1
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Wang Z, Vishwanathan N, Kowaliczko S, Ishii S. Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive. Microbiol Spectr 2023; 11:e0470922. [PMID: 36926990 PMCID: PMC10100939 DOI: 10.1128/spectrum.04709-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/18/2023] [Indexed: 03/17/2023] Open
Abstract
One of the major challenges for the bioremediation application of microbial nitrous oxide (N2O) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing N2O under aerobic conditions, the N2O reduction kinetics of phylogenetically diverse N2O reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II N2O-reducing bacteria in the presence or absence of oxygen (O2) by using a whole-cell assay with N2O and O2 microsensors. Among the seven strains tested, N2O reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced N2O in the presence of O2 but slower than in the absence of O2 (i.e., oxygen sensitive). N2O reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O2 was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant N2O reducers had higher oxygen consumption rates. The results suggest that the mechanism of O2 tolerance is not directly related to NosZ structure but is rather related to the scavenging of O2 in the cells and/or accessory proteins encoded by the nos cluster. IMPORTANCE Some bacteria can reduce N2O in the presence of O2, whereas others cannot. It is unclear whether this trait of aerobic N2O reduction is related to the phylogeny and structure of N2O reductase. The understanding of aerobic N2O reduction is critical for guiding emission control, due to the common concurrence of N2O and O2 in natural and engineered systems. This study provided the N2O reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant N2O reducers. Oxygen-tolerant N2O reducers rapidly consumed O2, which could help maintain the low O2 concentration in the cells and keep their N2O reductase active. These findings are important and useful when selecting N2O reducers for bioremediation applications.
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Affiliation(s)
- Zhiyue Wang
- Department of Civil and Environmental Engineering, University of Hawai'i, Honolulu, Hawai'i, USA
- Water Resources Research Center, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Nisha Vishwanathan
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Sophie Kowaliczko
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
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2
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Zhang L, Bill E, Kroneck PMH, Einsle O. A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Chem Sci 2021; 12:3239-3244. [PMID: 34164092 PMCID: PMC8179356 DOI: 10.1039/d0sc05204c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the only known enzyme reducing environmentally critical nitrous oxide (N2O) to dinitrogen (N2) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster CuZ remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N2OR in Escherichia coli. While no copper ion was found in the CuZ binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, SZ2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of SZ2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in CuZ and is thus of high mechanistic interest. Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.![]()
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
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3
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Zhang L, Bill E, Kroneck PMH, Einsle O. Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase. J Am Chem Soc 2020; 143:830-838. [DOI: 10.1021/jacs.0c10057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
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4
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Bennett SP, Torres MJ, Soriano-Laguna MJ, Richardson DJ, Gates AJ, Le Brun NE. nosX is essential for whole-cell N 2O reduction in Paracoccus denitrificans but not for assembly of copper centres of nitrous oxide reductase. MICROBIOLOGY-SGM 2020; 166:909-917. [PMID: 32886603 PMCID: PMC7660919 DOI: 10.1099/mic.0.000955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (N2OR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. N2OR contains two important copper cofactors (CuA and CuZ centres) that are essential for activity, and in copper-limited environments, N2OR fails to function, contributing to rising levels of atmospheric N2O and a major environmental challenge. Here we report studies of nosX, one of eight genes in the nos cluster of the soil dwelling α-proteobaterium Paraccocus denitrificans. A P. denitrificans ΔnosX deletion mutant failed to reduce N2O under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in N2OR activity. N2OR isolated from nosX-deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in in vitro assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the CuA and CuZ centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the N2OR-encoding nosZ gene. NosX is a homologue of the FAD-binding protein ApbE from Pseudomonas stutzeri, which functions in the flavinylation of another N2OR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of N2OR and cellular N2O reduction.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Maria J Torres
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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5
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Carreira C, Nunes RF, Mestre O, Moura I, Pauleta SR. The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase. J Biol Inorg Chem 2020; 25:927-940. [PMID: 32851479 DOI: 10.1007/s00775-020-01812-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 11/27/2022]
Abstract
Increasing atmospheric concentration of N2O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N2O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N2O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N2O. In addition, the biochemical properties of N2O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N2O reductase accessory genes. N2O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N2O reductase in an active state.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Rute F Nunes
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Olga Mestre
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal.
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6
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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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7
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Carreira C, Dos Santos MMC, Pauleta SR, Moura I. Proton-coupled electron transfer mechanisms of the copper centres of nitrous oxide reductase from Marinobacter hydrocarbonoclasticus - An electrochemical study. Bioelectrochemistry 2020; 133:107483. [PMID: 32120320 DOI: 10.1016/j.bioelechem.2020.107483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
Reduction of N2O to N2 is catalysed by nitrous oxide reductase in the last step of the denitrification pathway. This multicopper enzyme has an electron transferring centre, CuA, and a tetranuclear copper-sulfide catalytic centre, "CuZ", which exists as CuZ*(4Cu1S) or CuZ(4Cu2S). The redox behaviour of these metal centres in Marinobacter hydrocarbonoclasticus nitrous oxide reductase was investigated by potentiometry and for the first time by direct electrochemistry. The reduction potential of CuA and CuZ(4Cu2S) was estimated by potentiometry to be +275 ± 5 mV and +65 ± 5 mV vs SHE, respectively, at pH 7.6. A proton-coupled electron transfer mechanism governs CuZ(4Cu2S) reduction potential, due to the protonation/deprotonation of Lys397 with a pKox of 6.0 ± 0.1 and a pKred of 9.2 ± 0.1. The reduction potential of CuA, in enzyme samples with CuZ*(4Cu1S), is controlled by protonation of the coordinating histidine residues in a two-proton coupled electron transfer process. In the cyclic voltammograms, two redox pairs were identified corresponding to CuA and CuZ(4Cu2S), with no additional signals being detected that could be attributed to CuZ*(4Cu1S). However, an enhanced cathodic signal for the activated enzyme was observed under turnover conditions, which is explained by the binding of nitrous oxide to CuZ0(4Cu1S), an intermediate species in the catalytic cycle.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal; Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Margarida M C Dos Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal. http://docentes.fct.unl.pt/srp/
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
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8
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9
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Bennett SP, Soriano-Laguna MJ, Bradley JM, Svistunenko DA, Richardson DJ, Gates AJ, Le Brun NE. NosL is a dedicated copper chaperone for assembly of the Cu Z center of nitrous oxide reductase. Chem Sci 2019; 10:4985-4993. [PMID: 31183047 PMCID: PMC6530538 DOI: 10.1039/c9sc01053j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N2O) to dinitrogen. In addition to a binuclear CuA site that functions in electron transfer, the active site of N2OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed CuZ. In copper-limited environments, N2OR fails to function, resulting in truncation of denitrification and rising levels of N2O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N2O under copper-limited conditions. N2OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the CuA center were unaffected, while those corresponding to the CuZ center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the CuZ center of N2OR, and thus represents the first characterised assembly factor for the CuZ active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
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10
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Kroneck PMH. Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase. J Biol Inorg Chem 2017; 23:27-39. [PMID: 29218634 DOI: 10.1007/s00775-017-1510-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 01/19/2023]
Abstract
The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1.5+(CyS)2Cu1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.
