1
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Hird K, Campeciño JO, Lehnert N, Hegg EL. Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway. J Inorg Biochem 2024; 256:112542. [PMID: 38631103 DOI: 10.1016/j.jinorgbio.2024.112542] [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] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/19/2024]
Abstract
Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.
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Affiliation(s)
- Krystina Hird
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Julius O Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
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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: 92] [Impact Index Per Article: 30.7] [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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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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4
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Shahid S, Ali M, Legaspi-Humiston D, Wilcoxen J, Pacheco AA. A Kinetic Investigation of the Early Steps in Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite. Biochemistry 2021; 60:2098-2115. [PMID: 34143605 DOI: 10.1021/acs.biochem.1c00172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The decaheme enzyme cytochrome c nitrite reductase (ccNiR) catalyzes reduction of nitrite to ammonium in a six-electron, eight-proton process. With a strong reductant as the electron source, ammonium is the sole product. However, intermediates accumulate when weaker reductants are employed, facilitating study of the ccNiR mechanism. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated by using the weak reductants N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and ferrocyanide. In stopped-flow experiments, reduction of nitrite-loaded ccNiR by TMPD generated a transient intermediate, identified as FeH1II(NO2-), where FeH1 represents the ccNiR active site. FeH1II(NO2-) accumulated rapidly and was then more slowly converted to the two-electron-reduced moiety {FeH1NO}7; ccNiR was not reduced beyond the {FeH1NO}7 state. The midpoint potentials for sequential reduction of FeH1III(NO2-) to FeH1II(NO2-) and then to {FeH1NO}7 were estimated to be 130 and 370 mV versus the standard hydrogen electrode, respectively. FeH1II(NO2-) does not accumulate at equilibrium because its reduction to {FeH1NO}7 is so much easier than the reduction of FeH1III(NO2-) to FeH1II(NO2-). With weak reductants, free NO• was released from nitrite-loaded ccNiR. The release of NO• from {FeH1NO}7 is exceedingly slow (k ∼ 0.001 s-1), but it is somewhat faster (k ∼ 0.050 s-1) while FeH1III(NO2-) is being reduced to {FeH1NO}7; then, the release of NO• from the undetectable transient {FeH1NO}6 can compete with reduction of {FeH1NO}6 to {FeH1NO}7. CcNiR appears to be optimized to capture nitrite and minimize the release of free NO•. Nitrite capture is achieved by reducing bound nitrite with even weak electron donors, while NO• release is minimized by stabilizing the substitutionally inert {FeH1NO}7 over the more labile {FeH1NO}6.
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Affiliation(s)
- Shahid Shahid
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Mahbbat Ali
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Desiree Legaspi-Humiston
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - A Andrew Pacheco
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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5
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Sosa Alfaro V, Campeciño J, Tracy M, Elliott SJ, Hegg EL, Lehnert N. Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA). Biochemistry 2021; 60:1853-1867. [PMID: 34061493 DOI: 10.1021/acs.biochem.0c00977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via electron paramagnetic resonance (EPR) spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, 1 equiv at a time. The step-by-step reduction of the hemes was then followed using ultraviolet-visible absorption and EPR spectroscopy. EPR spectral simulations were used to elucidate the sequence of heme reduction within the pentaheme scaffold of NrfA and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow range from +10 mV (heme 5) to -226 mV (heme 3) (vs the standard hydrogen electrode). On the basis of quantitative analysis and simulation of the EPR data, we demonstrate that hemes 4 and 5 are reduced first (before the active site heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central heme 3, an H108M NrfA variant was generated where the reduction potential of heme 3 is shifted positively (from -226 to +48 mV). The H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 1% compared to that of the wild type. We propose that this is due to heme 3's important role as an electron gateway in the wild-type enzyme.
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Affiliation(s)
- Victor Sosa Alfaro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Julius Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew Tracy
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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7
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Amanullah S, Dey A. The role of porphyrin peripheral substituents in determining the reactivities of ferrous nitrosyl species. Chem Sci 2020; 11:5909-5921. [PMID: 32832056 PMCID: PMC7407271 DOI: 10.1039/d0sc01625j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/07/2020] [Indexed: 12/02/2022] Open
Abstract
Ferrous nitrosyl {FeNO}7 species is an intermediate common to the catalytic cycles of Cd1NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes.
