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Induced peroxidase activity of haem containing nitrate reductases revealed by protein film electrochemistry. J Electroanal Chem (Lausanne) 2013. [DOI: 10.1016/j.jelechem.2013.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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52
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Dahms SO, Kuester M, Streb C, Roth C, Sträter N, Than ME. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:284-97. [PMID: 23385464 PMCID: PMC3565441 DOI: 10.1107/s0907444912046008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/07/2012] [Indexed: 01/17/2023]
Abstract
Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.
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Affiliation(s)
- Sven O. Dahms
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Miriam Kuester
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Carsten Streb
- Institute of Inorganic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Egerlandstrasse 1, D-91058 Erlangen, Germany
| | - Christian Roth
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Universität Leipzig, D-04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Universität Leipzig, D-04103 Leipzig, Germany
| | - Manuel E. Than
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Abstract
A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, 1643 Boyce Hall, Riverside, CA 92521, USA.
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55
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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56
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Ma X, Schulzke C. Molybdenum and tungsten complexes of bis(phenolate) ligands, O,X,O (X=S or Se): Synthesis, characterization and catalytic oxygen atom transfer properties. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2012.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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57
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Nguyen N, Lough AJ, Fekl U. Rapid, Covalent Addition of Phosphine to Dithiolene in a Molybdenum Tris(dithiolene). A New Structural Model for Dimethyl Sulfoxide Reductase. Inorg Chem 2012; 51:6446-8. [DOI: 10.1021/ic301031b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Neilson Nguyen
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
- Department of Chemical
and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Alan J. Lough
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
| | - Ulrich Fekl
- Department of Chemistry, University of Toronto, Toronto, Ontario,
Canada M5S 3H6
- Department of Chemical
and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
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58
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da Silva SM, Pacheco I, Pereira IAC. Electron transfer between periplasmic formate dehydrogenase and cytochromes c in Desulfovibrio desulfuricans ATCC 27774. J Biol Inorg Chem 2012; 17:831-8. [DOI: 10.1007/s00775-012-0900-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/08/2012] [Indexed: 10/28/2022]
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Bueno E, Mesa S, Bedmar EJ, Richardson DJ, Delgado MJ. Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. Antioxid Redox Signal 2012; 16:819-52. [PMID: 22098259 PMCID: PMC3283443 DOI: 10.1089/ars.2011.4051] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, CSIC, Granada, Spain
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60
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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61
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Szilágyi A, Zhang Y, Závodszky P. Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures. J Mol Biol 2011; 415:221-35. [PMID: 22079367 DOI: 10.1016/j.jmb.2011.10.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/07/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
Abstract
Multidomain proteins form in evolution through the concatenation of domains, but structural domains may comprise multiple segments of the chain. In this work, we demonstrate that new multidomain architectures can evolve by an apparent three-dimensional swap of segments between structurally similar domains within a single-chain monomer. By a comprehensive structural search of the current Protein Data Bank (PDB), we identified 32 well-defined segment-swapped proteins (SSPs) belonging to 18 structural families. Nearly 13% of all multidomain proteins in the PDB may have a segment-swapped evolutionary precursor as estimated by more permissive searching criteria. The formation of SSPs can be explained by two principal evolutionary mechanisms: (i) domain swapping and fusion (DSF) and (ii) circular permutation (CP). By large-scale comparative analyses using structural alignment and hidden Markov model methods, it was found that the majority of SSPs have evolved via the DSF mechanism, and a much smaller fraction, via CP. Functional analyses further revealed that segment swapping, which results in two linkers connecting the domains, may impart directed flexibility to multidomain proteins and contributes to the development of new functions. Thus, inter-domain segment swapping represents a novel general mechanism by which new protein folds and multidomain architectures arise in evolution, and SSPs have structural and functional properties that make them worth defining as a separate group.