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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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11
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The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification. J Inorg Biochem 2017; 177:423-434. [PMID: 28927704 DOI: 10.1016/j.jinorgbio.2017.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/02/2017] [Accepted: 09/08/2017] [Indexed: 01/27/2023]
Abstract
The reduction of the potent greenhouse gas nitrous oxide requires a catalyst to overcome the large activation energy barrier of this reaction. Its biological decomposition to the inert dinitrogen can be accomplished by denitrifiers through nitrous oxide reductase, the enzyme that catalyzes the last step of the denitrification, a pathway of the biogeochemical nitrogen cycle. Nitrous oxide reductase is a multicopper enzyme containing a mixed valence CuA center that can accept electrons from small electron shuttle proteins, triggering electron flow to the catalytic sulfide-bridged tetranuclear copper "CuZ center". This enzyme has been isolated with its catalytic center in two forms, CuZ*(4Cu1S) and CuZ(4Cu2S), proven to be spectroscopic and structurally different. In the last decades, it has been a challenge to characterize the properties of this complex enzyme, due to the different oxidation states observed for each of its centers and the heterogeneity of its preparations. The substrate binding site in those two "CuZ center" forms and which is the active form of the enzyme is still a matter of debate. However, in the last years the application of different spectroscopies, together with theoretical calculations have been useful in answering these questions and in identifying intermediate species of the catalytic cycle. An overview of the spectroscopic, kinetics and structural properties of the two forms of the catalytic "CuZ center" is given here, together with the current knowledge on nitrous oxide reduction mechanism by nitrous oxide reductase and its intermediate species.
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12
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Yamaguchi T, Nihei Y, Sutherland DEK, Stillman MJ, Kohzuma T. Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin. Protein Sci 2017; 26:1921-1931. [PMID: 28691165 DOI: 10.1002/pro.3226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/11/2022]
Abstract
Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.
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Affiliation(s)
- Takahide Yamaguchi
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Yuko Nihei
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Duncan E K Sutherland
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Martin J Stillman
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Takamitsu Kohzuma
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
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13
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Johnston EM, Carreira C, Dell'Acqua S, Dey SG, Pauleta SR, Moura I, Solomon EI. Spectroscopic Definition of the Cu Z° Intermediate in Turnover of Nitrous Oxide Reductase and Molecular Insight into the Catalytic Mechanism. J Am Chem Soc 2017; 139:4462-4476. [PMID: 28228011 DOI: 10.1021/jacs.6b13225] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Spectroscopic methods and density functional theory (DFT) calculations are used to determine the geometric and electronic structure of CuZ°, an intermediate form of the Cu4S active site of nitrous oxide reductase (N2OR) that is observed in single turnover of fully reduced N2OR with N2O. Electron paramagnetic resonance (EPR), absorption, and magnetic circular dichroism (MCD) spectroscopies show that CuZ° is a 1-hole (i.e., 3CuICuII) state with spin density delocalized evenly over CuI and CuIV. Resonance Raman spectroscopy shows two Cu-S vibrations at 425 and 413 cm-1, the latter with a -3 cm-1 O18 solvent isotope shift. DFT calculations correlated to these spectral features show that CuZ° has a terminal hydroxide ligand coordinated to CuIV, stabilized by a hydrogen bond to a nearby lysine residue. CuZ° can be reduced via electron transfer from CuA using a physiologically relevant reductant. We obtain a lower limit on the rate of this intramolecular electron transfer (IET) that is >104 faster than the unobserved IET in the resting state, showing that CuZ° is the catalytically relevant oxidized form of N2OR. Terminal hydroxide coordination to CuIV in the CuZ° intermediate yields insight into the nature of N2O binding and reduction, specifying a molecular mechanism in which N2O coordinates in a μ-1,3 fashion to the fully reduced state, with hydrogen bonding from Lys397, and two electrons are transferred from the fully reduced μ4S2- bridged tetranuclear copper cluster to N2O via a single Cu atom to accomplish N-O bond cleavage.
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Affiliation(s)
- Esther M Johnston
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Cíntia Carreira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Campus da Caparica, 2829-516 Caparica, Portugal
| | - Simone Dell'Acqua
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Campus da Caparica, 2829-516 Caparica, Portugal
| | - Somdatta Ghosh Dey
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Sofia R Pauleta
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Campus da Caparica, 2829-516 Caparica, Portugal
| | - Isabel Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Campus da Caparica, 2829-516 Caparica, Portugal
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Tishchenko KI, Beloglazkina EK, Mazhuga AG, Zyk NV. Copper-containing enzymes: Site types and low-molecular-weight model compounds. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079978016010027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Qu Z, Bakken LR, Molstad L, Frostegård Å, Bergaust LL. Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions. Environ Microbiol 2016; 18:2951-63. [PMID: 26568281 DOI: 10.1111/1462-2920.13128] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 11/27/2022]
Abstract
Oxygen is known to repress denitrification at the transcriptional and metabolic levels. It has been a common notion that nitrous oxide reductase (N2 OR) is the most sensitive enzyme among the four N-oxide reductases involved in denitrification, potentially leading to increased N2 O production under suboxic or fluctuating oxygen conditions. We present detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of e(-) -flow to O2 and N2 O under various O2 regimes. Transcription of nosZ took place concomitantly with that of narG under suboxic conditions, whereas transcription of nirS and norB was inhibited until O2 levels approached 0 μM in the liquid. Catalytically functional N2 OR was synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2 O reduction rates were 10 times higher when anaerobic pre-cultures were subjected to the same conditions. Upon oxygen exposure, there was an incomplete and transient inactivation of N2 OR that could be ascribed to its lower ability to compete for electrons compared with terminal oxidases. The demonstrated reduction of N2 O at high O2 partial pressure and low N2 O concentrations by a bacterium not known as a typical aerobic denitrifier may provide one clue to the understanding of why some soils appear to act as sinks rather than sources for atmospheric N2 O.
