1
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Zhao Y, Duan H, Erler D, Yuan Z, Ye L. Decoupling the simultaneous effects of NO 2-, pH and free nitrous acid on N 2O and NO production from enriched nitrifying activated sludge. WATER RESEARCH 2023; 245:120609. [PMID: 37713792 DOI: 10.1016/j.watres.2023.120609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
In the pursuit of energy and carbon neutrality, nitrogen removal technologies have been developed featuring nitrite (NO2-) accumulation. However, high NO2- accumulations are often associated with stimulated greenhouse gas (i.e., nitrous oxide, N2O) emissions. Furthermore, the coexistence of free nitrous acid (FNA) formed by NO2- and proton (pH) makes the consequence of NO2- accumulation on N2O emissions complicated. The concurrent three factors, NO2-, pH and FNA may play different roles on N2O and nitric oxide (NO) emissions simultaneously, which has not been systematically studied. This study aims to decouple the effects of NO2- (0-200 mg N/L), pH (6.5-8) and FNA (0-0.15 mg N/L) on the N2O and NO production rates and the production pathways by ammonia oxidizing bacteria (AOB), with the use of a series of precisely executed batch tests and isotope site-preference analysis. Results suggested the dominant factors affecting the N2O production rate were NO2- and FNA concentrations, while pH alone played a relatively insignificant role. The most influential factor shifted from NO2- to FNA as FNA concentrations increased from 0 to 0.15 mg N/L. At concentrations below 0.0045 mg HNO2-N/L, nitrite rather than FNA played a significant role stimulating N2O production at elevated nitrite concentrations. The inhibition effect of FNA emerged with further increase of FNA between 0.0045-0.015 mg HNO2-N/L, weakening the promoting effect of increased nitrite. While at concentrations above 0.015 mg HNO2-N/L, FNA inhibited N2O production especially from nitrifier denitrification pathway with the level of inhibition linearly correlated with the FNA concentration. pH and the nitrite concentration regulated the production pathways, with elevated pH promoting the nitrifier nitrification pathway, while elevated NO2- concentrations promoting the nitrifier denitrification pathway. In contrast to N2O, NO emission was less susceptible to FNA at concentrations up to 0.015 mg N/L but was stimulated by increasing NO2- concentrations. This study, for the first time, distinguished the effects of pH, NO2- and FNA on N2O and NO production, thereby providing support to the design and operation of novel nitrogen removal systems with NO2- accumulation.
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Affiliation(s)
- Yingfen Zhao
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Haoran Duan
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia; The Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Dirk Erler
- Centre for Coastal Biogeochemistry, School of Environmental Science and Engineering, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Zhiguo Yuan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Liu Ye
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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2
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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: 132] [Impact Index Per Article: 33.0] [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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3
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Kato M, Nakagawa S, Tosha T, Shiro Y, Masuda Y, Nakata K, Yagi I. Surface-Enhanced Infrared Absorption Spectroscopy of Bacterial Nitric Oxide Reductase under Electrochemical Control Using a Vibrational Probe of Carbon Monoxide. J Phys Chem Lett 2018; 9:5196-5200. [PMID: 30141632 DOI: 10.1021/acs.jpclett.8b02581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nitric oxide reductases (NORs) reduce nitric oxide to nitrous oxide in the denitrification pathway of the global nitrogen cycle. NORs contain four iron cofactors and the NO reduction occurs at the heme b3/nonheme FeB binuclear active site. The determination of reduction potentials of the iron cofactors will help us elucidate the enzymatic reaction mechanism. However, previous reports on these potentials remain controversial. Herein, we performed electrochemical and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements of Pseudomonas aeruginosa NOR immobilized on gold electrodes. Cyclic voltammograms exhibited two reduction peaks at -0.11 and -0.44 V vs SHE, and a SEIRA spectrum using a vibrational probe of CO showed a characteristic band at 1972 cm-1 at -0.4 V vs SHE, which was assigned to νCO of heme b3-CO. Our results suggest that the reduction of heme b3 initiates the enzymatic NO reduction.
