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Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P. Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins. BMC Biol 2023; 21:47. [PMID: 36855050 PMCID: PMC9976466 DOI: 10.1186/s12915-023-01546-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (FeB) cofactor insertion into cytochrome c-dependent nitric oxide reductase (cNOR). cNOR catalyzes NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed FeB insertion, and the general mechanism of the MoxR/VWA interacting protein families. RESULTS We show that NorQ-catalyzed ATP hydrolysis, an intact VWA domain in NorD, and specific surface carboxylates on cNOR are all features required for cNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that "plugs" the NorQ ring pore to the VWA domain of NorD with a protruding "finger" inserting through the pore and suggest this binding mode to be general for MoxR/VWA couples. CONCLUSIONS Based on our results, we present a tentative model for the mechanism of NorQD-catalyzed cNOR remodeling and suggest many of its features to be applicable to the whole MoxR/VWA family.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden. .,Present Address: Department of Biochemistry, University of Potsdam, 14476, Potsdam, Germany.
| | - Sofia Appelgren
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden. .,Swedish Cryo-EM Facility, Science for Life Laboratory Stockholm University, Solna, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.
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2
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Tao W, Carter S, Trevino R, Zhang W, Shafaat HS, Zhang S. Reductive NO Coupling at Dicopper Center via a [Cu 2(NO) 2] 2+ Diamond-Core Intermediate. J Am Chem Soc 2022; 144:22633-22640. [PMID: 36469729 DOI: 10.1021/jacs.2c09523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Treatment of a dicopper(I,I) complex with excess amounts of NO leads to the formation of a dicopper dinitrosyl [Cu2(NO)2]2+ complex capable of (i) releasing two equivalents of NO reversibly in 90% yield and (ii) reacting with another equivalent of NO to afford N2O and dicopper nitrosyl oxo species [Cu2(NO)(O)]2+. Resonance Raman characterization of the [Cu2(NO)2]2+ complex shows a 15N-sensitive N═O stretch at 1527.6 cm-1 and two Cu-N stretches at 390.6 and 414.1 cm-1, supporting a symmetric diamond-core structure with bis-μ-NO ligands. The conversion of [Cu2(NO)2]2+ to [Cu2(NO)O]2+ occurs via a rate-limiting reaction with NO and bypasses the dicopper oxo intermediate, a mechanism distinct from that of diFe-mediated NO reduction to N2O.
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Affiliation(s)
- Wenjie Tao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Samantha Carter
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Regina Trevino
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Weiyao Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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3
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Matsumura H, Faponle AS, Hagedoorn PL, Tosha T, de Visser SP, Moënne-Loccoz P. Mechanism of substrate inhibition in cytochrome-c dependent NO reductases from denitrifying bacteria (cNORs). J Inorg Biochem 2022; 231:111781. [DOI: 10.1016/j.jinorgbio.2022.111781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022]
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4
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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5
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6
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Blomberg MRA. Activation of O 2 and NO in heme-copper oxidases - mechanistic insights from computational modelling. Chem Soc Rev 2021; 49:7301-7330. [PMID: 33006348 DOI: 10.1039/d0cs00877j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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7
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Takeda H, Kimura T, Nomura T, Horitani M, Yokota A, Matsubayashi A, Ishii S, Shiro Y, Kubo M, Tosha T. Timing of NO Binding and Protonation in the Catalytic Reaction of Bacterial Nitric Oxide Reductase as Established by Time-Resolved Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan
| | - Azusa Yokota
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Akiko Matsubayashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Shoko Ishii
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
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8
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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9
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Carrasco MC, Hematian S. (Hydr)oxo-bridged heme complexes: From structure to reactivity. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619300258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Iron–porphyrins ([Formula: see text] hemes) are present throughout the biosphere and perform a wide range of functions, particularly those that involve complex multiple-electron redox processes. Some common heme enzymes involved in these processes include cytochrome P450, heme/copper oxidase or heme/non-heme diiron nitric oxide reductase. Consequently, the (hydr)oxo-bridged heme species have been studied for the important roles that they play in many life processes or for their application for catalysis and preparation of new functional materials. This review encompasses important synthetic, structural and reactivity aspects of the (hydr)oxo-bridged heme constructs that govern their function and application. The properties and reactivity of the bridging (hydr)oxo moieties are directly dictated by the coordination environment of the heme core, the nature and ligation of the second metal center attached to the (hydr)oxo group, the presence or absence of a linker, and the degree of flexibility around that linker within the scaffold. Here, we summarize the structural features of all known (hydr)oxo-bridged heme constructs and use those to categorize and thus, provide a more comprehensive picture of structure–function relationships.