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Affiliation(s)
- Zhi Qu
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars R Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Lars Molstad
- Department of Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway
| | - Linda L Bergaust
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, N-1432, Ås, Norway.
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Johnston EM, Dell'Acqua S, Pauleta SR, Moura I, Solomon EI. Protonation state of the Cu 4S 2 Cu Z site in nitrous oxide reductase: redox dependence and insight into reactivity. Chem Sci 2015; 6:5670-5679. [PMID: 26417423 PMCID: PMC4583207 DOI: 10.1039/c5sc02102b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/03/2015] [Indexed: 11/21/2022] Open
Abstract
Spectroscopic and computational methods have been used to determine the protonation state of the edge sulfur ligand in the Cu4S2 CuZ form of the active site of nitrous oxide reductase (N2OR) in its 3CuICuII (1-hole) and 2CuI2CuII (2-hole) redox states. The EPR, absorption, and MCD spectra of 1-hole CuZ indicate that the unpaired spin in this site is evenly delocalized over CuI, CuII, and CuIV. 1-hole CuZ is shown to have a μ2-thiolate edge ligand from the observation of S-H bending modes in the resonance Raman spectrum at 450 and 492 cm-1 that have significant deuterium isotope shifts (-137 cm-1) and are not perturbed up to pH 10. 2-hole CuZ is characterized with absorption and resonance Raman spectroscopies as having two Cu-S stretching vibrations that profile differently. DFT models of the 1-hole and 2-hole CuZ sites are correlated to these spectroscopic features to determine that 2-hole CuZ has a μ2-sulfide edge ligand at neutral pH. The slow two electron (+1 proton) reduction of N2O by 1-hole CuZ is discussed and the possibility of a reaction between 2-hole CuZ and O2 is considered.
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Affiliation(s)
- Esther M. Johnston
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Simone Dell'Acqua
- Dipartimento di Chimica , Università di Pavia , Via Taramelli 12 , 27100 Pavia , Italy
| | - Sofia R. Pauleta
- UCIBIO , REQUIMTE , Departamento de Química , Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Isabel Moura
- UCIBIO , REQUIMTE , Departamento de Química , Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Edward I. Solomon
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
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Ishii S, Song Y, Rathnayake L, Tumendelger A, Satoh H, Toyoda S, Yoshida N, Okabe S. Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules. Environ Microbiol 2014; 16:3168-80. [PMID: 24650173 DOI: 10.1111/1462-2920.12458] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 03/16/2014] [Indexed: 11/28/2022]
Abstract
The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.
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Affiliation(s)
- Satoshi Ishii
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1147] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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Johnston EM, Dell'Acqua S, Ramos S, Pauleta SR, Moura I, Solomon EI. Determination of the active form of the tetranuclear copper sulfur cluster in nitrous oxide reductase. J Am Chem Soc 2014; 136:614-7. [PMID: 24364717 DOI: 10.1021/ja411500p] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N2OR has been found to have two structural forms of its tetranuclear copper active site, the 4CuS Cu(Z)* form and the 4Cu2S Cu(Z) form. EPR, resonance Raman, and MCD spectroscopies have been used to determine the redox states of these sites under different reductant conditions, showing that the Cu(Z)* site accesses the 1-hole and fully reduced redox states, while the Cu(Z) site accesses the 2-hole and 1-hole redox states. Single-turnover reactions of N2OR for Cu(Z) and Cu(Z)* poised in these redox states and steady-state turnover assays with different proportions of Cu(Z) and Cu(Z)* show that only fully reduced Cu(Z)* is catalytically competent in rapid turnover with N2O.
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Affiliation(s)
- Esther M Johnston
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
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20
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No laughing matter: the unmaking of the greenhouse gas dinitrogen monoxide by nitrous oxide reductase. Met Ions Life Sci 2014; 14:177-210. [PMID: 25416395 DOI: 10.1007/978-94-017-9269-1_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The gas nitrous oxide (N₂O) is generated in a variety of abiotic, biotic, and anthropogenic processes and it has recently been under scrutiny for its role as a greenhouse gas. A single enzyme, nitrous oxide reductase, is known to reduce N₂O to uncritical N₂, in a two-electron reduction process that is catalyzed at two unusual metal centers containing copper. Nitrous oxide reductase is a bacterial metalloprotein from the metabolic pathway of denitrification, and it forms a 130 kDa homodimer in which the two metal sites CuA and CuZ from opposing monomers are brought into close contact to form the active site of the enzyme. CuA is a binuclear, valence-delocalized cluster that accepts and transfers a single electron. The CuA site of nitrous oxide reductase is highly similar to that of respiratory heme-copper oxidases, but in the denitrification enzyme the site additionally undergoes a conformational change on a ligand that is suggested to function as a gate for electron transfer from an external donor protein. CuZ, the tetranuclear active center of nitrous oxide reductase, is isolated under mild and anoxic conditions as a unique [4Cu:2S] cluster. It is easily desulfurylated to yield a [4Cu:S] state termed CuZ (*) that is functionally distinct. The CuZ form of the cluster is catalytically active, while CuZ (*) is inactive as isolated in the [3Cu(1+):1Cu(2+)] state. However, only CuZ (*) can be reduced to an all-cuprous state by sodium dithionite, yielding a form that shows higher activities than CuZ. As the possibility of a similar reductive activation in the periplasm is unconfirmed, the mechanism and the actual functional state of the enzyme remain under debate. Using enzyme from anoxic preparations with CuZ in the [4Cu:2S] state, N2O was shown to bind between the CuA and CuZ sites, suggesting direct electron transfer from CuA to the substrate after its activation by CuZ.