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Affiliation(s)
- Masaru Kato
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN) , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
| | | | - Takehiko Tosha
- RIKEN , SPring-8 Center , Kouto, Sayo , Hyogo 679-5148 , Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | | | | | - Ichizo Yagi
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN) , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
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4
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Blum JM, Su Q, Ma Y, Valverde-Pérez B, Domingo-Félez C, Jensen MM, Smets BF. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production. Environ Microbiol 2018; 20:1623-1640. [DOI: 10.1111/1462-2920.14063] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Jan-Michael Blum
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Qingxian Su
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Yunjie Ma
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Borja Valverde-Pérez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
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5
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Sakurai N, Kataoka K, Sugaya N, Shimodaira T, Iwamoto M, Shoda M, Horiuchi H, Kiyono M, Ohta Y, Triwiyono B, Seo D, Sakurai T. Heterologous expression of Halomonas halodenitrificans nitric oxide reductase and its N-terminally truncated NorC subunit in Escherichia coli. J Inorg Biochem 2017; 169:61-67. [PMID: 28131879 DOI: 10.1016/j.jinorgbio.2017.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/30/2016] [Accepted: 01/20/2017] [Indexed: 11/29/2022]
Abstract
Halomonas halodenitrificans nitric oxide reductase (NOR) is the membrane-bound heterodimer complex of NorC, which contains a low-spin heme c center, and NorB, which contains a low-spin heme b center, a high-spin heme b3 center, and a non-heme FeB center. The soluble domain of NorC, NorC* (ΔMet1-Val37) was heterologously expressed in Escherichia coli using expression plasmids harboring the truncated norC gene deleted of its 84 5'-terminal nucleotides. Analogous scission of the N-terminal helix as the membrane anchor took place when the whole norC gene was used. NorC* exhibited spectra typical of a low-spin heme c. In addition, NorC* functioned as the acceptor of an electron from a cytochrome c isolated from the periplasm of H. halodenitrificans and small reducing reagents. The redox potential of NorC* shifted ca. 40mV in the negative direction from that of NorC. Unlike NorC, recombinant NorB was not heterologously expressed. However, recombinant NOR (rNOR) could be expressed in E. coli by using a plasmid harboring all genes in the nor operon, norCBQDX, from which the three hairpin loops (mRNA) were deleted, and by using the ccm genes for the maturation of C-type heme. rNOR exhibited the same spectroscopic properties and reactivity to NO and O2 as NOR, although its enzymatic activity toward NO was considerably decreased. These results on the expression of rNOR and NorC* will allow us to develop more profound studies on the properties of the four Fe centers and the reaction mechanism of NOR from this halophilic denitrifying bacterium.
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Affiliation(s)
- Nobuhiko Sakurai
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan.
| | - Kunishige Kataoka
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Noriko Sugaya
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takaki Shimodaira
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Mie Iwamoto
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Munehiro Shoda
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Hajime Horiuchi
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Miyuki Kiyono
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yasuke Ohta
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan
| | - Bambang Triwiyono
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan
| | - Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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6
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Ghosh C, Mukherjee S, Seal M, Dey SG. Peroxidase to Cytochrome b Type Transition in the Active Site of Heme-Bound Amyloid β Peptides Relevant to Alzheimer’s Disease. Inorg Chem 2016; 55:1748-57. [DOI: 10.1021/acs.inorgchem.5b02683] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Soumya Mukherjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Manas Seal
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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7
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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: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
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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8
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Blomberg MR, Siegbahn PE. Why is the reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR) not electrogenic? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:826-33. [DOI: 10.1016/j.bbabio.2013.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/27/2013] [Accepted: 04/13/2013] [Indexed: 11/29/2022]
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9
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Shiro Y, Sugimoto H, Tosha T, Nagano S, Hino T. Structural basis for nitrous oxide generation by bacterial nitric oxide reductases. Philos Trans R Soc Lond B Biol Sci 2012; 367:1195-203. [PMID: 22451105 DOI: 10.1098/rstb.2011.0310] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The crystal structure of the bacterial nitric oxide reductase (cNOR) from Pseudomonas aeruginosa is reported. Its overall structure is similar to those of the main subunit of aerobic and micro-aerobic cytochrome oxidases (COXs), in agreement with the hypothesis that all these enzymes are members of the haem-copper oxidase superfamily. However, substantial structural differences between cNOR and COX are observed in the catalytic centre and the delivery pathway of the catalytic protons, which should be reflected in functional differences between these respiratory enzymes. On the basis of the cNOR structure, we propose a possible reaction mechanism of nitric oxide reduction to nitrous oxide as a working hypothesis.
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10
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Electrochemical titrations and reaction time courses monitored in situ by magnetic circular dichroism spectroscopy. Anal Biochem 2011; 419:110-6. [DOI: 10.1016/j.ab.2011.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/24/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
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11
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Hino T, Nagano S, Sugimoto H, Tosha T, Shiro Y. Molecular structure and function of bacterial nitric oxide reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:680-7. [PMID: 22001779 DOI: 10.1016/j.bbabio.2011.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/29/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
Abstract
The crystal structure of the membrane-integrated nitric oxide reductase cNOR from Pseudomonas aeruginosa was determined. The smaller NorC subunit of cNOR is comprised of 1 trans-membrane helix and a hydrophilic domain, where the heme c is located, while the larger NorB subunit consists of 12 trans-membrane helices, which contain heme b and the catalytically active binuclear center (heme b(3) and non-heme Fe(B)). The roles of the 5 well-conserved glutamates in NOR are discussed, based on the recently solved structure. Glu211 and Glu280 appear to play an important role in the catalytic reduction of NO at the binuclear center by functioning as a terminal proton donor, while Glu215 probably contributes to the electro-negative environment of the catalytic center. Glu135, a ligand for Ca(2+) sandwiched between two heme propionates from heme b and b(3), and the nearby Glu138 appears to function as a structural factor in maintaining a protein conformation that is suitable for electron-coupled proton transfer from the periplasmic region to the active site. On the basis of these observations, the possible molecular mechanism for the reduction of NO by cNOR is discussed. This article is part of a Special Issue entitled: Respiratory Oxidases.