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Affiliation(s)
- András Szilágyi
- Institute of Enzymology, Hungarian Academy of Sciences, Karolina út 29, H-1113 Budapest, Hungary
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62
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Wang TH, Chen YH, Huang JY, Liu KC, Ke SC, Chu HA. Enzyme kinetics, inhibitors, mutagenesis and electron paramagnetic resonance analysis of dual-affinity nitrate reductase in unicellular N(2)-fixing cyanobacterium Cyanothece sp. PCC 8801. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:1369-1376. [PMID: 21821424 DOI: 10.1016/j.plaphy.2011.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/12/2011] [Indexed: 05/31/2023]
Abstract
The assimilatory nitrate reductase (NarB) of N(2)-fixing cyanobacterium Cyanothece sp. PCC 8801 is a monomeric enzyme with dual affinity for substrate nitrate. We purified the recombinant NarB of Cyanothece sp. PCC 8801 and further investigated it by enzyme kinetics analysis, site-directed mutagenesis, inhibitor kinetics analysis, and electron paramagnetic resonance (EPR) spectroscopy. The NarB showed 2 kinetic regimes at pH 10.5 or 8 and electron-donor conditions methyl viologen or ferredoxin (Fd). Fd-dependent NR assay revealed NarB with very high affinity for nitrate (K(m)1, ∼1μM; K(m)2, ∼270μM). Metal analysis and EPR results showed that NarB contains a Mo cofactor and a [4Fe-4S] cluster. In addition, the R352A mutation on the proposed nitrate-binding site of NarB greatly altered both high- and low-affinity kinetic components. Furthermore, the effect of azide on the NarB of Cyanothece sp. PCC 8801 was more complex than that on the NarB of Synechococcus sp. PCC 7942 with its single kinetic regime. With 1mM azide, the kinetics of the wild-type NarB was transformed from 2 kinetic regimes to hyperbolic kinetics, and its activity was enhanced significantly under medium nitrate concentrations. Moreover, EPR results also suggested a structural difference between the two NarBs. Taken together, our results show that the NarB of Cyanothece sp. PCC 8801 contains only a single Mo-catalytic center, and we rule out that the enzyme has 2 independent, distinct catalytic sites. In addition, the NarB of Cyanothece sp. PCC 8801 may have a regulatory nitrate-binding site.
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Affiliation(s)
- Tung-Hei Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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63
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Samuel PP, Horn S, Döring A, Havelius KGV, Reschke S, Leimkühler S, Haumann M, Schulzke C. A Crystallographic and Mo K-Edge XAS Study of Molybdenum Oxo Bis-, Mono-, and Non-Dithiolene Complexes - First-Sphere Coordination Geometry and Noninnocence of Ligands. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100331] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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64
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Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration – Genes, enzymes and environmental distribution. J Biotechnol 2011; 155:104-17. [DOI: 10.1016/j.jbiotec.2010.12.025] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 12/07/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023]
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65
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Marom H, Antonov S, Popowski Y, Gozin M. Selective Sulfoxidation of Thioethers and Thioaryl Boranes with Nitrate, Promoted by a Molybdenum–Copper Catalytic System. J Org Chem 2011; 76:5240-6. [DOI: 10.1021/jo2001808] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hanit Marom
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Svetlana Antonov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yanay Popowski
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Gozin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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66
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Majumdar A, Sarkar S. Bioinorganic chemistry of molybdenum and tungsten enzymes: A structural–functional modeling approach. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.11.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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67
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Magalon A, Fedor JG, Walburger A, Weiner JH. Molybdenum enzymes in bacteria and their maturation. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.12.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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68
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69
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70
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Holm RH, Solomon EI, Majumdar A, Tenderholt A. Comparative molecular chemistry of molybdenum and tungsten and its relation to hydroxylase and oxotransferase enzymes. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.10.017] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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71
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Rauschenbach I, Yee N, Häggblom MM, Bini E. Energy metabolism and multiple respiratory pathways revealed by genome sequencing ofDesulfurispirillum indicumstrain S5. Environ Microbiol 2011; 13:1611-21. [DOI: 10.1111/j.1462-2920.2011.02473.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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72
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Ferroni FM, Rivas MG, Rizzi AC, Lucca ME, Perotti NI, Brondino CD. Nitrate reduction associated with respiration in Sinorhizobium meliloti 2011 is performed by a membrane-bound molybdoenzyme. Biometals 2011; 24:891-902. [PMID: 21432624 DOI: 10.1007/s10534-011-9442-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