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Affiliation(s)
- Maria C. Carrasco
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro 27402, USA
| | - Shabnam Hematian
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro 27402, USA
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10
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Wijeratne GB, Bhadra M, Siegler MA, Karlin KD. Copper(I) Complex Mediated Nitric Oxide Reductive Coupling: Ligand Hydrogen Bonding Derived Proton Transfer Promotes N 2O (g) Release. J Am Chem Soc 2019; 141:17962-17967. [PMID: 31621325 DOI: 10.1021/jacs.9b07286] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A cuprous chelate bearing a secondary sphere hydrogen bonding functionality, [(PV-tmpa)CuI]+, transforms •NO(g) to N2O(g) in high-yields in methanol. Ligand derived proton transfer facilitates N-O bond cleavage of a putative hyponitrite intermediate releasing N2O(g), underscoring the crucial balance between H-bonding capabilities and acidities in (bio)chemical •NO(g) coupling systems.
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Affiliation(s)
- Gayan B Wijeratne
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Mayukh Bhadra
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Maxime A Siegler
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kenneth D Karlin
- Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States
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11
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Sabuncu S, Reed JH, Lu Y, Moënne-Loccoz P. Nitric Oxide Reductase Activity in Heme-Nonheme Binuclear Engineered Myoglobins through a One-Electron Reduction Cycle. J Am Chem Soc 2018; 140:17389-17393. [PMID: 30512937 DOI: 10.1021/jacs.8b11037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
FeBMbs are structural and functional models of native bacterial nitric oxide reductases (NORs) generated through engineering of myoglobin. These biosynthetic models replicate the heme-nonheme diiron site of NORs and allow substitutions of metal centers and heme cofactors. Here, we provide evidence for multiple NOR turnover in monoformyl-heme-containing FeBMb1 proteins loaded with FeII, CoII, or ZnII metal ions at the FeB site (FeII/CoII/ZnII-FeBMb1(MF-heme)). FTIR detection of the ν(NNO) band of N2O at 2231 cm-1 provides a direct quantitative measurement of the product in solution. A maximum number of turnover is observed with FeII-FeBMb1(MF-heme), but the NOR activity is retained when the FeB site is loaded with ZnII. These data support the viability of a one-electron semireduced pathway for the reduction of NO at binuclear centers in reducing conditions.
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Affiliation(s)
- Sinan Sabuncu
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
| | - Julian H Reed
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
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12
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Blomberg MRA, Ädelroth P. Mechanisms for enzymatic reduction of nitric oxide to nitrous oxide - A comparison between nitric oxide reductase and cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1223-1234. [PMID: 30248312 DOI: 10.1016/j.bbabio.2018.09.368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022]
Abstract
Cytochrome c oxidases (CcO) reduce O2 to H2O in the respiratory chain of mitochondria and many aerobic bacteria. In addition, some species of CcO can also reduce NO to N2O and water while others cannot. Here, the mechanism for NO-reduction in CcO is investigated using quantum mechanical calculations. Comparison is made to the corresponding reaction in a "true" cytochrome c-dependent NO reductase (cNOR). The calculations show that in cNOR, where the reduction potentials are low, the toxic NO molecules are rapidly reduced, while the higher reduction potentials in CcO lead to a slower or even impossible reaction, consistent with experimental observations. In both enzymes the reaction is initiated by addition of two NO molecules to the reduced active site, forming a hyponitrite intermediate. In cNOR, N2O can then be formed using only the active-site electrons. In contrast, in CcO, one proton-coupled reduction step most likely has to occur before N2O can be formed, and furthermore, proton transfer is most likely rate-limiting. This can explain why different CcO species with the same heme a3-Cu active site differ with respect to NO reduction efficiency, since they have a varying number and/or properties of proton channels. Finally, the calculations also indicate that a conserved active site valine plays a role in reducing the rate of NO reduction in CcO.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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13