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12
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Timóteo CG, Pereira AS, Martins CE, Naik SG, Duarte AG, Moura JJG, Tavares P, Huynh BH, Moura I. Low-spin heme b(3) in the catalytic center of nitric oxide reductase from Pseudomonas nautica. Biochemistry 2011; 50:4251-62. [PMID: 21452843 DOI: 10.1021/bi101605p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Respiratory nitric oxide reductase (NOR) was purified from membrane extract of Pseudomonas (Ps.) nautica cells to homogeneity as judged by polyacrylamide gel electrophoresis. The purified protein is a heterodimer with subunits of molecular masses of 54 and 18 kDa. The gene encoding both subunits was cloned and sequenced. The amino acid sequence shows strong homology with enzymes of the cNOR class. Iron/heme determinations show that one heme c is present in the small subunit (NORC) and that approximately two heme b and one non-heme iron are associated with the large subunit (NORB), in agreement with the available data for enzymes of the cNOR class. Mössbauer characterization of the as-purified, ascorbate-reduced, and dithionite-reduced enzyme confirms the presence of three heme groups (the catalytic heme b(3) and the electron transfer heme b and heme c) and one redox-active non-heme Fe (Fe(B)). Consistent with results obtained for other cNORs, heme c and heme b in Ps. nautica cNOR were found to be low-spin while Fe(B) was found to be high-spin. Unexpectedly, as opposed to the presumed high-spin state for heme b(3), the Mössbauer data demonstrate unambiguously that heme b(3) is, in fact, low-spin in both ferric and ferrous states, suggesting that heme b(3) is six-coordinated regardless of its oxidation state. EPR spectroscopic measurements of the as-purified enzyme show resonances at the g ∼ 6 and g ∼ 2-3 regions very similar to those reported previously for other cNORs. The signals at g = 3.60, 2.99, 2.26, and 1.43 are attributed to the two charge-transfer low-spin ferric heme c and heme b. Previously, resonances at the g ∼ 6 region were assigned to a small quantity of uncoupled high-spin Fe(III) heme b(3). This assignment is now questionable because heme b(3) is low-spin. On the basis of our spectroscopic data, we argue that the g = 6.34 signal is likely arising from a spin-spin coupled binuclear center comprising the low-spin Fe(III) heme b(3) and the high-spin Fe(B)(III). Activity assays performed under various reducing conditions indicate that heme b(3) has to be reduced for the enzyme to be active. But, from an energetic point of view, the formation of a ferrous heme-NO as an initial reaction intermediate for NO reduction is disfavored because heme [FeNO](7) is a stable product. We suspect that the presence of a sixth ligand in the Fe(II)-heme b(3) may weaken its affinity for NO and thus promotes, in the first catalytic step, binding of NO at the Fe(B)(II) site. The function of heme b(3) would then be to orient the Fe(B)-bound NO molecules for the formation of the N-N bond and to provide reducing equivalents for NO reduction.
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Affiliation(s)
- Cristina G Timóteo
- Requimte, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Monte de Caparica, Portugal
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13
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Field SJ, Roldan MD, Marritt SJ, Butt JN, Richardson DJ, Watmough NJ. Electron transfer to the active site of the bacterial nitric oxide reductase is controlled by ligand binding to heme b₃. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:451-7. [PMID: 21296048 DOI: 10.1016/j.bbabio.2011.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 01/26/2011] [Accepted: 01/30/2011] [Indexed: 10/18/2022]
Abstract
The active site of the bacterial nitric oxide reductase from Paracoccus denitrificans contains a dinuclear centre comprising heme b₃ and non heme iron (Fe(B)). These metal centres are shown to be at isopotential with midpoint reduction potentials of E(m) ≈ +80 mV. The midpoint reduction potentials of the other two metal centres in the enzyme, heme c and heme b, are greater than the dinuclear centre suggesting that they act as an electron receiving/storage module. Reduction of the low-spin heme b causes structural changes at the dinuclear centre which allow access to substrate molecules. In the presence of the substrate analogue, CO, the midpoint reduction potential of heme b₃ is raised to a region similar to that of heme c and heme b. This leads us to suggest that reduction of the electron transfer hemes leads to an opening of the active site which allows substrate to bind and in turn raises the reduction potential of the active site such that electrons are only delivered to the active site following substrate binding.