Ferrous nitrosyl {FeNO}7 species is an intermediate common to the catalytic cycles of Cd1NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes. The former reduces NO2– to NO in the denitrification pathway while the latter reduces NO2– to NH4+ in a dissimilatory nitrite reduction. With very similar electron transfer partners and heme based active sites, the origin of this difference in reactivity has remained unexplained. Differences in the structure of the heme d1 (Cd1NiR), which bears electron-withdrawing groups and has saturated pyrroles, relative to heme c (CcNiR) are often invoked to explain these reactivities. A series of iron porphyrinoids, designed to model the electron-withdrawing peripheral substitution as well as the saturation present in heme d1 in Cd1NiR, and their NO adducts were synthesized and their properties were investigated. The data clearly show that the presence of electron-withdrawing groups (EWGs) and saturated pyrroles together in a synthetic porphyrinoid (FeDEsC) weakens the Fe–NO bond in {FeNO}7 adducts along with decreasing the bond dissociation free energies (BDFENH) of the {FeHNO}8 species. The EWG raises the E° of the {FeNO}7/8 process, making the electron transfer (ET) facile, but decreases the pKa of {FeNO}8 species, making protonation (PT) difficult, while saturation has the opposite effect. The weakening of the Fe–NO bonding biases the {FeNO}7 species of FeDEsC for NO dissociation, as in Cd1NiR, which is otherwise set-up for a proton-coupled electron transfer (PCET) to form an {FeHNO}8 species eventually leading to its further reduction to NH4+.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja SC Mullick Road , Kolkata , India - 700032 .
| | - Abhishek Dey
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja SC Mullick Road , Kolkata , India - 700032 .
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8
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Seefeldt LC, Yang ZY, Lukoyanov DA, Harris DF, Dean DR, Raugei S, Hoffman BM. Reduction of Substrates by Nitrogenases. Chem Rev 2020; 120:5082-5106. [PMID: 32176472 DOI: 10.1021/acs.chemrev.9b00556] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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9
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Ali M, Stein N, Mao Y, Shahid S, Schmidt M, Bennett B, Pacheco AA. Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism. J Am Chem Soc 2019; 141:13358-13371. [DOI: 10.1021/jacs.9b03036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahbbat Ali
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Natalia Stein
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Yingxi Mao
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Shahid Shahid
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Marius Schmidt
- Department of Physics, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
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10
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Lintuluoto M, Lintuluoto JM. Intra-electron transfer induced by protonation in copper-containing nitrite reductase. Metallomics 2018. [DOI: 10.1039/c7mt00323d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Electron transfer between two Cu sites in the enzyme induced by protonation of remote catalytic residues.
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Affiliation(s)
- Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
- Kyoto 606-8522
- Japan
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11
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Lintuluoto M, Yamada C, Lintuluoto JM. QM/MM Calculation of the Enzyme Catalytic Cycle Mechanism for Copper- and Zinc-Containing Superoxide Dismutase. J Phys Chem B 2017; 121:7235-7246. [DOI: 10.1021/acs.jpcb.7b03589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Chiaki Yamada
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
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12
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Parey K, Fielding AJ, Sörgel M, Rachel R, Huber H, Ziegler C, Rajendran C. In meso
crystal structure of a novel membrane-associated octaheme cytochrome c
from the Crenarchaeon Ignicoccus hospitalis. FEBS J 2016; 283:3807-3820. [DOI: 10.1111/febs.13870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 08/31/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian Parey
- Department of Structural Biology; Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Alistair J. Fielding
- School of Chemistry and the Photon Science Institute; University of Manchester; UK
| | - Matthias Sörgel
- Biogeochemistry Department; Max Planck Institute for Chemistry; Mainz Germany
| | - Reinhard Rachel
- Department of Microbiology; University of Regensburg; Germany
| | - Harald Huber
- Department of Microbiology; University of Regensburg; Germany
| | | | - Chitra Rajendran
- Department of Structural Biology; University of Regensburg; Germany
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13
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Lintuluoto M, Lintuluoto JM. DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase. Biochemistry 2016; 55:4697-707. [DOI: 10.1021/acs.biochem.6b00423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho,
Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
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14
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Timmons AJ, Symes MD. Converting between the oxides of nitrogen using metal-ligand coordination complexes. Chem Soc Rev 2016; 44:6708-22. [PMID: 26158348 DOI: 10.1039/c5cs00269a] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The oxides of nitrogen (chiefly NO, NO3(-), NO2(-) and N2O) are key components of the natural nitrogen cycle and are intermediates in a range of processes of enormous biological, environmental and industrial importance. Nature has evolved numerous enzymes which handle the conversion of these oxides to/from other small nitrogen-containing species and there also exist a number of heterogeneous catalysts that can mediate similar reactions. In the chemical space between these two extremes exist metal-ligand coordination complexes that are easier to interrogate than heterogeneous systems and simpler in structure than enzymes. In this Tutorial Review, we will examine catalysts for the inter-conversions of the various nitrogen oxides that are based on such complexes, looking in particular at more recent examples that take inspiration from the natural systems.