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Kahle M, Ter Beek J, Hosler JP, Ädelroth P. The insertion of the non-heme Fe B cofactor into nitric oxide reductase from P. denitrificans depends on NorQ and NorD accessory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1051-1058. [PMID: 29874552 DOI: 10.1016/j.bbabio.2018.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Bacterial NO reductases (NOR) catalyze the reduction of NO into N2O, either as a step in denitrification or as a detoxification mechanism. cNOR from Paracoccus (P.) denitrificans is expressed from the norCBQDEF operon, but only the NorB and NorC proteins are found in the purified NOR complex. Here, we established a new purification method for the P. denitrificans cNOR via a His-tag using heterologous expression in E. coli. The His-tagged enzyme is both structurally and functionally very similar to non-tagged cNOR. We were also able to express and purify cNOR from the structural genes norCB only, in absence of the accessory genes norQDEF. The produced protein is a stable NorCB complex containing all hemes and it can bind gaseous ligands (CO) to heme b3, but it is catalytically inactive. We show that this deficient cNOR lacks the non-heme iron cofactor FeB. Mutational analysis of the nor gene cluster revealed that it is the norQ and norD genes that are essential to form functional cNOR. NorQ belongs to the family of MoxR P-loop AAA+ ATPases, which are in general considered to facilitate enzyme activation processes often involving metal insertion. Our data indicates that NorQ and NorD work together in order to facilitate non-heme Fe insertion. This is noteworthy since in many cases Fe cofactor binding occurs spontaneously. We further suggest a model for NorQ/D-facilitated metal insertion into cNOR.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Josy Ter Beek
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jonathan P Hosler
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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14
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Wijeratne GB, Hematian S, Siegler MA, Karlin KD. Copper(I)/NO (g) Reductive Coupling Producing a trans-Hyponitrite Bridged Dicopper(II) Complex: Redox Reversal Giving Copper(I)/NO (g) Disproportionation. J Am Chem Soc 2017; 139:13276-13279. [PMID: 28820592 PMCID: PMC5630263 DOI: 10.1021/jacs.7b07808] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A copper complex, [CuI(tmpa)(MeCN)]+, effectively reductively couples NO(g) at RT in methanol (MeOH), giving a structurally characterized hyponitrito-dicopper(II) adduct. Hydrogen-bonding from MeOH is critical for the hyponitrite complex formation and stabilization. This complex exhibits the reverse redox process in aprotic solvents, giving CuI + NO(g), leading to CuI-mediated NO(g)-disproportionation. The relationship of this chemistry to biological iron and/or copper mediated NO(g) reductive coupling to give N2O(g) is discussed.
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Affiliation(s)
| | | | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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15
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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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16
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Blomberg MRA, Siegbahn PEM. Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR). J Comput Chem 2016; 37:1810-8. [DOI: 10.1002/jcc.24396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory; Stockholm University; Stockholm SE-106 91 Sweden
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory; Stockholm University; Stockholm SE-106 91 Sweden
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17
