TMPD) as the electron donor were characteristic for both P. stutzeri cbb3-CcOs. Our work provides the basis for further mutagenesis studies of each of the two cbb3 isoforms specifically.
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Peroxidase activity of a myoglobin mutant with three distal histidines forming a metal-binding site: Implications for the cross-reactivity of cytochrome c oxidase. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tosha T, Shiro Y. Crystal structures of nitric oxide reductases provide key insights into functional conversion of respiratory enzymes. IUBMB Life 2013; 65:217-26. [DOI: 10.1002/iub.1135] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 12/25/2012] [Indexed: 11/08/2022]
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Al-Attar S, de Vries S. Energy transduction by respiratory metallo-enzymes: From molecular mechanism to cell physiology. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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