The purification and biochemical characterization of the respiratory membrane-bound nitrate reductase from Sinorhizobium meliloti 2011 (Sm NR) is reported together with the optimal conditions for cell growth and enzyme production. The best biomass yield was obtained under aerobic conditions in a fed-batch system using Luria-Bertani medium with glucose as carbon source. The highest level of Sm NR production was achieved using microaerobic conditions with the medium supplemented with both nitrate and nitrite. Sm NR is a mononuclear Mo-protein belonging to the DMSO reductase family isolated as a heterodimeric enzyme containing two subunits of 118 and 45 kDa. Protein characterization by mass spectrometry showed homology with respiratory nitrate reductases. UV-Vis spectra of as-isolated and dithionite reduced Sm NR showed characteristic absorption bands of iron-sulfur and heme centers. Kinetic studies indicate that Sm NR follows a Michaelis-Menten mechanism (K (m) = 97 ± 11 μM, V = 9.4 ± 0.5 μM min(-1), and k (cat) = 12.1 ± 0.6 s(-1)) and is inhibited by azide, chlorate, and cyanide with mixed inhibition patterns. Physiological and kinetic studies indicate that molybdenum is essential for NR activity and that replacement of this metal for tungsten inhibits the enzyme. Although no narGHI gene cluster has been annotated in the genome of rhizobia, the biochemical characterization indicates that Sm NR is a Mo-containing NR enzyme with molecular organization similar to NarGHI.
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Affiliation(s)
- Felix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina
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73
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Coelho C, González PJ, Moura JG, Moura I, Trincão J, João Romão M. The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states. J Mol Biol 2011; 408:932-48. [PMID: 21419779 DOI: 10.1016/j.jmb.2011.03.016] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 11/19/2022]
Abstract
The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit (NapA, 91 kDa) containing the molybdenum active site plus one [4Fe-4S] cluster, as well as a small subunit (NapB, 17 kDa), which is a diheme c-type cytochrome involved in electron transfer. Crystals of the oxidized form of the enzyme diffracted beyond 1.5 Å at the European Synchrotron Radiation Facility. This is the highest resolution reported to date for a nitrate reductase, providing true atomic details of the protein active center, and this showed further evidence on the molybdenum coordination sphere, corroborating previous data on the related Desulfovibrio desulfuricans NapA. The molybdenum atom is bound to a total of six sulfur atoms, with no oxygen ligands or water molecules in the vicinity. In the present work, we were also able to prepare partially reduced crystals that revealed two alternate conformations of the Mo-coordinating cysteine. This crystal form was obtained by soaking dithionite into crystals grown in the presence of the ionic liquid [C(4)mim]Cl(-). In addition, UV-Vis and EPR spectroscopy studies showed that the periplasmic nitrate reductase from C. necator might work at unexpectedly high redox potentials when compared to all periplasmic nitrate reductases studied to date.
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Affiliation(s)
- Catarina Coelho
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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74
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Gates AJ, Kemp GL, To CY, Mann J, Marritt SJ, Mayes AG, Richardson DJ, Butt JN. The relationship between redox enzyme activity and electrochemical potential—cellular and mechanistic implications from protein film electrochemistry. Phys Chem Chem Phys 2011; 13:7720-31. [DOI: 10.1039/c0cp02887h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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75
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Carbajal-Rodríguez I, Stöveken N, Satola B, Wübbeler JH, Steinbüchel A. Aerobic degradation of mercaptosuccinate by the gram-negative bacterium Variovorax paradoxus strain B4. J Bacteriol 2011; 193:527-39. [PMID: 21075928 PMCID: PMC3019817 DOI: 10.1128/jb.00793-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/29/2010] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Variovorax paradoxus strain B4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (MS). During growth with MS this strain released significant amounts of sulfate into the medium. Tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using MS as a carbon source. In six of these mutants, Tn5::mob insertions were mapped in a putative gene encoding a molybdenum (Mo) cofactor biosynthesis protein (moeA). In two further mutants the Tn5::mob insertion was mapped in the gene coding for a putative molybdopterin (MPT) oxidoreductase. In contrast to the wild type, these eight mutants also showed no growth on taurine. In another mutant a gene putatively encoding a 3-hydroxyacyl-coenzyme A dehydrogenase (paaH2) was disrupted by transposon insertion. Upon subcellular fractionation of wild-type cells cultivated with MS as sole carbon and sulfur source, MPT oxidoreductase activity was detected in only the cytoplasmic fraction. Cells grown with succinate, taurine, or gluconate as a sole carbon source exhibited no activity or much lower activity. MPT oxidoreductase activity in the cytoplasmic fraction of the Tn5::mob-induced mutant Icr6 was 3-fold lower in comparison to the wild type. Therefore, a new pathway for MS catabolism in V. paradoxus strain B4 is proposed: (i) MPT oxidoreductase catalyzes the conversion of MS first into sulfinosuccinate (a putative organo-sulfur compound composed of succinate and a sulfino group) and then into sulfosuccinate by successive transfer of oxygen atoms, (ii) sulfosuccinate is cleaved into oxaloacetate and sulfite, and (iii) sulfite is oxidized to sulfate.