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Affiliation(s)
- Sarah J Field
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR47TJ, UK
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14
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Lachmann P, Huang Y, Reimann J, Flock U, Adelroth P. Substrate control of internal electron transfer in bacterial nitric-oxide reductase. J Biol Chem 2010; 285:25531-7. [PMID: 20547487 DOI: 10.1074/jbc.m110.123984] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric -oxide reductase (NOR) from Paracoccus denitrificans catalyzes the reduction of nitric oxide (NO) to nitrous oxide (N(2)O) (2NO + 2H(+) + 2e(-) -->N(2)O + H(2)O) by a poorly understood mechanism. NOR contains two low spin hemes c and b, one high spin heme b(3), and a non-heme iron Fe(B). Here, we have studied the reaction between fully reduced NOR and NO using the "flow-flash" technique. Fully (four-electron) reduced NOR is capable of two turnovers with NO. Initial binding of NO to reduced heme b(3) occurs with a time constant of approximately 1 micros at 1.5 mM NO, in agreement with earlier studies. This reaction is [NO]-dependent, ruling out an obligatory binding of NO to Fe(B) before ligation to heme b(3). Oxidation of hemes b and c occurs in a biphasic reaction with rate constants of 50 s(-1) and 3 s(-1) at 1.5 mM NO and pH 7.5. Interestingly, this oxidation is accelerated as [NO] is lowered; the rate constants are 120 s(-1) and 12 s(-1) at 75 microM NO. Protons are taken up from solution concomitantly with oxidation of the low spin hemes, leading to an acceleration at low pH. This effect is, however, counteracted by a larger degree of substrate inhibition at low pH. Our data thus show that substrate inhibition in NOR, previously observed during multiple turnovers, already occurs during a single oxidative cycle. Thus, NO must bind to its inhibitory site before electrons redistribute to the active site. The further implications of our data for the mechanism of NO reduction by NOR are discussed.
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Affiliation(s)
- Peter Lachmann
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Wang J, Schopfer MP, Puiu SC, Sarjeant AAN, Karlin KD. Reductive coupling of nitrogen monoxide (*NO) facilitated by heme/copper complexes. Inorg Chem 2010; 49:1404-19. [PMID: 20030370 DOI: 10.1021/ic901431r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interactions of nitrogen monoxide (*NO; nitric oxide) with transition metal centers continue to be of great interest, in part due to their importance in biochemical processes. Here, we describe *NO((g)) reductive coupling chemistry of possible relevance to that process (i.e., nitric oxide reductase (NOR) biochemistry), which occurs at the heme/Cu active site of cytochrome c oxidases (CcOs). In this report, heme/Cu/*NO((g)) activity is studied using 1:1 ratios of heme and copper complex components, (F(8))Fe (F(8) = tetrakis(2,6-difluorophenyl)porphyrinate(2-)) and [(tmpa)Cu(I)(MeCN)](+) (TMPA = tris(2-pyridylmethyl)amine). The starting point for heme chemistry is the mononitrosyl complex (F(8))Fe(NO) (lambda(max) = 399 (Soret), 541 nm in acetone). Variable-temperature (1)H and (2)H NMR spectra reveal a broad peak at delta = 6.05 ppm (pyrrole) at room temperature (RT), which gives rise to asymmetrically split pyrrole peaks at 9.12 and 8.54 ppm at -80 degrees C. A new heme dinitrosyl species, (F(8))Fe(NO)(2), obtained by bubbling (F(8))Fe(NO) with *NO((g)) at -80 degrees C, could be reversibly formed, as monitored by UV-vis (lambda(max) = 426 (Soret), 538 nm in acetone), EPR (silent), and NMR spectroscopies; that is, the mono-NO complex was regenerated upon warming to RT. (F(8))Fe(NO)(2) reacts with [(tmpa)Cu(I)(MeCN)](+) and 2 equiv of acid to give [(F(8))Fe(III)](+), [(tmpa)Cu(II)(solvent)](2+), and N(2)O((g)), fitting the stoichiometric *NO((g)) reductive coupling reaction: 2*NO((g)) + Fe(II) + Cu(I) + 2H(+) --> N(2)O((g)) + Fe(III) + Cu(II) + H(2)O, equivalent to one enzyme turnover. Control reaction chemistry shows that both iron and copper centers are required for the NOR-type chemistry observed and that, if acid is not present, half the *NO is trapped as a (F(8))Fe(NO) complex, while the remaining nitrogen monoxide undergoes copper complex promoted disproportionation chemistry. As part of this study, [(F(8))Fe(III)]SbF(6) was synthesized and characterized by X-ray crystallography, along with EPR (77 K: g = 5.84 and 6.12 in CH(2)Cl(2) and THF, respectively) and variable-temperature NMR spectroscopies. These structural and physical properties suggest that at RT this complex consists of an admixture of high and intermediate spin states.