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Woolfenden HC, Gates AJ, Bocking C, Blyth MG, Richardson DJ, Moulton V. Modeling the effect of copper availability on bacterial denitrification. Microbiologyopen 2013; 2:756-65. [PMID: 23913488 PMCID: PMC3831637 DOI: 10.1002/mbo3.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 11/10/2022] Open
Abstract
When denitrifying bacteria such as Paracoccus denitrificans respire anaerobically they convert nitrate to dinitrogen gas via a pathway which includes the potent greenhouse gas, nitrous oxide (N2O). The copper-dependent enzyme Nitrous Oxide reductase (Nos) catalyzes the reduction of N2O to dinitrogen. In low-copper conditions, recent experiments in chemostats have demonstrated that Nos efficiency decreases resulting in significant N2O emissions. For the first time, a chemostat-based mathematical model is developed that describes the anaerobic denitrification pathway based on Michaelis–Menten kinetics and published kinetic parameters. The model predicts steady-state enzyme levels from experimental data. For low copper concentrations, the predicted Nos level is significantly reduced, whereas the levels for the non copper-dependent reductases in the pathway remain relatively unaffected. The model provides time courses for the pathway metabolites that accurately reflect previously published experimental data. In the absence of experimental data purely predictive analyses can also be readily performed by calculating the relative Nos level directly from the copper concentration. Here, the model quantitatively estimates the increasing level of emitted N2O as the copper level decreases.
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Affiliation(s)
- Hugh C Woolfenden
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K
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Dell'Acqua S, Pauleta SR, Moura JJG, Moura I. Biochemical characterization of the purple form of Marinobacter hydrocarbonoclasticus nitrous oxide reductase. Philos Trans R Soc Lond B Biol Sci 2012; 367:1204-12. [PMID: 22451106 DOI: 10.1098/rstb.2011.0311] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitrous oxide reductase (N(2)OR) catalyses the final step of the denitrification pathway-the reduction of nitrous oxide to nitrogen. The catalytic centre (CuZ) is a unique tetranuclear copper centre bridged by inorganic sulphur in a tetrahedron arrangement that can have different oxidation states. Previously, Marinobacter hydrocarbonoclasticus N(2)OR was isolated with the CuZ centre as CuZ*, in the [1Cu(2+) : 3Cu(+)] redox state, which is redox inert and requires prolonged incubation under reductive conditions to be activated. In this work, we report, for the first time, the isolation of N(2)OR from M. hydrocarbonoclasticus in the 'purple' form, in which the CuZ centre is in the oxidized [2Cu(2+) : 2Cu(+)] redox state and is redox active. This form of the enzyme was isolated in the presence of oxygen from a microaerobic culture in the presence of nitrate and also from a strictly anaerobic culture. The purple form of the enzyme was biochemically characterized and was shown to be a redox active species, although it is still catalytically non-competent, as its specific activity is lower than that of the activated fully reduced enzyme and comparable with that of the enzyme with the CuZ centre in either the [1Cu(2+) : 3Cu(+)] redox state or in the redox inactive CuZ* state.
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Affiliation(s)
- Simone Dell'Acqua
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Bergaust L, van Spanning RJM, Frostegård Å, Bakken LR. Expression of nitrous oxide reductase in Paracoccus denitrificans is regulated by oxygen and nitric oxide through FnrP and NNR. MICROBIOLOGY-SGM 2011; 158:826-834. [PMID: 22174385 PMCID: PMC3541799 DOI: 10.1099/mic.0.054148-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The reductases performing the four steps of denitrification are controlled by a network of transcriptional regulators and ancillary factors responding to intra- and extracellular signals, amongst which are oxygen and N oxides (NO and NO2–). Although many components of the regulatory network have been identified, there are gaps in our understanding of their role(s) in controlling the expression of the various reductases, in particular the environmentally important N2O reductase (N2OR). We investigated denitrification phenotypes of Paracoccus denitrificans mutants deficient in: (i) regulatory proteins (three FNR-type transcriptional regulators, NarR, NNR and FnrP, and NirI, which is involved in transcription activation of the structural nir cluster); (ii) functional enzymes (NO reductase and N2OR); or (iii) ancillary factors involved in N2O reduction (NirX and NosX). A robotized incubation system allowed us to closely monitor changes in concentrations of oxygen and all gaseous products during the transition from oxic to anoxic respiration. Strains deficient in NO reductase were able to grow during denitrification, despite reaching micromolar concentrations of NO, but were unable to return to oxic respiration. The FnrP mutant showed linear anoxic growth in a medium with nitrate as the sole NOx, but exponential growth was restored by replacing nitrate with nitrite. We interpret this as nitrite limitation, suggesting dual transcriptional control of respiratory nitrate reductase (NAR) by FnrP and NarR. Mutations in either NirX or NosX did not affect the phenotype, but the double mutant lacked the potential to reduce N2O. Finally, we found that FnrP and NNR are alternative and equally effective inducers of N2OR.
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Affiliation(s)
- Linda Bergaust
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Rob J. M. van Spanning
- Department of Molecular Cell Biology, Faculty of Earth and Life Science, VU University, Amsterdam, The Netherlands
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R. Bakken
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
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25
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Electrochemical titrations and reaction time courses monitored in situ by magnetic circular dichroism spectroscopy. Anal Biochem 2011; 419:110-6. [DOI: 10.1016/j.ab.2011.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/24/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
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26
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Dell'Acqua S, Pauleta SR, Moura I, Moura JJG. The tetranuclear copper active site of nitrous oxide reductase: the CuZ center. J Biol Inorg Chem 2011; 16:183-94. [PMID: 21240533 DOI: 10.1007/s00775-011-0753-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 01/03/2011] [Indexed: 01/24/2023]
Abstract
This review focuses on the novel CuZ center of nitrous oxide reductase, an important enzyme owing to the environmental significance of the reaction it catalyzes, reduction of nitrous oxide, and the unusual nature of its catalytic center, named CuZ. The structure of the CuZ center, the unique tetranuclear copper center found in this enzyme, opened a novel area of research in metallobiochemistry. In the last decade, there has been progress in defining the structure of the CuZ center, characterizing the mechanism of nitrous oxide reduction, and identifying intermediates of this reaction. In addition, the determination of the structure of the CuZ center allowed a structural interpretation of the spectroscopic data, which was supported by theoretical calculations. The current knowledge of the structure, function, and spectroscopic characterization of the CuZ center is described here. We would like to stress that although many questions have been answered, the CuZ center remains a scientific challenge, with many hypotheses still being formed.