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Matsumura H, Chakraborty S, Reed J, Lu Y, Moënne-Loccoz P. Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (Fe(B)Mbs): Insights into the Mechanism of Denitrifying NO Reductases. Biochemistry 2016; 55:2091-9. [PMID: 27003474 DOI: 10.1021/acs.biochem.5b01109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Denitrifying NO reductases are transmembrane protein complexes that utilize a heme/nonheme diiron center at their active sites to reduce two NO molecules to the innocuous gas N2O. Fe(B)Mb proteins, with their nonheme iron sites engineered into the heme distal pocket of sperm whale myoglobin, are attractive models for studying the molecular details of the NO reduction reaction. Spectroscopic and structural studies of Fe(B)Mb constructs have confirmed that they reproduce the metal coordination spheres observed at the active site of the cytochrome c-dependent NO reductase from Pseudomonas aeruginosa. Exposure of Fe(B)Mb to excess NO, as examined by analytical and spectroscopic techniques, results primarily in the formation of a five-coordinate heme-nitrosyl complex without N2O production. However, substitution of the outer-sphere residue Ile107 with a glutamic acid (i.e., I107E) decreases the formation rate of the five-coordinate heme-nitrosyl complex and allows for the substoichiometric production of N2O. Here, we aim to better characterize the formation of the five-coordinate heme-nitrosyl complex and to explain why the level of N2O production increases with the I107E substitution. We follow the formation of the five-coordinate heme-nitrosyl inhibitory complex through the sequential exposure of Fe(B)Mb to different NO isotopomers using rapid-freeze-quench resonance Raman spectroscopy. The data show that the complex is formed by the displacement of the proximal histidine by a new NO molecule after the weakening of the Fe(II)-His bond in the intermediate six-coordinate low-spin (6cLS) heme-nitrosyl complex. These results lead us to explore diatomic migration within the scaffold of myoglobin and whether substitutions at residue 107 can be sufficient to control access to the proximal heme cavities. Results on a new Fe(B)Mb construct with an I107F substitution (Fe(B)Mb3) show an increased rate for the formation of the five-coordinate low-spin heme-nitrosyl complex without N2O production. Taken together, our results suggest that production of N2O from the [6cLS heme {FeNO}(7)/{Fe(B)NO}(7)] trans iron-nitrosyl dimer intermediate requires a proton transfer event facilitated by an outer-sphere residue such as E107 in Fe(B)Mb2 and E280 in P. aeruginosa cNOR.
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Affiliation(s)
- Hirotoshi Matsumura
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Saumen Chakraborty
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Julian Reed
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Pierre Moënne-Loccoz
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
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18
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Chakraborty S, Reed J, Sage JT, Branagan NC, Petrik ID, Miner KD, Hu MY, Zhao J, Alp EE, Lu Y. Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies. Inorg Chem 2015; 54:9317-29. [PMID: 26274098 PMCID: PMC4677664 DOI: 10.1021/acs.inorgchem.5b01105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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This Forum Article focuses on recent
advances in structural and spectroscopic studies of biosynthetic models
of nitric oxide reductases (NORs). NORs are complex metalloenzymes
found in the denitrification pathway of Earth’s nitrogen cycle
where they catalyze the proton-dependent two-electron reduction of
nitric oxide (NO) to nitrous oxide (N2O). While much progress
has been made in biochemical and biophysical studies of native NORs
and their variants, a clear mechanistic understanding of this important
metalloenzyme related to its function is still elusive. We report
herein UV–vis and nuclear resonance vibrational spectroscopy
(NRVS) studies of mononitrosylated intermediates of the NOR reaction
of a biosynthetic model. The ability to selectively substitute metals
at either heme or nonheme metal sites allows the introduction of independent 57Fe probe atoms at either site, as well as allowing the preparation
of analogues of stable reaction intermediates by replacing either
metal with a redox inactive metal. Together with previous structural
and spectroscopic results, we summarize insights gained from studying
these biosynthetic models toward understanding structural features
responsible for the NOR activity and its mechanism. The outlook on
NOR modeling is also discussed, with an emphasis on the design of
models capable of catalytic turnovers designed based on close mimics
of the secondary coordination sphere of native NORs. New insights into nitric oxide reductases (NORs) are obtained. Using
nuclear resonance vibrational spectroscopy, we probe both iron atoms
in mononitrosylated intermediates of the NOR reaction in a biosynthetic
protein model that reveal new insights into the structural and electronic
features responsible for the NOR activity and its likely mechanism.