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Affiliation(s)
- Jun Wang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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16
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Mitigating release of the potent greenhouse gas N(2)O from the nitrogen cycle - could enzymic regulation hold the key? Trends Biotechnol 2009; 27:388-97. [PMID: 19497629 DOI: 10.1016/j.tibtech.2009.03.009] [Citation(s) in RCA: 247] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 11/21/2022]
Abstract
When faced with a shortage of oxygen, many bacterial species use nitrate to support respiration via the process of denitrification. This takes place extensively in nitrogen-rich soils and generates the gaseous products nitric oxide (NO), nitrous oxide (N(2)O) and dinitrogen (N(2)). The denitrifying bacteria protect themselves from the endogenous cytotoxic NO produced by converting it to N(2)O, which can be released into the atmosphere. However, N(2)O is a potent greenhouse gas and hence the activity of the enzyme that breaks down N(2)O has a crucial role in restricting its atmospheric levels. Here, we review the current understanding of the process by which N(2)O is produced and destroyed and discuss the potential for feeding this into new approaches for combating N(2)O release.
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Abstract
The two-subunit cytochrome bc complex (NorBC) isolated from membranes of the model denitrifying soil bacterium Paracoccus denitrificans is the best-characterized example of the bacterial respiratory nitric oxide reductases. These are members of the super-family of haem-copper oxidases and are characterized by the elemental composition of their active site, which contains non-haem iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is catalysed. The reaction requires the presence of two substrate molecules at the active site along with the controlled input of two electrons and two protons from the same side of the membrane. In the present paper, we consider progress towards understanding the pathways of electron and proton transfer in NOR and how this information can be integrated with evidence for the likely modes of substrate binding at the active site to propose a revised and experimentally testable reaction mechanism.
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Flock U, Lachmann P, Reimann J, Watmough NJ, Adelroth P. Exploring the terminal region of the proton pathway in the bacterial nitric oxide reductase. J Inorg Biochem 2009; 103:845-50. [PMID: 19332356 DOI: 10.1016/j.jinorgbio.2009.02.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 02/12/2009] [Accepted: 02/20/2009] [Indexed: 12/01/2022]
Abstract
The c-type nitric oxide reductase (cNOR) from Paracoccus (P.) denitrificans is an integral membrane protein that catalyzes NO reduction; 2NO+2e(-)+2H(+)-->N(2)O+H(2)O. It is also capable of catalyzing the reduction of oxygen to water, albeit more slowly than NO reduction. cNORs are divergent members of the heme-copper oxidase superfamily (HCuOs) which reduce NO, do not pump protons, and the reaction they catalyse is non-electrogenic. All known cNORs have been shown to have five conserved glutamates (E) in the catalytic subunit, by P. denitrificans numbering, the E122, E125, E198, E202 and E267. The E122 and E125 are presumed to face the periplasm and the E198, E202 and E267 are located in the interior of the membrane, close to the catalytic site. We recently showed that the E122 and E125 define the entry point of the proton pathway leading from the periplasm into the active site [U. Flock, F.H. Thorndycroft, A.D. Matorin, D.J. Richardson, N.J. Watmough, P. Adelroth, J. Biol. Chem. 283 (2008) 3839-3845]. Here we present results from the reaction between fully reduced NOR and oxygen on the alanine variants of the E198, E202 and E267. The initial binding of O(2) to the active site was unaffected by these mutations. In contrast, proton uptake to the bound O(2) was significantly inhibited in both the E198A and E267A variants, whilst the E202A NOR behaved essentially as wildtype. We propose that the E198 and E267 are involved in terminating the proton pathway in the region close to the active site in NOR.
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Affiliation(s)
- Ulrika Flock
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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19
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Abstract
A functional heme/nonheme nitric oxide reductase (NOR) model is presented. The fully reduced diiron compound reacts with two equivalents of NO leading to the formation of one equivalent of N(2)O and the bis-ferric product. NO binds to both heme Fe and nonheme Fe complexes forming individual ferrous nitrosyl species. The mixed-valence species with an oxidized heme and a reduced nonheme Fe(B) does not show NO reduction activity. These results are consistent with a so-called "trans" mechanism for the reduction of NO by bacterial NOR.
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20
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Yeung N, Lu Y. One heme, diverse functions: using biosynthetic myoglobin models to gain insights into heme-copper oxidases and nitric oxide reductases. Chem Biodivers 2008; 5:1437-1454. [PMID: 18729107 PMCID: PMC2770894 DOI: 10.1002/cbdv.200890134] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Natasha Yeung
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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21
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Field SJ, Thorndycroft FH, Matorin AD, Richardson DJ, Watmough NJ. The respiratory nitric oxide reductase (NorBC) from Paracoccus denitrificans. Methods Enzymol 2008; 437:79-101. [PMID: 18433624 DOI: 10.1016/s0076-6879(07)37005-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The two subunit cytochrome bc complex (NorBC) isolated from membranes of the model denitrifying soil bacterium Paracoccus denitrificans is the best characterized example of the bacterial respiratory nitric oxide reductases. These are members of the superfamily of heme-copper oxidases and are characterized by the elemental composition of their active site, which contains nonheme iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is catalyzed. This chapter describes methods for the purification and characterization of both native nitric oxide reductase from P. denitrificans and a recombinant form of the enzyme expressed in Escherichia coli, which enables site-directed mutagenesis of the catalytic subunit NorB. Examples are given of electronic absorption and electron paramagnetic resonance spectra that characterize the enzyme in a number of redox states, along with a method for the routine assay of the complex using its natural electron donor pseudoazurin.