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Affiliation(s)
- Irma Carbajal-Rodríguez
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Nadine Stöveken
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Barbara Satola
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
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Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1167-73. [PMID: 20944207 PMCID: PMC2954201 DOI: 10.1107/s1744309110007517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/26/2010] [Indexed: 11/16/2022]
Abstract
The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
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Affiliation(s)
- Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - L. Aravind
- National Institutes of Health, Bethesda, MD, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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77
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Abstract
Proteins that reside partially or completely outside the bacterial cytoplasm require specialized pathways to facilitate their localization. Globular proteins that function in the periplasm must be translocated across the hydrophobic barrier of the inner membrane. While the Sec pathway transports proteins in a predominantly unfolded conformation, the Tat pathway exports folded protein substrates. Protein transport by the Tat machinery is powered solely by the transmembrane proton gradient, and there is no requirement for nucleotide triphosphate hydrolysis. Proteins are targeted to the Tat machinery by N-terminal signal peptides that contain a consensus twin arginine motif. In Escherichia coli and Salmonella there are approximately thirty proteins with twin arginine signal peptides that are transported by the Tat pathway. The majority of these bind complex redox cofactors such as iron sulfur clusters or the molybdopterin cofactor. Here we describe what is known about Tat substrates in E. coli and Salmonella, the function and mechanism of Tat protein export, and how the cofactor insertion step is coordinated to ensure that only correctly assembled substrates are targeted to the Tat machinery.
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78
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Cremades E, Echeverría J, Alvarez S. The Trigonal Prism in Coordination Chemistry. Chemistry 2010; 16:10380-96. [DOI: 10.1002/chem.200903032] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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79
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Resolution of two native monomeric 90kDa nitrate reductase active proteins from Shewanella gelidimarina and the sequence of two napA genes. Biochem Biophys Res Commun 2010; 398:13-8. [DOI: 10.1016/j.bbrc.2010.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 06/01/2010] [Indexed: 11/22/2022]
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80
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Szaleniec M, Borowski T, Schühle K, Witko M, Heider J. Ab Inito Modeling of Ethylbenzene Dehydrogenase Reaction Mechanism. J Am Chem Soc 2010; 132:6014-24. [DOI: 10.1021/ja907208k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Szaleniec
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Karola Schühle
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Malgorzata Witko
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Johann Heider
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
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81
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Abad Andrade CE, Ma X, Meyer-Klaucke W, Schulzke C. The difference one ligand atom makes – An altered oxygen transfer reaction mechanism caused by an exchange of selenium for sulfur. Polyhedron 2010. [DOI: 10.1016/j.poly.2009.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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82
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Hanson GR, Lane I. Dimethylsulfoxide (DMSO) Reductase, a Member of the DMSO Reductase Family of Molybdenum Enzymes. METALS IN BIOLOGY 2010. [DOI: 10.1007/978-1-4419-1139-1_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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83
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Xie H, Cao Z. Enzymatic Reduction of Nitrate to Nitrite: Insight from Density Functional Calculations. Organometallics 2009. [DOI: 10.1021/om9008197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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84