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Affiliation(s)
| | | | - J Timothy Sage
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Nicole C Branagan
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | | | | | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
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19
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Al-Attar S, de Vries S. An electrogenic nitric oxide reductase. FEBS Lett 2015; 589:2050-7. [PMID: 26149211 DOI: 10.1016/j.febslet.2015.06.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Nitric oxide reductases (Nors) are members of the heme-copper oxidase superfamily that reduce nitric oxide (NO) to nitrous oxide (N₂O). In contrast to the proton-pumping cytochrome oxidases, Nors studied so far have neither been implicated in proton pumping nor have they been experimentally established as electrogenic. The copper-A-dependent Nor from Bacillus azotoformans uses cytochrome c₅₅₁ as electron donor but lacks menaquinol activity, in contrast to our earlier report (Suharti et al., 2001). Employing reduced phenazine ethosulfate (PESH) as electron donor, the main NO reduction pathway catalyzed by Cu(A)Nor reconstituted in liposomes involves transmembrane cycling of the PES radical. We show that Cu(A)Nor reconstituted in liposomes generates a proton electrochemical gradient across the membrane similar in magnitude to cytochrome aa₃, highlighting that bacilli using Cu(A)Nor can exploit NO reduction for increased cellular ATP production compared to organisms using cNor.
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Affiliation(s)
- Sinan Al-Attar
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands
| | - Simon de Vries
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands.
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20
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Duarte AG, Cordas CM, Moura JJ, Moura I. Steady-state kinetics with nitric oxide reductase (NOR): New considerations on substrate inhibition profile and catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:375-84. [DOI: 10.1016/j.bbabio.2014.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 12/28/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
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21
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Matsumura H, Hayashi T, Chakraborty S, Lu Y, Moënne-Loccoz P. The production of nitrous oxide by the heme/nonheme diiron center of engineered myoglobins (Fe(B)Mbs) proceeds through a trans-iron-nitrosyl dimer. J Am Chem Soc 2014; 136:2420-31. [PMID: 24432820 PMCID: PMC4004238 DOI: 10.1021/ja410542z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Denitrifying NO reductases are transmembrane
protein complexes
that are evolutionarily related to heme/copper terminal oxidases.
They utilize a heme/nonheme diiron center to reduce two NO molecules
to N2O. Engineering a nonheme FeB site within
the heme distal pocket of sperm whale myoglobin has offered well-defined
diiron clusters for the investigation of the mechanism of NO reduction
in these unique active sites. In this study, we use FTIR spectroscopy
to monitor the production of N2O in solution and to show
that the presence of a distal FeBII is not sufficient
to produce the expected product. However, the addition of a glutamate
side chain peripheral to the diiron site allows for 50% of a productive
single-turnover reaction. Unproductive reactions are characterized
by resonance Raman spectroscopy as dinitrosyl complexes, where one
NO molecule is bound to the heme iron to form a five-coordinate low-spin
{FeNO}7 species with ν(FeNO)heme and ν(NO)heme at 522 and 1660 cm–1, and a second NO
molecule is bound to the nonheme FeB site with a ν(NO)FeB at 1755 cm–1. Stopped-flow UV–vis
absorption coupled with rapid-freeze-quench resonance Raman spectroscopy
provide a detailed map of the reaction coordinates leading to the
unproductive iron-nitrosyl dimer. Unexpectedly, NO binding to FeB is kinetically favored and occurs prior to the binding of
a second NO to the heme iron, leading to a (six-coordinate low-spin
heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl complex
with characteristic ν(FeNO)heme at 570 ± 2 cm–1 and ν(NO)FeB at 1755 cm–1. Without the addition of a peripheral glutamate, the dinitrosyl
complex is converted to a dead-end product after the dissociation
of the proximal histidine of the heme iron, but the added peripheral
glutamate side chain in FeBMb2 lowers the rate of dissociation
of the promixal histidine which in turn allows the (six-coordinate
low-spin heme-nitrosyl/FeB-nitrosyl) transient dinitrosyl
complex to decay with production of N2O at a rate of 0.7
s–1 at 4 °C. Taken together, our results support
the proposed trans mechanism of NO reduction in NORs.