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Affiliation(s)
- Sarah J Field
- Center for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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22
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Collman JP, Yan YL, Lei J, Dinolfo PH. Active-site models of bacterial nitric oxide reductase featuring tris-histidyl and glutamic acid mimics: influence of a carboxylate ligand on Fe(B) binding and the heme Fe/Fe(B) redox potential. Inorg Chem 2007; 45:7581-3. [PMID: 16961346 PMCID: PMC2593900 DOI: 10.1021/ic0609150] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Active-site models of bacterial nitric oxide reductase (NOR) featuring a heme Fe and a trisimidazole- and glutaric acid-bound non-heme Fe (Fe(B)) have been synthesized. These models closely replicate the proposed active site of native NORs. Examination of these models shows that the glutamic acid mimic is required for both Fe(B) retention in the distal binding site and proper modulation of the redox potentials of both the heme and non-heme Fe's.
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Affiliation(s)
- James P Collman
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
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Moënne-Loccoz P. Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins. Nat Prod Rep 2007; 24:610-20. [PMID: 17534533 PMCID: PMC3028592 DOI: 10.1039/b604194a] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitric oxide (NO) plays an important role in cell signalling and in the mammalian immune response to infection. On its own, NO is a relatively inert radical, and when it is used as a signalling molecule, its concentration remains within the picomolar range. However, at infection sites, the NO concentration can reach the micromolar range, and reactions with other radical species and transition metals lead to a broad toxicity. Under aerobic conditions, microorganisms cope with this nitrosative stress by oxidizing NO to nitrate (NO3−). Microbial hemoglobins play an essential role in this NO-detoxifying process. Under anaerobic conditions, detoxification occurs via a 2-electron reduction of two NO molecules to N2O. In many bacteria and archaea, this NO-reductase reaction is catalyzed by diiron proteins. Despite the importance of this reaction in providing microorganisms with a resistance to the mammalian immune response, its mechanism remains ill-defined. Because NO is an obligatory intermediate of the denitrification pathway, respiratory NO reductases also provide resistance to toxic concentrations of NO. This family of enzymes is the focus of this review. Respiratory NO reductases are integral membrane protein complexes that contain a norB subunit evolutionarily related to subunit I of cytochrome c oxidase (Cc O). NorB anchors one high-spin heme b3 and one non-heme iron known as FeB, i.e ., analogous to CuB in Cc O. A second group of diiron proteins with NO-reductase activity is comprised of the large family of soluble flavoprotein A found in strict and facultative anaerobic bacteria and archaea. These soluble detoxifying NO reductases contain a non-heme diiron cluster with a Fe–Fe distance of 3.4 Å and are only briefly mentioned here as a promising field of research. This article describes possible mechanisms of NO reduction to N2O in denitrifying NO-reductase (NOR) proteins and critically reviews recent experimental results. Relevant theoretical model calculations and spectroscopic studies of the NO-reductase reaction in heme/copper terminal oxidases are also overviewed.
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Affiliation(s)
- Pierre Moënne-Loccoz
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, 20,000 NW Walker Road, Beaverton, Oregon 97006-8921, USA.
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24
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Blomberg LM, Blomberg MRA, Siegbahn PEM. Reduction of nitric oxide in bacterial nitric oxide reductase--a theoretical model study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:240-52. [PMID: 16774734 DOI: 10.1016/j.bbabio.2006.04.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2006] [Revised: 04/07/2006] [Accepted: 04/07/2006] [Indexed: 11/24/2022]
Abstract
The mechanism of the nitric oxide reduction in a bacterial nitric oxide reductase (NOR) has been investigated in two model systems of the heme-b(3)-Fe(B) active site using density functional theory (B3LYP). A model with an octahedral coordination of the non-heme Fe(B) consisting of three histidines, one glutamate and one water molecule gave an energetically feasible reaction mechanism. A tetrahedral coordination of the non-heme iron, corresponding to the one of Cu(B) in cytochrome oxidase, gave several very high barriers which makes this type of coordination unlikely. The first nitric oxide coordinates to heme b(3) and is partly reduced to a more nitroxyl anion character, which activates it toward an attack from the second NO. The product in this reaction step is a hyponitrite dianion coordinating in between the two irons. Cleaving an NO bond in this intermediate forms an Fe(B) (IV)O and nitrous oxide, and this is the rate determining step in the reaction mechanism. In the model with an octahedral coordination of Fe(B) the intrinsic barrier of this step is 16.3 kcal/mol, which is in good agreement with the experimental value of 15.9 kcal/mol. However, the total barrier is 21.3 kcal/mol, mainly due to the endergonic reduction of heme b(3) taken from experimental reduction potentials. After nitrous oxide has left the active site the ferrylic Fe(B) will form a mu-oxo bridge to heme b(3) in a reaction step exergonic by 45.3 kcal/mol. The formation of a quite stable mu-oxo bridge between heme b(3) and Fe(B) is in agreement with this intermediate being the experimentally observed resting state in oxidized NOR. The formation of a ferrylic non-heme Fe(B) in the proposed reaction mechanism could be one reason for having an iron as the non-heme metal ion in NOR instead of a Cu as in cytochrome oxidase.