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Affiliation(s)
- Simone Dell'Acqua
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Bingham SJ, Rasmussen T, Farrar J, Wolverson D, Thomson AJ. Magnetic circular dichroism anisotropy of the CuAcentre of nitrous oxide reductase from coherent Raman detected electron spin resonance spectroscopy. Mol Phys 2010. [DOI: 10.1080/00268970701732985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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A new CuZ active form in the catalytic reduction of N2O by nitrous oxide reductase from Pseudomonas nautica. J Biol Inorg Chem 2010; 15:967-76. [DOI: 10.1007/s00775-010-0658-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 04/04/2010] [Indexed: 10/19/2022]
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Mitigating release of the potent greenhouse gas N(2)O from the nitrogen cycle - could enzymic regulation hold the key? Trends Biotechnol 2009; 27:388-97. [PMID: 19497629 DOI: 10.1016/j.tibtech.2009.03.009] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 11/21/2022]
Abstract
When faced with a shortage of oxygen, many bacterial species use nitrate to support respiration via the process of denitrification. This takes place extensively in nitrogen-rich soils and generates the gaseous products nitric oxide (NO), nitrous oxide (N(2)O) and dinitrogen (N(2)). The denitrifying bacteria protect themselves from the endogenous cytotoxic NO produced by converting it to N(2)O, which can be released into the atmosphere. However, N(2)O is a potent greenhouse gas and hence the activity of the enzyme that breaks down N(2)O has a crucial role in restricting its atmospheric levels. Here, we review the current understanding of the process by which N(2)O is produced and destroyed and discuss the potential for feeding this into new approaches for combating N(2)O release.
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Liu X, Gao C, Zhang A, Jin P, Wang L, Feng L. Thenosgene cluster from gram-positive bacteriumGeobacillus thermodenitrificansNG80-2 and functional characterization of the recombinant NosZ. FEMS Microbiol Lett 2008; 289:46-52. [DOI: 10.1111/j.1574-6968.2008.01362.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Dell’Acqua S, Pauleta SR, Monzani E, Pereira AS, Casella L, Moura JJG, Moura I. Electron Transfer Complex between Nitrous Oxide Reductase and Cytochrome c552 from Pseudomonas nautica: Kinetic, Nuclear Magnetic Resonance, and Docking Studies. Biochemistry 2008; 47:10852-62. [DOI: 10.1021/bi801375q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simone Dell’Acqua
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Sofia R. Pauleta
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Enrico Monzani
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Alice S. Pereira
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Luigi Casella
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Isabel Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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32
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Bar-Nahum I, York JT, Young VG, Tolman WB. Novel reactivity of side-on (disulfido)dicopper complexes supported by bi- and tridentate nitrogen donors: impact of axial coordination. Angew Chem Int Ed Engl 2008; 47:533-6. [PMID: 18058868 DOI: 10.1002/anie.200704690] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Itsik Bar-Nahum
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA
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Bar-Nahum I, York J, Young V, Tolman W. Novel Reactivity of Side-On (Disulfido)dicopper Complexes Supported by Bi- and Tridentate Nitrogen Donors: Impact of Axial Coordination. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Fujita K, Chan JM, Bollinger JA, Alvarez ML, Dooley DM. Anaerobic purification, characterization and preliminary mechanistic study of recombinant nitrous oxide reductase from Achromobacter cycloclastes. J Inorg Biochem 2007; 101:1836-44. [PMID: 17681606 DOI: 10.1016/j.jinorgbio.2007.06.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 06/04/2007] [Accepted: 06/06/2007] [Indexed: 11/20/2022]
Abstract
An overexpression system for nitrous oxide reductase (N(2)OR), an enzyme that catalyzes the conversion of N(2)O to N(2) and H(2)O, has been developed in Achromobacter cycloclastes. Anaerobically purified A. cycloclastes recombinant N(2)OR (AcN(2)OR) has on average 4.5 Cu and 1.2 S per monomer. Upon reduction by methyl viologen, AcN(2)OR displays a high specific activity: 124 U/mg at 25 degrees C. Anaerobically purified AcN(2)OR displays a unique absorption spectrum. UV-visible and EPR spectra, combined with kinetics studies, indicate that the as-purified form of the enzyme is predominately a mixture of the fully-reduced Cu(Z)=[4Cu(I)] state and the Cu(Z)=[3Cu(I).Cu(II)] state, with the latter readily reducible by reduced forms of viologens. CD spectra of the as-purified AcN(2)OR over a range of pH values reveal perturbations of the protein conformation induced by pH variations, although the principal secondary structure elements are largely unaltered. Further, the activity of AcN(2)OR in D(2)O is significantly decreased compared with that in H(2)O, indicative of a significant solvent isotope effect on N(2)O reduction. These data are in good agreement with conclusions reached in recent studies on the effect of pH on catalysis by N(2)OR [K. Fujita, D.M. Dooley, Inorg. Chem. 46 (2007) 613-615].
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Affiliation(s)
- Koyu Fujita
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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36
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York JT, Bar-Nahum I, Tolman WB. Structural Diversity in Copper−Sulfur Chemistry: Synthesis of Novel Cu/S Clusters through Metathesis Reactions. Inorg Chem 2007; 46:8105-7. [PMID: 17824695 DOI: 10.1021/ic700760p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the ultimate goal of understanding the Cu(4)S cluster in nitrous oxide reductase, studies of the fundamental chemistry of nitrogen-donor ligand-supported copper-sulfur species have been pursued. Reactions of Cu(II)X(2) (X = Cl(-) or CF(3)SO(3)(-)), N,N,N',N'-tetramethyl-trans-(1R,2R)-diaminocyclohexane, and Li(2)S or Na(2)S(2) yielded clusters that contain [Cu(2)(micro-S(2))(2)](2+), [Cu(3)(micro-S)(2)](3+), [Cu(4)(micro-S(2))(2)](4+), and/or [Cu(6)(micro-S(2))(4)](4+) cores, depending on the specific reaction conditions, notably the nature of X and the sulfur source used. Copper(II) and/or Copper(III) and variable sulfur oxidation levels, including S(2-), S(2)(2-), and S(2)(-*), were identified by X-ray crystallography and spectroscopy.