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Affiliation(s)
- Hirotoshi Matsumura
- Divison of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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22
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Pirota V, Gennarini F, Dondi D, Monzani E, Casella L, Dell'Acqua S. Dinuclear heme and non-heme metal complexes as bioinspired catalysts for oxidation reactions. NEW J CHEM 2014. [DOI: 10.1039/c3nj01279d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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23
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Shoji M, Hanaoka K, Kondo D, Sato A, Umeda H, Katsumasa Kamiya, Shiraishi K. A QM/MM study of nitric oxide reductase-catalysed N2O formation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.830200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Synthetic Models of Copper–Nitrosyl Species Proposed as Intermediates in Biological Denitrification. STRUCTURE AND BONDING 2013. [DOI: 10.1007/430_2013_93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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25
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Unexpected weak magnetic exchange coupling between haem and non-haem iron in the catalytic site of nitric oxide reductase (NorBC) from Paracoccus denitrificans1. Biochem J 2013; 451:389-94. [DOI: 10.1042/bj20121406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacterial NOR (nitric oxide reductase) is a major source of the powerful greenhouse gas N2O. NorBC from Paracoccus denitrificans is a heterodimeric multi-haem transmembrane complex. The active site, in NorB, comprises high-spin haem b3 in close proximity with non-haem iron, FeB. In oxidized NorBC, the active site is EPR-silent owing to exchange coupling between FeIII haem b3 and FeBIII (both S=5/2). On the basis of resonance Raman studies [Moënne-Loccoz, Richter, Huang, Wasser, Ghiladi, Karlin and de Vries (2000) J. Am. Chem. Soc. 122, 9344–9345], it has been assumed that the coupling is mediated by an oxo-bridge and subsequent studies have been interpreted on the basis of this model. In the present study we report a VFVT (variable-field variable-temperature) MCD (magnetic circular dichroism) study that determines an isotropic value of J=−1.7 cm−1 for the coupling. This is two orders of magnitude smaller than that encountered for oxo-bridged diferric systems, thus ruling out this configuration. Instead, it is proposed that weak coupling is mediated by a conserved glutamate residue.
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26
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Berto TC, Speelman AL, Zheng S, Lehnert N. Mono- and dinuclear non-heme iron–nitrosyl complexes: Models for key intermediates in bacterial nitric oxide reductases. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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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: 3.3] [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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28
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Blomberg MRA, Siegbahn PEM. Mechanism for N2O Generation in Bacterial Nitric Oxide Reductase: A Quantum Chemical Study. Biochemistry 2012; 51:5173-86. [DOI: 10.1021/bi300496e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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29
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Shiro Y. Structure and function of bacterial nitric oxide reductases: nitric oxide reductase, anaerobic enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1907-13. [PMID: 22425814 DOI: 10.1016/j.bbabio.2012.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/01/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
The crystal structures of bacterial nitric oxide reductases (NOR) from Pseudomonas aeruginosa and Geobacillus stearothermophilus were reported. The structural characteristics of these enzymes, especially at the catalytic site and on the pathway that catalytic protons are delivered, are compared, and the corresponding regions of aerobic and micro-aerobic cytochrome oxidases, O(2) reducing enzymes, which are evolutionarily related to NOR are discussed. On the basis of these structural comparisons, a mechanism for the reduction of NO to produce N(2)O by NOR, and the possible molecular evolution of the proton pumping ability of the respiratory enzymes is discussed. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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30
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Arikawa Y, Onishi M. Reductive N–N coupling of NO molecules on transition metal complexes leading to N2O. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.10.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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31
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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: 3.5] [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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32
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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: 2.3] [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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Arikawa Y, Matsumoto N, Asayama T, Umakoshi K, Onishi M. Conversion of oxido-bridged dinuclear ruthenium complex to dicationic dinitrosyl ruthenium complex using proton and nitric oxide: Completion of NO reduction cycle. Dalton Trans 2011; 40:2148-50. [DOI: 10.1039/c0dt01002b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, Murata T, Iwata S, Shiro Y. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 2010; 330:1666-70. [PMID: 21109633 DOI: 10.1126/science.1195591] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N(2)O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resolution. The structure reveals details of the catalytic binuclear center. The non-heme iron (Fe(B)) is coordinated by three His and one Glu ligands, but a His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the NOR reaction are probably provided from the extracellular side.
