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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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2
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Selamoglu N, Önder Ö, Öztürk Y, Khalfaoui-Hassani B, Blaby-Haas CE, Garcia BA, Koch HG, Daldal F. Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins. Metallomics 2020; 12:572-591. [PMID: 32149296 PMCID: PMC7192791 DOI: 10.1039/c9mt00314b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/28/2020] [Indexed: 12/20/2022]
Abstract
Copper (Cu) is an essential, but toxic, micronutrient for living organisms and cells have developed sophisticated response mechanisms towards both the lack and the excess of Cu in their environments. In this study, we achieved a global view of Cu-responsive changes in the prokaryotic model organism Rhodobacter capsulatus using label-free quantitative differential proteomics. Semi-aerobically grown cells under heterotrophic conditions in minimal medium (∼0.3 μM Cu) were compared with cells supplemented with either 5 μM Cu or with 5 mM of the Cu-chelator bathocuproine sulfonate. Mass spectrometry based bottom-up proteomics of unfractionated cell lysates identified 2430 of the 3632 putative proteins encoded by the genome, producing a robust proteome dataset for R. capsulatus. Use of biological and technical replicates for each growth condition yielded high reproducibility and reliable quantification for 1926 of the identified proteins. Comparison of cells grown under Cu-excess or Cu-depleted conditions to those grown under minimal Cu-sufficient conditions revealed that 75 proteins exhibited statistically significant (p < 0.05) abundance changes, ranging from 2- to 300-fold. A subset of the highly Cu-responsive proteins was orthogonally probed using molecular genetics, validating that several of them were indeed involved in cellular Cu homeostasis.
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Affiliation(s)
- Nur Selamoglu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Blum JM, Su Q, Ma Y, Valverde-Pérez B, Domingo-Félez C, Jensen MM, Smets BF. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production. Environ Microbiol 2018; 20:1623-1640. [DOI: 10.1111/1462-2920.14063] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Jan-Michael Blum
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Qingxian Su
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Yunjie Ma
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Borja Valverde-Pérez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
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Xie H, Liu C, Chen X, Lei Q, Fang W, Zhou T. Theoretically exploring the key role of the Lys412 residue in the conversion of N2O to N2by nitrous oxide reductase from Achromobacter cycloclastes. NEW J CHEM 2015. [DOI: 10.1039/c5nj01339a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The active CuZcluster of NOR provides strong back-donation to coordinated N2O and activates the O atom of the N2O group facilitating H-bonding and protonationviathe Lys412 residue.
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Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Chengcheng Liu
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Xuelin Chen
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Qunfang Lei
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Wenjun Fang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Tao Zhou
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
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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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6
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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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8
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Direct electron transfer from pseudoazurin to nitrous oxide reductase in catalytic N2O reduction. J Inorg Biochem 2012; 115:163-73. [DOI: 10.1016/j.jinorgbio.2012.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 11/22/2022]
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9
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Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4729-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Dell'acqua S, Moura I, Moura JJG, Pauleta SR. The electron transfer complex between nitrous oxide reductase and its electron donors. J Biol Inorg Chem 2011; 16:1241-54. [PMID: 21739254 DOI: 10.1007/s00775-011-0812-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/20/2011] [Indexed: 11/25/2022]
Abstract
Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N(2)OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N(2)OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N(2)OR, or an electrostatic nature, in the case of P. denitrificans N(2)OR and A. cycloclastes N(2)OR. A set of well-conserved residues on the N(2)OR surface were identified as being part of the electron transfer pathway from the redox partner to N(2)OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N(2)OR sequence). Moreover, we built a model for Wolinella succinogenes N(2)OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N(2)OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N(2)OR domain is similar to that found in the other electron transfer complexes.
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Affiliation(s)
- Simone Dell'acqua
- REQUIMTE/CQFB, Departamento de Química, Universidade Nova de Lisboa, Caparica, Portugal
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11
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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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12
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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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13
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Bizzarri AR, Brunori E, Bonanni B, Cannistraro S. Docking and molecular dynamics simulation of the Azurin–Cytochrome c551 electron transfer complex. J Mol Recognit 2007; 20:122-31. [PMID: 17407190 DOI: 10.1002/jmr.820] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We coupled protein-protein docking procedure with molecular dynamics (MD) simulation to investigate the electron transfer (ET) complex Azurin-Cytochrome c551 whose transient character makes difficult a direct experimental investigation. The ensemble of complexes generated by the docking algorithm are filtered according to both the distance between the metal ions in the redox centres of the two proteins and to the involvement of suitable residues at the interface. The resulting best complex (BC) is characterized by a distance of 1.59 nm and involves Val23 and Ile59 of Cytochrome c551. The ET properties have been evaluated in the framework of the Pathways model and compared with experimental data. A 60 ns long MD simulation, carried on at full hydration, evidenced that the two protein molecules retain their mutual spatial positions upon forming the complex. An analysis of the ET properties of the complex, monitored at regular time intervals, has revealed that several different ET paths are possible, with the occasional intervening of water molecules. Furthermore, the temporal evolution of the geometric distance between the two redox centres is characterized by very fast fluctuations around an average value of 1.6 nm, with periodic jumps at 2 nm with a frequency of about 70 MHz. Such a behaviour is discussed in connection with a nonlinear dynamics of protein systems and its possible implications in the ET process are explored.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy.
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14
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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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15
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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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16
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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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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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