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Affiliation(s)
- L Mattias Blomberg
- Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden.
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25
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Abstract
The NOR (nitric oxide reductase) from Paracoccus denitrificans catalyses the two-electron reduction of NO to N2O (2NO+2H++2e−→N2O+H2O). The NOR is a divergent member of the superfamily of haem-copper oxidases, oxygen-reducing enzymes which couple the reduction of oxygen with translocation of protons across the membrane. In contrast, reduction of NO catalysed by NOR is non-electrogenic which, since electrons are supplied from the periplasmic side of the membrane, implies that the protons needed for NO reduction are also taken from the periplasm. Thus NOR must contain a proton-transfer pathway leading from the periplasmic side of the membrane into the catalytic site. The proton pathway has not been identified, and the mechanism and timing of proton transfer during NO reduction is unknown. To address these questions, we have studied the reaction between NOR and the chemically less reactive oxidant O2 [Flock, Watmough and Ädelroth (2005) Biochemistry 44, 10711–10719]. When fully reduced NOR reacts with O2, proton-coupled electron transfer occurs in a reaction that is rate-limited by internal proton transfer from a group with a pKa of 6.6. This group is presumably an amino acid residue close to the active site that acts as a proton donor also during NO reduction. The results are discussed in the framework of a structural model that identifies possible candidates for the proton donor as well as for the proton-transfer pathway.
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Affiliation(s)
- U Flock
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
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26
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Flock U, Watmough NJ, Adelroth P. Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen. Biochemistry 2005; 44:10711-9. [PMID: 16060680 DOI: 10.1021/bi050524h] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The respiratory nitric oxide reductase (NOR) from Paracoccus denitrificans catalyzes the two-electron reduction of NO to N(2)O (2NO + 2H(+) + 2e(-) --> N(2)O + H(2)O), which is an obligatory step in the sequential reduction of nitrate to dinitrogen known as denitrification. NOR has four redox-active cofactors, namely, two low-spin hemes c and b, one high-spin heme b(3), and a non-heme iron Fe(B), and belongs to same superfamily as the oxygen-reducing heme-copper oxidases. NOR can also use oxygen as an electron acceptor; this catalytic activity was investigated in this study. We show that the product in the steady-state reduction of oxygen is water. A single turnover of the fully reduced NOR with oxygen was initiated using the flow-flash technique, and the progress of the reaction monitored by time-resolved optical absorption spectroscopy. Two major phases with time constants of 40 micros and 25 ms (pH 7.5, 1 mM O(2)) were observed. The rate constant for the faster process was dependent on the O(2) concentration and is assigned to O(2) binding to heme b(3) at a bimolecular rate constant of 2 x 10(7) M(-)(1) s(-)(1). The second phase (tau = 25 ms) involves oxidation of the low-spin hemes b and c, and is coupled to the uptake of protons from the bulk solution. The rate constant for this phase shows a pH dependence consistent with rate limitation by proton transfer from an internal group with a pK(a) = 6.6. This group is presumably an amino acid residue that is crucial for proton transfer to the catalytic site also during NO reduction.
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Affiliation(s)
- Ulrika Flock
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
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27
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Sakurai T, Nakashima S, Kataoka K, Seo D, Sakurai N. Diverse NO reduction by Halomonas halodenitrificans nitric oxide reductase. Biochem Biophys Res Commun 2005; 333:483-7. [PMID: 15950940 DOI: 10.1016/j.bbrc.2005.05.149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 05/19/2005] [Indexed: 11/25/2022]
Abstract
Reduction of the four Fe centers is not required to initiate the reaction of the Halomonas halodenitrificans nitric oxide reductase (NOR) based on the facts that NOR in the form that ferric heme b(3) and non-heme iron (Fe(B)) are not bridged and/or the interaction between them is weakened and reversibly binds NO molecules, and that NOR in the form that only heme b(3) is oxidized reacts with NO molecules.
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Affiliation(s)
- Takeshi Sakurai
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.