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Affiliation(s)
- Tomoya Hino
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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35
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Xu N, Yi J, Richter-Addo GB. Linkage isomerization in heme-NOx compounds: understanding NO, nitrite, and hyponitrite interactions with iron porphyrins. Inorg Chem 2010; 49:6253-66. [PMID: 20666385 DOI: 10.1021/ic902423v] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nitric oxide (NO) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. Much of their physiological relevance stems from their interactions with the iron centers in heme proteins. The chemical reactivities displayed by the heme-NOx species (NOx = NO, nitrite, hyponitrite) are a function of the binding modes of the NOx ligands. Hence, an understanding of the types of binding modes extant in heme-NOx compounds is important if we are to unravel the inherent chemical properties of these NOx metabolites. In this Forum Article, the experimentally characterized linkage isomers of heme-NOx models and proteins are presented and reviewed. Nitrosyl linkage isomers of synthetic iron and ruthenium porphyrins have been generated by photolysis at low temperatures and characterized by spectroscopy and density functional theory calculations. Nitrite linkage isomers in synthetic metalloporphyrin derivatives have been generated from photolysis experiments and in low-temperature matrices. In the case of nitrite adducts of heme proteins, both N and O binding have been determined crystallographically, and the role of the distal H-bonding residue in myoglobin in directing the O-binding mode of nitrite has been explored using mutagenesis. To date, only one synthetic metalloporphyrin complex containing a hyponitrite ligand (displaying an O-binding mode) has been characterized by crystallography. This is contrasted with other hyponitrite binding modes experimentally determined for coordination compounds and computationally for NO reductase enzymes. Although linkage isomerism in heme-NOx derivatives is still in its infancy, opportunities now exist for a detailed exploration of the existence and stabilities of the metastable states in both heme models and heme proteins.
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Affiliation(s)
- Nan Xu
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA
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Soldatova AV, Ibrahim M, Olson JS, Czernuszewicz RS, Spiro TG. New light on NO bonding in Fe(III) heme proteins from resonance Raman spectroscopy and DFT modeling. J Am Chem Soc 2010; 132:4614-25. [PMID: 20218710 DOI: 10.1021/ja906233m] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Visible and ultraviolet resonance Raman (RR) spectra are reported for Fe(III)(NO) adducts of myoglobin variants with altered polarity in the distal heme pockets. The stretching frequencies of the Fe(III)-NO and N-O bonds, nu(FeN) and nu(NO), are negatively correlated, consistent with backbonding. However, the correlation shifts to lower nu(NO) for variants lacking a distal histidine. DFT modeling reproduces the shifted correlations and shows the shift to be associated with the loss of a lone-pair donor interaction from the distal histidine that selectively strengthens the N-O bond. However, when the model contains strongly electron-withdrawing substituents at the heme beta-positions, nu(FeN) and nu(NO) become positively correlated. This effect results from Fe(III)-N-O bending, which is induced by lone-pair donation to the N(NO) atom. Other mechanisms for bending are discussed, which likewise lead to a positive nu(FeN)/nu(NO) correlation, including thiolate ligation in heme proteins and electron-donating meso-substituents in heme models. The nu(FeN)/nu(NO) data for the Fe(III) complexes are reporters of heme pocket polarity and the accessibility of lone pair, Lewis base donors. Implications for biologically important processes, including NO binding, reductive nitrosylation, and NO reduction, are discussed.
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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Goodrich LE, Paulat F, Praneeth VKK, Lehnert N. Electronic Structure of Heme-Nitrosyls and Its Significance for Nitric Oxide Reactivity, Sensing, Transport, and Toxicity in Biological Systems. Inorg Chem 2010; 49:6293-316. [DOI: 10.1021/ic902304a] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Lauren E. Goodrich
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Florian Paulat
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - V. K. K. Praneeth
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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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: 28] [Impact Index Per Article: 2.0] [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: 42] [Impact Index Per Article: 3.0] [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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Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin. Proc Natl Acad Sci U S A 2010; 107:8581-6. [PMID: 20421510 DOI: 10.1073/pnas.1000526107] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative Fe(B) site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by approximately 110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a approximately 100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the Fe(B) site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.