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Affiliation(s)
- Andrew J Timmons
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
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15
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Lintuluoto M, Lintuluoto JM. DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase. Biochemistry 2015; 55:210-23. [DOI: 10.1021/acs.biochem.5b00542] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
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16
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Bykov D, Neese F. Six-Electron Reduction of Nitrite to Ammonia by Cytochrome c Nitrite Reductase: Insights from Density Functional Theory Studies. Inorg Chem 2015; 54:9303-16. [DOI: 10.1021/acs.inorgchem.5b01506] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmytro Bykov
- qLEAP Center
for Theoretical Chemistry, Department of Chemistry, Aarhus University, Gustav
Wieds Vej 10A, DK-8000 Aarhus C, Denmark
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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17
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Sundararajan M, Neese F. Distal Histidine Modulates the Unusual O-Binding of Nitrite to Myoglobin: Evidence from the Quantum Chemical Analysis of EPR Parameters. Inorg Chem 2015; 54:7209-17. [DOI: 10.1021/acs.inorgchem.5b00557] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mahesh Sundararajan
- Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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18
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Lockwood CWJ, Burlat B, Cheesman MR, Kern M, Simon J, Clarke TA, Richardson DJ, Butt JN. Resolution of Key Roles for the Distal Pocket Histidine in Cytochrome c Nitrite Reductases. J Am Chem Soc 2015; 137:3059-68. [DOI: 10.1021/ja512941j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | - Melanie Kern
- Microbial
Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Jörg Simon
- Microbial
Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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19
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Bauß A, Koslowski T. Storage, transport, release: heme versatility in nitrite reductase electron transfer studied by molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:4483-91. [DOI: 10.1039/c4cp04383a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni.
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Affiliation(s)
- Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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20
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Shaw S, Lukoyanov D, Danyal K, Dean DR, Hoffman BM, Seefeldt LC. Nitrite and hydroxylamine as nitrogenase substrates: mechanistic implications for the pathway of N₂ reduction. J Am Chem Soc 2014; 136:12776-83. [PMID: 25136926 PMCID: PMC4160268 DOI: 10.1021/ja507123d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Investigations of reduction of nitrite
(NO2–) to ammonia (NH3) by
nitrogenase indicate a limiting
stoichiometry, NO2– + 6e– + 12ATP + 7H+ → NH3 + 2H2O + 12ADP + 12Pi. Two intermediates freeze-trapped during
NO2– turnover by nitrogenase variants
and investigated by Q-band ENDOR/ESEEM are identical to states, denoted H and I, formed
on the pathway of N2 reduction. The proposed NO2– reduction intermediate hydroxylamine (NH2OH) is a nitrogenase substrate for which the H and I reduction intermediates
also can be trapped. Viewing N2 and NO2– reductions in light of their common reduction intermediates
and of NO2– reduction by multiheme cytochrome
c nitrite reductase (ccNIR) leads us to propose that NO2– reduction by nitrogenase begins with the generation
of NO2H bound to a state in which the active-site FeMo-co
(M) has accumulated two [e–/H+] (E2), stored as a (bridging) hydride and proton. Proton
transfer to NO2H and H2O loss leaves M–[NO+]; transfer of the E2 hydride to
the [NO+] directly to form HNO bound to FeMo-co is one
of two alternative means for avoiding formation of a terminal M–[NO] thermodynamic “sink”. The N2 and NO2– reduction pathways
converge upon reduction of NH2NH2 and NH2OH bound states to form state H with [−NH2] bound to M. Final reduction
converts H to I, with NH3 bound to M. The results
presented here, combined with the parallels with ccNIR, support a
N2 fixation mechanism in which liberation of the first
NH3 occurs upon delivery of five [e–/H+] to N2, but a total of seven [e–/H+] to FeMo-co when obligate H2 evolution
is considered, and not earlier in the reduction process.