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Affiliation(s)
- John T York
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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Caruso R, Fina D, Peluso I, Fantini MC, Tosti C, Del Vecchio Blanco G, Paoluzi OA, Caprioli F, Andrei F, Stolfi C, Romano M, Ricci V, MacDonald TT, Pallone F, Monteleone G. IL-21 is highly produced in Helicobacter pylori-infected gastric mucosa and promotes gelatinases synthesis. THE JOURNAL OF IMMUNOLOGY 2007; 178:5957-65. [PMID: 17442980 DOI: 10.4049/jimmunol.178.9.5957] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicobacter pylori (Hp) infection is associated with gastric inflammation and ulceration. The pathways of tissue damage in Hp-infected subjects are complex, but evidence indicates that T cell-derived cytokines enhance the synthesis of matrix metalloproteinases (MMP) that contribute to mucosal ulceration and epithelial damage. In this study, we have examined the role of the T cell cytokine IL-21 in Hp-infected gastric mucosa and evaluated whether IL-21 regulates MMP production by gastric epithelial cells. We show that IL-21 is constitutively expressed in gastric mucosa and is more abundant in biopsy specimens and purified mucosal CD3(+) T cells from Hp-infected patients compared with normal patients and disease controls. We also demonstrate that IL-21R is expressed by primary gastric epithelial cells, as well as by the gastric epithelial cell lines AGS and MKN28. Consistently, AGS cells respond to IL-21 by increasing production of MMP-2 and MMP-9, but not MMP-1, MMP-3, MMP-7, or tissue inhibitors of MMP. Analysis of signaling pathways leading to MMP production reveals that IL-21 enhances NF-kappaB but not MAPK activation, and inhibition of NF-kappaB activation reduces IL-21-induced MMP-2 and MMP-9 production. Finally, we show that treatment of Hp-infected gastric explants with anti-IL-21 reduces epithelial cell-derived MMP-2 and MMP-9 production. These data indicate that IL-21 is overexpressed in Hp-infected gastric mucosa where it could contribute to increased epithelial gelatinase production.
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Affiliation(s)
- Roberta Caruso
- Department of Internal Medicine and Centre of Excellence for Genomic Risk Assessment in Multifactorial and Complex Diseases, University of Rome Tor Vergata, Rome, Italy
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38
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Ghosh S, Gorelsky SI, George SD, Chan JM, Cabrito I, Dooley DM, Moura JJG, Moura I, Solomon EI. Spectroscopic, computational, and kinetic studies of the mu4-sulfide-bridged tetranuclear CuZ cluster in N2O reductase: pH effect on the edge ligand and its contribution to reactivity. J Am Chem Soc 2007; 129:3955-65. [PMID: 17352474 PMCID: PMC2597388 DOI: 10.1021/ja068059e] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the CuZ site in Pseudomonas nautica (Pn) nitrous oxide reductase (N2OR) and Achromobacter cycloclastes (Ac) N2OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN2OR at high pH shows that the 415 cm-1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm-1 18O shift, implying significant Cu-O character, demonstrating the presence of a OH- ligand at the CuICuIV edge. From DFT calculations, protonation of either the OH- to H2O or the mu4-S2- to mu4-SH- would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the CuICuIV edge ligand show that the position of the OH- ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pKa approximately 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E degrees and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu4S(im)7OH]2+ to the fully reduced 4CuI active form for turnover.
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Affiliation(s)
- Somdatta Ghosh
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Serge I. Gorelsky
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Serena DeBeer George
- Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA 94309, USA
| | - Jeannine M. Chan
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Inês Cabrito
- Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-114 Caparica, Portugal
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - José J. G. Moura
- Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-114 Caparica, Portugal
| | - Isabel Moura
- Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-114 Caparica, Portugal
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- CORRESPONDING AUTHOR FOOTNOTE: All correspondence should be addressed to
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Zumft WG, Kroneck PMH. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 2006; 52:107-227. [PMID: 17027372 DOI: 10.1016/s0065-2911(06)52003-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.
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Affiliation(s)
- Walter G Zumft
- Institute of Applied Biosciences, Division of Molecular Microbiology, University of Karlsruhe, D-76128 Karlsruhe, Germany
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40
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Paraskevopoulos K, Antonyuk SV, Sawers RG, Eady RR, Hasnain SS. Insight into Catalysis of Nitrous Oxide Reductase from High-resolution Structures of Resting and Inhibitor-bound Enzyme from Achromobacter cycloclastes. J Mol Biol 2006; 362:55-65. [PMID: 16904686 DOI: 10.1016/j.jmb.2006.06.064] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 06/26/2006] [Accepted: 06/27/2006] [Indexed: 11/15/2022]
Abstract
The difficult chemistry of nitrous oxide (N2O) reduction to gaseous nitrogen (N2) in biology is catalysed by the novel micro4-sulphide-bridged tetranuclear Cuz cluster of the N2O reductases (N2OR). Two spectroscopically distinct forms of this cluster have been identified as CuZ and CuZ*. We have obtained a 1.86 A resolution crystal structure of the pink-purple species of N2OR from Achromobacter cycloclastes (AcN2OR) isolated under aerobic conditions. This structure reveals a previously unobserved ligation with two oxygen atoms from H2O/OH- coordinated to Cu1 and Cu4 of the catalytic centre. We ascribe this structure to be that of the CuZ form of the cluster, since the previously reported structures of two blue species of N2ORs, also isolated aerobically, have characterised the redox inactive CuZ* form, revealing a single water molecule at Cu4. Exposure of the as-isolated AcN2OR to sodium iodide led to reduction of the electron-donating CuA site and the formation of a blue species. Structure determination of this adduct at 1.7 A resolution showed that iodide was bound at the CuZ site bridging the Cu1 and Cu4 ions. This structure represents the first observation of an inhibitor bound to the Cu1-Cu4 edge of the catalytic cluster, providing clear evidence for this being the catalytic edge in N2ORs. These structures, together with the published structural and spectroscopic data, give fresh insight into the mode of substrate binding, reduction and catalysis.
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41
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Zumft WG. Biogenesis of the bacterial respiratory CuA, Cu-S enzyme nitrous oxide reductase. J Mol Microbiol Biotechnol 2006; 10:154-66. [PMID: 16645312 DOI: 10.1159/000091562] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nitrous oxide reductase (NosZ, EC 1.7.99.6) is the terminal oxidoreductase of a respiratory electron transfer chain that transforms nitrous oxide to dinitrogen. The enzyme carries six Cu atoms. Two are arranged in the mixed-valent binuclear CuA site, and four make up the mu4-sulfide-bridged Cu cluster, CuZ. The biogenesis of a catalytically active NosZ requires auxiliary functions for metal center assembly in the periplasm. Both Tat and Sec pathways share the task to transport the various Nos proteins to their functional sites. Biogenesis of NosZ requires an ABC transporter complex and the periplasmic Cu chaperone NosL. Sustaining whole-cell NosZ function depends on the periplasmic, FAD-containing protein NosX, and the membrane-bound iron-sulfur flavoprotein NosR. Most components with a biogenetic function are now amenable to structural studies.
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Affiliation(s)
- Walter G Zumft
- Institute of Applied Biosciences, Division of Molecular Microbiology, University of Karlsruhe, Karlsruhe, Germany.