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Rational design of a structural and functional nitric oxide reductase. Nature 2009; 462:1079-82. [PMID: 19940850 PMCID: PMC4297211 DOI: 10.1038/nature08620] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/29/2009] [Indexed: 01/13/2023]
Abstract
Protein design provides an ultimate test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. While progress has been made in designing proteins that mimic native proteins structurally1–3, it is more difficult to design functional proteins4–8. In comparison to recent successes in designing non-metalloproteins4,6,7,9,10, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes5,8,11–20, since protein metal binding sites are much more varied than non-metal containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal binding site properties in silico, as many of the parameters for metal binding sites, such as force fields are ill-defined. Therefore, the successful design of a structural and functional metalloprotein will greatly advance the field of protein design and our understanding of enzymes. Here, we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a heme/non-heme FeB center that is remarkably similar to that in the crystal structure. This designed protein also exhibits NOR activity. This is the first designed protein that models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.
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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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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: 1.2] [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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Ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:919-24. [DOI: 10.1016/j.bbabio.2008.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/03/2008] [Accepted: 03/19/2008] [Indexed: 11/18/2022]
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Pinakoulaki E, Varotsis C. Resonance Raman Spectroscopy of Nitric Oxide Reductase and cbb3 Heme-Copper Oxidase. J Phys Chem B 2008; 112:1851-7. [DOI: 10.1021/jp077295o] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus, and Department of Chemistry, University of Crete, 71003 Voutes, Heraklion, Crete, Greece
| | - Constantinos Varotsis
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus, and Department of Chemistry, University of Crete, 71003 Voutes, Heraklion, Crete, Greece
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Hayashi T, Lin IJ, Chen Y, Fee JA, Moënne-Loccoz P. Fourier transform infrared characterization of a CuB-nitrosyl complex in cytochrome ba3 from Thermus thermophilus: relevance to NO reductase activity in heme-copper terminal oxidases. J Am Chem Soc 2007; 129:14952-8. [PMID: 17997553 DOI: 10.1021/ja074600a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two heme-copper terminal oxidases of Thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (NO) to nitrous oxide (N2O) [Giuffre, A.; Stubauer, G.; Sarti, P.; Brunori, M.; Zumft, W. G.; Buse, G.; Soulimane, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14718-14723]. While it is well-established that NO binds to the reduced heme a3 to form a low-spin heme {FeNO}7 species, the role CuB plays in the binding of the second NO remains unclear. Here we present low-temperature FTIR photolysis experiments carried out on the NO complex formed by addition of NO to fully reduced cytochrome ba3. Low-temperature UV-vis, EPR, and RR spectroscopies confirm the binding of NO to the heme a3 and the efficiency of the photolysis at 30 K. The nu(NO) modes from the light-induced FTIR difference spectra are isolated from other perturbed vibrations using 15NO and 15N18O. The nu(N-O)a3 is observed at 1622 cm-1, and upon photolysis, it is replaced by a new nu(N-O) at 1589 cm-1 assigned to a CuB-nitrosyl complex. This N-O stretching frequency is more than 100 cm-1 lower than those reported for Cu-NO models with three N-ligands and for CuB+-NO in bovine aa3. Because the UV-vis and RR data do not support a bridging configuration between CuB and heme a3 for the photolyzed NO, we assign the exceptionally low nu(NO) to an O-bound (eta1-O) or a side-on (eta2-NO) CuB-nitrosyl complex. From this study, we propose that, after binding of a first NO molecule to the heme a3 of fully reduced Tt ba3, the formation of an N-bound {CuNO}11 is prevented, and the addition of a second NO produces an O-bond CuB-hyponitrite species bridging CuB and Fea3. In contrast, bovine cytochrome c oxidase is believed to form an N-bound CuB-NO species; the [{FeNO}7{CuNO}11] complex is suggested here to be an inhibitory complex.
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Affiliation(s)
- Takahiro Hayashi
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Arikawa Y, Asayama T, Moriguchi Y, Agari S, Onishi M. Reversible N-N coupling of NO ligands on dinuclear ruthenium complexes and subsequent N2O evolution: relevance to nitric oxide reductase. J Am Chem Soc 2007; 129:14160-1. [PMID: 17973393 DOI: 10.1021/ja0763504] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasuhiro Arikawa
- Department of Applied Chemistry, Faculty of Engineering, Nagasaki University, Bunkyo-machi 1-14, Nagasaki 852-8521, Japan
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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: 1.5] [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: 5.3] [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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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: 3.4] [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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