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Affiliation(s)
- Sudipta Shaw
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322, United States
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21
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Judd ET, Stein N, Pacheco AA, Elliott SJ. Hydrogen bonding networks tune proton-coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia. Biochemistry 2014; 53:5638-46. [PMID: 25137350 PMCID: PMC4159211 DOI: 10.1021/bi500854p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Multielectron
multiproton reactions play an important role in both
biological systems and chemical reactions involved in energy storage
and manipulation. A key strategy employed by nature in achieving such
complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron seven-proton
reduction of nitrite to ammonia. While a catalytic mechanism for ccNiR
has been proposed on the basis of studies combining computation and
crystallography, there have been few studies directly addressing the
nature of the proton-coupled events that are predicted to occur along
the nitrite reduction pathway. Here we use protein film voltammetry
to directly interrogate the proton-coupled steps that occur during
nitrite reduction by ccNiR. We find that conversion of nitrite to
ammonia by ccNiR adsorbed to graphite electrodes is defined by two
distinct phases; one is proton-coupled, and the other is not. Mutation
of key active site residues (H257, R103, and Y206) modulates these
phases and specifically alters the properties of the detected proton-dependent
step but does not inhibit the ability of ccNiR to conduct the full
reduction of nitrite to ammonia. We conclude that the active site
residues examined are responsible for tuning the protonation steps
that occur during catalysis, likely through an extensive hydrogen
bonding network, but are not necessarily required for the reaction
to proceed. These results provide important insight into how enzymes
can specifically tune proton- and electron transfer steps to achieve
high turnover numbers in a physiological pH range.
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Affiliation(s)
- Evan T Judd
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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22
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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23
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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24
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Abstract
The global biogeochemical nitrogen cycle is essential for life on Earth. Many of the underlying biotic reactions are catalyzed by a multitude of prokaryotic and eukaryotic life forms whereas others are exclusively carried out by microorganisms. The last century has seen the rise of a dramatic imbalance in the global nitrogen cycle due to human behavior that was mainly caused by the invention of the Haber-Bosch process. Its main product, ammonia, is a chemically reactive and biotically favorable form of bound nitrogen. The anthropogenic supply of reduced nitrogen to the biosphere in the form of ammonia, for example during environmental fertilization, livestock farming, and industrial processes, is mandatory in feeding an increasing world population. In this chapter, environmental ammonia pollution is linked to the activity of microbial metalloenzymes involved in respiratory energy metabolism and bioenergetics. Ammonia-producing multiheme cytochromes c are discussed as paradigm enzymes.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287, Darmstadt, Germany,
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25
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Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2013; 19:97-112. [DOI: 10.1007/s00775-013-1065-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/05/2013] [Indexed: 11/25/2022]
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26
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Design and synthesis of novel 3,5-bis-N-(aryl/heteroaryl) carbamoyl-4-aryl-1,4-dihydropyridines as small molecule BACE-1 inhibitors. Bioorg Med Chem 2013; 21:6893-909. [DOI: 10.1016/j.bmc.2013.09.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 11/23/2022]
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27
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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28
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Contrasting catalytic profiles of multiheme nitrite reductases containing CxxCK heme-binding motifs. J Biol Inorg Chem 2013; 18:655-67. [DOI: 10.1007/s00775-013-1011-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
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29
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Ebadi A, Razzaghi-Asl N, Khoshneviszadeh M, Miri R. Comparative amino acid decomposition analysis of potent type I p38α inhibitors. ACTA ACUST UNITED AC 2013; 21:41. [PMID: 23714278 PMCID: PMC3680208 DOI: 10.1186/2008-2231-21-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/25/2013] [Indexed: 12/21/2022]
Abstract
Background and purpose of the study p38α is a member of mitogen-activated protein kinases (MAPK) considered as a prominent target in development of anti-inflammatory agents. Any abnormality in the phosphorylation process leads to the different human diseases such as cancer, diabetes and inflammatory diseases. Several small molecule p38α inhibitors have been developed up to now. In this regard, structural elucidation of p38 inhibitors needs to be done enabling us in rational lead development strategies. Methods Various interactions of three potent inhibitors with p38α active site have been evaluated in terms of binding energies and bond lengths via density function theory and MD simulations. Results Our comparative study showed that both ab initio and MD simulation led to the relatively similar results in pharmacophore discrimination of p38α inhibitors. Conclusion The results of the present study may find their usefulness in pharmacophore based modification of p38α inhibitors.
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Affiliation(s)
- Ahmad Ebadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, PO Box 3288-71345, Shiraz, Iran.