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42
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Gorelsky SI, Ghosh S, Solomon EI. Mechanism of N2O reduction by the mu4-S tetranuclear CuZ cluster of nitrous oxide reductase. J Am Chem Soc 2006; 128:278-90. [PMID: 16390158 DOI: 10.1021/ja055856o] [Citation(s) in RCA: 272] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction thermodynamics and potential energy surfaces are calculated using density functional theory to investigate the mechanism of the reductive cleavage of the N-O bond by the mu(4)-sulfide-bridged tetranuclear Cu(Z) site of nitrous oxide reductase. The Cu(Z) cluster provides an exogenous ligand-binding site, and, in its fully reduced 4Cu(I) state, the cluster turns off binding of stronger donor ligands while enabling the formation of the Cu(Z)-N(2)O complex through enhanced Cu(Z) --> N(2)O back-donation. The two copper atoms (Cu(I) and Cu(IV)) at the ligand-binding site of the cluster play a crucial role in the enzymatic function, as these atoms are directly involved in bridged N(2)O binding, bending the ligand to a configuration that resembles the transition state (TS) and contributing the two electrons for N(2)O reduction. The other atoms of the Cu(Z) cluster are required for extensive back-bonding with minimal sigma ligand-to-metal donation for the N(2)O activation. The low reaction barrier (18 kcal mol(-)(1)) of the direct cleavage of the N-O bond in the Cu(Z)-N(2)O complex is due to the stabilization of the TS by a strong Cu(IV)(2+)-O(-) bond. Due to the charge transfer from the Cu(Z) cluster to the N(2)O ligand, noncovalent interactions with the protein environment stabilize the polar TS and reduce the activation energy to an extent dependent on the strength of proton donor. After the N-O bond cleavage, the catalytic cycle consists of a sequence of alternating protonation/one-electron reduction steps which return the Cu(Z) cluster to the fully reduced (4Cu(I)) state for future turnover.
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Affiliation(s)
- Serge I Gorelsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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43
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Wunsch P, Körner H, Neese F, van Spanning RJM, Kroneck PMH, Zumft WG. NosX function connects to nitrous oxide (N2O) reduction by affecting the CuZcenter of NosZ and its activity in vivo. FEBS Lett 2005; 579:4605-9. [PMID: 16087179 DOI: 10.1016/j.febslet.2005.07.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 07/14/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
The effect of loss of the 34-kDa periplasmic NosX protein on the properties of N2O reductase was investigated with an N2O-respiration negative, double mutant of the paralogous genes nosX and nirX of Paracoccus denitrificans. In spite of absence of whole-cell N2O-reducing activity, the purified reductase was catalytically active, which attributes NosX a physiological role in sustaining the reaction cycle. N2O reductase exhibited the spectroscopic features of Cu(A) and the redox-inert, paramagnetic state, Cu(Z)*, of the catalytic center. Cu(Z)*, hitherto considered the result of spontaneous reaction of the reductase with dioxygen, attains cellular significance.
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Affiliation(s)
- Patrick Wunsch
- Institute of Applied Biosciences, Division of Molecular Microbiology, University of Karlsruhe, D-76128 Karlsruhe, Germany
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44
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Wunsch P, Zumft WG. Functional domains of NosR, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration. J Bacteriol 2005; 187:1992-2001. [PMID: 15743947 PMCID: PMC1064061 DOI: 10.1128/jb.187.6.1992-2001.2005] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial nitrous oxide (N2O) respiration depends on the polytopic membrane protein NosR for the expression of N2O reductase from the nosZ gene. We constructed His-tagged NosR and purified it from detergent-solubilized membranes of Pseudomonas stutzeri ATCC 14405. NosR is an iron-sulfur flavoprotein with redox centers positioned at opposite sides of the cytoplasmic membrane. The flavin cofactor is presumably bound covalently to an invariant threonine residue of the periplasmic domain. NosR also features conserved CX3CP motifs, located C-terminally of the transmembrane helices TM4 and TM6. We genetically manipulated nosR with respect to these different domains and putative functional centers and expressed recombinant derivatives in a nosR null mutant, MK418nosR::Tn5. NosR's function was studied by its effects on N2O respiration, NosZ synthesis, and the properties of purified NosZ proteins. Although all recombinant NosR proteins allowed the synthesis of NosZ, a loss of N2O respiration was observed upon deletion of most of the periplasmic domain or of the C-terminal parts beyond TM2 or upon modification of the cysteine residues in a highly conserved motif, CGWLCP, following TM4. Nonetheless, NosZ purified from the recombinant NosR background exhibited in vitro catalytic activity. Certain NosR derivatives caused an increase in NosZ of the spectral contribution from a modified catalytic Cu site. In addition to its role in nosZ expression, NosR supports in vivo N2O respiration. We also discuss its putative functions in electron donation and redox activation.
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Affiliation(s)
- Patrick Wunsch
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Karlsruhe, Germany
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45
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Rasmussen T, Brittain T, Berks BC, Watmough NJ, Thomson AJ. Formation of a cytochrome c–nitrous oxide reductase complex is obligatory for N2O reduction by Paracoccus pantotrophus. Dalton Trans 2005:3501-6. [PMID: 16234931 DOI: 10.1039/b501846c] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitrous oxide reductase (N2OR) catalyses the final step of bacterial denitrification, the two-electron reduction of nitrous oxide (N2O) to dinitrogen (N2). N2OR contains two metal centers; a binuclear copper center, CuA, that serves to receive electrons from soluble donors, and a tetranuclear copper-sulfide center, CuZ, at the active site. Stopped flow experiments at low ionic strengths reveal rapid electron transfer (kobs=150 s-1) between reduced horse heart (HH) cytochrome c and the CuA center in fully oxidized N2OR. When fully reduced N2OR was mixed with oxidized cytochrome c, a similar rate of electron transfer was recorded for the reverse reaction, followed by a much slower internal electron transfer from CuZ to CuA(kobs=0.1-0.4 s-1). The internal electron transfer process is likely to represent the rate-determining step in the catalytic cycle. Remarkably, in the absence of cytochrome c, fully reduced N2OR is inert towards its substrate, even though sufficient electrons are stored to initiate a single turnover. However, in the presence of reduced cytochrome c and N2O, a single turnover occurs after a lag-phase. We propose that a conformational change in N2OR is induced by its specific interaction with cytochrome c that in turn either permits electron transfer between CuA and CuZ or controls the rate of N2O decomposition at the active site.