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28
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Kumita H, Matsuura K, Hino T, Takahashi S, Hori H, Fukumori Y, Morishima I, Shiro Y. NO Reduction by Nitric-oxide Reductase from Denitrifying Bacterium Pseudomonas aeruginosa. J Biol Chem 2004; 279:55247-54. [PMID: 15504726 DOI: 10.1074/jbc.m409996200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric-oxide reductase (NOR) of a denitrifying bacterium catalyzes NO reduction to N(2)O at the binuclear catalytic center consisting of high spin heme b(3) and non-heme Fe(B). The structures of the reaction intermediates in the single turnover of the NO reduction by NOR from Pseudomonas aeruginosa were investigated using optical absorption and EPR spectroscopies combined with an originally designed freeze-quench device. In the EPR spectrum of the sample, in which the fully reduced NOR was mixed with an NO solution and quenched at 0.5 ms after the mixing, two characteristic signals for the ferrous Fe(B)-NO and the penta-coordinated ferrous heme b(3)-NO species were observed. The CO inhibition of its formation indicated that two NO molecules were simultaneously distributed into the two irons of the same binuclear center of the enzyme in this state. The time- and temperature-dependent EPR spectral changes indicated that the species that appeared at 0.5 ms is a transient reaction intermediate prior to the N(2)O formation, in good agreement with the so-called "trans" mechanism. It was also found that the final state of the enzyme in the single turnover cycle is the fully oxidized state, in which the mu-oxo-bridged ligand is absent between the two irons of its binuclear center, unlike the resting form of NOR as isolated. On the basis of these present findings, we propose a newly developed mechanism for the NO reduction reaction conducted by NOR.
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Affiliation(s)
- Hideyuki Kumita
- RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
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29
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Heering HA, Wiertz FGM, Dekker C, de Vries S. Direct Immobilization of Native Yeast Iso-1 Cytochrome c on Bare Gold: Fast Electron Relay to Redox Enzymes and Zeptomole Protein-Film Voltammetry. J Am Chem Soc 2004; 126:11103-12. [PMID: 15339197 DOI: 10.1021/ja046737w] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic voltammetry shows that yeast iso-1-cytochrome c (YCC), chemisorbed on a bare gold electrode via Cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. Vectorially immobilized YCC relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (NIR) and nitric oxide reductase from Paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. On a microelectrode, we measured nitrite turnover by approximately 80 zmol (49 000 molecules) of NIR, coadsorbed on 0.65 amol (390 000 molecules) of YCC.
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Affiliation(s)
- Hendrik A Heering
- Contribution from the Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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30
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Grönberg KLC, Watmough NJ, Thomson AJ, Richardson DJ, Field SJ. Redox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies. J Biol Chem 2004; 279:17120-5. [PMID: 14766741 DOI: 10.1074/jbc.m400824200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial respiratory nitric-oxide reductase (NOR) catalyzes the respiratory detoxification of nitric oxide in bacteria and Archaea. It is a member of the well known super-family of heme-copper oxidases but has a [heme Fe-non-heme Fe] active site rather than the [heme Fe-Cu(B)] active site normally associated with oxygen reduction. Paracoccus denitrificans NOR is spectrally characterized by a ligand-to-metal charge transfer absorption band at 595 nm, which arises from the high spin ferric heme iron of a micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site. On reduction of the nonheme iron, the micro-oxo bridge is broken, and the ferric heme iron is hydroxylated or hydrated, depending on the pH. At present, the catalytic cycle of NOR is a matter of much debate, and it is not known to which redox state(s) of the enzyme nitric oxide can bind. This study has used cyanide to probe the nature of the active site in a number of different redox states. Our observations suggest that the micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site represents a closed or resting state of NOR that can be opened by reduction of the non-heme iron.
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Affiliation(s)
- Karin L C Grönberg
- School of Biological Sciences and School of Chemical Sciences and Pharmacy, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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31
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Pitcher RS, Cheesman MR, Watmough NJ. Molecular and spectroscopic analysis of the cytochrome cbb(3) oxidase from Pseudomonas stutzeri. J Biol Chem 2002; 277:31474-83. [PMID: 12070166 DOI: 10.1074/jbc.m204103200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome cbb(3) oxidase, a member of the heme-copper oxidase superfamily, is characterized by its high affinity for oxygen while retaining the ability to pump protons. These attributes are central to its proposed role in the microaerobic metabolism of proteobacteria. We have completed the first detailed spectroscopic characterization of a cytochrome cbb(3) oxidase, the enzyme purified from Pseudomonas stutzeri. A combination of UV-visible and magnetic CD spectroscopies clearly identified four low-spin hemes and the high-spin heme of the active site. This heme complement is in good agreement with our analysis of the primary sequence of the ccoNOPQ operon and biochemical analysis of the complex. Near-IR magnetic CD spectroscopy revealed the unexpected presence of a low-spin bishistidine-coordinated c-type heme in the complex. This was shown to be one of two c-type hemes in the CcoP subunit by separately expressing the subunit in Escherichia coli. Separate expression of CcoP also allowed us to unambiguously assign each of the signals associated with low-spin ferric hemes present in the X-band EPR spectrum of the oxidized enzyme. This work both underpins future mechanistic studies on this distinctive class of bacterial oxidases and raises questions concerning the role of CcoP in electron delivery to the catalytic subunit.
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Affiliation(s)
- Robert S Pitcher
- Centre for Metalloprotein Spectroscopy and Biology and the School of Biological Sciences, University of East Anglia, Norfolk NR4 7TJ, United Kingdom
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