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30
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Tikhonova T, Tikhonov A, Trofimov A, Polyakov K, Boyko K, Cherkashin E, Rakitina T, Sorokin D, Popov V. Comparative structural and functional analysis of two octaheme nitrite reductases from closely relatedThioalkalivibriospecies. FEBS J 2012; 279:4052-61. [DOI: 10.1111/j.1742-4658.2012.08811.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tamara Tikhonova
- Bach Institute of Biochemistry; Russian Academy of Sciences, Leninskii pr. 33; Moscow 119071; Russia
| | - Alexey Tikhonov
- Bach Institute of Biochemistry; Russian Academy of Sciences, Leninskii pr. 33; Moscow 119071; Russia
| | | | | | | | - Eugene Cherkashin
- National Research Centre ‘Kurchatov Institute’, Academic Kurchatov sq. 1; Moscow 123182; Russia
| | - Tatiana Rakitina
- National Research Centre ‘Kurchatov Institute’, Academic Kurchatov sq. 1; Moscow 123182; Russia
| | - Dmitry Sorokin
- Winogradsky Institute of Microbiology; Russian Academy of Sciences, Leninskii pr. 32a; Moscow 119991; Russia
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31
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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32
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Todorovic S, Rodrigues ML, Matos D, Pereira IAC. Redox properties of lysine- and methionine-coordinated hemes ensure downhill electron transfer in NrfH2A4 nitrite reductase. J Phys Chem B 2012; 116:5637-43. [PMID: 22519292 DOI: 10.1021/jp301356m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The multiheme NrfHA nitrite reductase is a menaquinol:nitrite oxidoreductase that catalyzes the 6-electron reduction of nitrite to ammonia in a reaction that involves eight protons. X-ray crystallography of the enzyme from Desulfovibrio vulgaris revealed that the biological unit, NrfH2A4, houses 28 c-type heme groups, 22 of them with low spin and 6 with pentacoordinated high spin configuration. The high spin hemes, which are the electron entry and exit points of the complex, carry a highly unusual coordination for c-type hemes, lysine and methionine as proximal ligands in NrfA and NrfH, respectively. Employing redox titrations followed by X-band EPR spectroscopy and surface-enhanced resonance Raman spectroelectrochemistry, we provide the first experimental evidence for the midpoint redox potential of the NrfH menaquinol-interacting methionine-coordinated heme (-270 ± 10 mV, z = 0.96), identified by the use of the inhibitor HQNO, a structural analogue of the physiological electron donor. The redox potential of the catalytic lysine-coordinated high spin heme of NrfA is -50 ± 10 mV, z = 0.9. These values determined for the integral NrfH2A4 complex indicate that a driving force for a downhill electron transfer is ensured in this complex.
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Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa , Av. da Republica, 2780-157 Oeiras, Portugal
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33
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Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA. Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system. J Biol Inorg Chem 2012; 17:647-62. [PMID: 22382353 PMCID: PMC3412176 DOI: 10.1007/s00775-012-0885-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein "small tetraheme c" replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 °C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-Å-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Evan T. Judd
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Bilal Sayyed
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Tyler Goelzer
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Sean J. Elliott
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Marius Schmidt
- Department of Physics, 1900 E. Kenwood Blvd, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
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34
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Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2012; 17:741-60. [DOI: 10.1007/s00775-012-0893-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
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35
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Kern M, Volz J, Simon J. The oxidative and nitrosative stress defence network of Wolinella succinogenes: cytochrome c nitrite reductase mediates the stress response to nitrite, nitric oxide, hydroxylamine and hydrogen peroxide. Environ Microbiol 2011; 13:2478-94. [PMID: 21672122 DOI: 10.1111/j.1462-2920.2011.02520.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microorganisms employ diverse mechanisms to withstand physiological stress conditions exerted by reactive or toxic oxygen and nitrogen species such as hydrogen peroxide, organic hydroperoxides, superoxide anions, nitrite, hydroxylamine, nitric oxide or NO-generating compounds. This study identified components of the oxidative and nitrosative stress defence network of Wolinella succinogenes, an exceptional Epsilonproteobacterium that lacks both catalase and haemoglobins. Various gene deletion-insertion mutants were constructed, grown by either fumarate respiration or respiratory nitrate ammonification and subjected to disc diffusion, growth and viability assays under stress conditions. It was demonstrated that mainly two periplasmic multihaem c-type cytochromes, namely cytochrome c peroxidase and cytochrome c nitrite reductase (NrfA), mediated resistance to hydrogen peroxide. Two AhpC-type peroxiredoxin isoenzymes were shown to be involved in protection against different organic hydroperoxides. The phenotypes of two superoxide dismutase mutants lacking either SodB or SodB2 implied that both isoenzymes play important roles in oxygen and superoxide stress defence although they are predicted to reside in the cytoplasm and periplasm respectively. NrfA and a cytoplasmic flavodiiron protein (Fdp) were identified as key components of nitric oxide detoxification. In addition, NrfA (but not the hybrid cluster protein Hcp) was found to mediate resistance to hydroxylamine stress. The results indicate the presence of a robust oxidative and nitrosative stress defence network and identify NrfA as a multifunctional cytochrome c involved in both anaerobic respiration and stress protection.
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Affiliation(s)
- Melanie Kern
- Institute of Microbiology and Genetics, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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