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Affiliation(s)
- Tim Rasmussen
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, UK NR4 7TJ
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46
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Abstract
Denitrification represents an important part of the biogeochemical cycle of the essential element nitrogen. It constitutes the predominant pathway of the reductive dissimilation of nitrate in the environment. Via four enzymatic reactions, nitrate is transformed stepwise to nitrite (NO2-), nitric oxide (NO), and nitrous oxide (N2O), to finally yield dinitrogen gas (N2). All steps within this metabolic pathway are catalyzed by complex multi-site metalloenzymes with unique spectroscopic and structural features. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO reductase.
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Affiliation(s)
- Oliver Einsle
- Abt. Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
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47
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Ghosh S, Gorelsky SI, Chen P, Cabrito I, Moura JJG, Moura I, Solomon EI. Activation of N2O Reduction by the Fully Reduced μ4-Sulfide Bridged Tetranuclear CuZ Cluster in Nitrous Oxide Reductase. J Am Chem Soc 2003; 125:15708-9. [PMID: 14677937 DOI: 10.1021/ja038344n] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tetranuclear CuZ cluster catalyzes the two-electron reduction of N2O to N2 and H2O in the enzyme nitrous oxide reductase. This study shows that the fully reduced 4CuI form of the cluster correlates with the catalytic activity of the enzyme. This is the first demonstration that the S = 1/2 form of CuZ can be further reduced. Complementary DFT calculations support the experimental findings and demonstrate that N2O binding in a bent mu-1,3-bridging mode to the 4CuI form is most efficient due to strong back-bonding from two reduced copper atoms. This back-donation activates N2O for electrophilic attack by a proton.
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Affiliation(s)
- Somdatta Ghosh
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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48
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Wunsch P, Herb M, Wieland H, Schiek UM, Zumft WG. Requirements for Cu(A) and Cu-S center assembly of nitrous oxide reductase deduced from complete periplasmic enzyme maturation in the nondenitrifier Pseudomonas putida. J Bacteriol 2003; 185:887-96. [PMID: 12533464 PMCID: PMC142834 DOI: 10.1128/jb.185.3.887-896.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial nitrous oxide (N(2)O) reductase is the terminal oxidoreductase of a respiratory process that generates dinitrogen from N(2)O. To attain its functional state, the enzyme is subjected to a maturation process which involves the protein-driven synthesis of a unique copper-sulfur cluster and metallation of the binuclear Cu(A) site in the periplasm. There are seven putative maturation factors, encoded by nosA, nosD, nosF, nosY, nosL, nosX, and sco. We wanted to determine the indispensable proteins by expressing nos genes from Pseudomonas stutzeri in the nondenitrifying organism Pseudomonas putida. An in silico study of denitrifying bacteria revealed that nosL, nosX (or a homologous gene, apbE), and sco, but not nosA, coexist consistently with the N(2)O reductase structural gene and other maturation genes. Nevertheless, we found that expression of only three maturation factors (periplasmic protein NosD, cytoplasmic NosF ATPase, and the six-helix integral membrane protein NosY) together with nosRZ in trans was sufficient to produce catalytically active holo-N(2)O reductase in the nondenitrifying background. We suggest that these obligatory factors are required for Cu-S center assembly. Using a mutational approach with P. stutzeri, we also studied NosA, the Cu-containing outer membrane protein previously thought to have Cu insertase function, and ScoP, a putative membrane-anchored chaperone for Cu(A) metallation. Both of these were found to be dispensable elements for N(2)O reductase biosynthesis. Our experimental and in silico data were integrated in a model of N(2)O reductase maturation.
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Affiliation(s)
- Patrick Wunsch
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, D-76128 Karlsruhe, Germany
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49
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Haltia T, Brown K, Tegoni M, Cambillau C, Saraste M, Mattila K, Djinovic-Carugo K. Crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 A resolution. Biochem J 2003; 369:77-88. [PMID: 12356332 PMCID: PMC1223067 DOI: 10.1042/bj20020782] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2002] [Revised: 09/17/2002] [Accepted: 09/30/2002] [Indexed: 11/17/2022]
Abstract
N2O is generated by denitrifying bacteria as a product of NO reduction. In denitrification, N2O is metabolized further by the enzyme N2O reductase (N2OR), a multicopper protein which converts N2O into dinitrogen and water. The structure of N2OR remained unknown until the recent elucidation of the structure of the enzyme isolated from Pseudomonas nautica. In the present paper, we report the crystal structure of a blue form of the enzyme that was purified under aerobic conditions from Paracoccus denitrificans. N2OR is a head-to-tail homodimer stabilized by a multitude of interactions including two calcium sites located at the intermonomeric surface. Each monomer is composed of two domains: a C-terminal cupredoxin domain that carries the dinuclear electron entry site known as Cu(A), and an N-terminal seven-bladed beta-propeller domain which hosts the active-site centre Cu(Z). The electrons are transferred from Cu(A) to Cu(Z) across the subunit interface. Cu(Z) is a tetranuclear copper cluster in which the four copper ions (Cu1 to Cu4) are ligated by seven histidine imidazoles, a hydroxyl or water oxygen and a bridging inorganic sulphide. A bound chloride ion near the Cu(Z) active site shares one of the ligand imidazoles of Cu1. This arrangement probably influences the redox potential of Cu1 so that this copper is stabilized in the cupric state. The treatment of N2OR with H2O2 or cyanide causes the disappearance of the optical band at 640 nm, attributed to the Cu(Z) centre. The crystal structure of the enzyme soaked with H2O2 or cyanide suggests that an average of one copper of the Cu(Z) cluster has been lost. The lowest occupancy is observed for Cu3 and Cu4. A docking experiment suggests that N(2)O binds between Cu1 and Cu4 so that the oxygen of N2O replaces the oxygen ligand of Cu4. Certain ligand imidazoles of Cu1 and Cu2, as well as of Cu4, are located at the dimer interface. Particularly those of Cu2 and Cu4 are parts of a bonding network which couples these coppers to the Cu(A) centre in the neighbouring monomer. This structure may provide an efficient electron transfer path for reduction of the bound N2O.
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Affiliation(s)
- Tuomas Haltia
- Institute of Biomedicine/Biochemistry, P.O. Box 63, Biomedicum Helsinki, Haartmaninkatu 8, FIN-00014 University of Helsinki, Helsinki, Finland.
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