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Simpson PJL, Richardson DJ, Codd R. The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB. MICROBIOLOGY-SGM 2009; 156:302-312. [PMID: 19959582 DOI: 10.1099/mic.0.034421-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the bacterial periplasm, the reduction of nitrate to nitrite is catalysed by a periplasmic nitrate reductase (NAP) system, which is a species-dependent assembly of protein subunits encoded by the nap operon. The reduction of nitrate catalysed by NAP takes place in the 90 kDa NapA subunit, which contains a Mo-bis-molybdopterin guanine dinucleotide cofactor and one [4Fe-4S] iron-sulfur cluster. A review of the nap operons in the genomes of 19 strains of Shewanella shows that most genomes contain two nap operons. This is an unusual feature of this genus. The two NAP isoforms each comprise three isoform-specific subunits - NapA, a di-haem cytochrome NapB, and a maturation chaperone NapD - but have different membrane-intrinsic subunits, and have been named NAP-alpha (NapEDABC) and NAP-beta (NapDAGHB). Sixteen Shewanella genomes encode both NAP-alpha and NAP-beta. The genome of the vigorous denitrifier Shewanella denitrificans OS217 encodes only NAP-alpha and the genome of the respiratory nitrate ammonifier Shewanella oneidensis MR-1 encodes only NAP-beta. This raises the possibility that NAP-alpha and NAP-beta are associated with physiologically distinct processes in the environmentally adaptable genus Shewanella.
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Affiliation(s)
- Philippa J L Simpson
- Centre for Heavy Metals Research, School of Chemistry, University of Sydney, New South Wales 2006, Australia
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich NR4 TJ7, UK
| | - Rachel Codd
- School of Medical Sciences (Pharmacology) and Bosch Institute, University of Sydney, New South Wales 2006, Australia.,Centre for Heavy Metals Research, School of Chemistry, University of Sydney, New South Wales 2006, Australia
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85
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The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. J Comput Chem 2009; 30:2466-84. [DOI: 10.1002/jcc.21280] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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86
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Biochemistry, physiology and biotechnology of sulfate-reducing bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2009; 68:41-98. [PMID: 19426853 DOI: 10.1016/s0065-2164(09)01202-7] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The production of biosulfide by SRB has led to immobilization of toxic metals and reduction of textile dyes, although the process remains unresolved, SRB play a role in anaerobic methane oxidation which not only contributes to carbon cycle activities but also depletes an important industrial energy reserve.
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87
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Hofmann M. Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA. J Biol Inorg Chem 2009; 14:1023-35. [DOI: 10.1007/s00775-009-0545-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
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88
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Richey C, Chovanec P, Hoeft SE, Oremland RS, Basu P, Stolz JF. Respiratory arsenate reductase as a bidirectional enzyme. Biochem Biophys Res Commun 2009; 382:298-302. [DOI: 10.1016/j.bbrc.2009.03.045] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/04/2009] [Indexed: 11/30/2022]
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89
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Tarasova NB, Gorshkov OV, Petrova OE. Activity of nitrate reductase in Desulfovibrio vulgaris VKM 1388. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709020040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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90
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Groysman S, Holm RH. Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites. Biochemistry 2009; 48:2310-20. [PMID: 19206188 PMCID: PMC2765533 DOI: 10.1021/bi900044e] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few have even been closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases.
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Affiliation(s)
- Stanislav Groysman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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91
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Glass JB, Wolfe-Simon F, Anbar AD. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae. GEOBIOLOGY 2009; 7:100-23. [PMID: 19320747 DOI: 10.1111/j.1472-4669.2009.00190.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Marine primary producers adapted over eons to the changing chemistry of the oceans. Because a number of metalloenzymes are necessary for N assimilation, changes in the availability of transition metals posed a particular challenge to the supply of this critical nutrient that regulates marine biomass and productivity. Integrating recently developed geochemical, biochemical, and genetic evidence, we infer that the use of metals in N assimilation - particularly Fe and Mo - can be understood in terms of the history of metal availability through time. Anoxic, Fe-rich Archean oceans were conducive to the evolution of Fe-using enzymes that assimilate abiogenic NH(4)(+) and NO(2)(-). The N demands of an expanding biosphere were satisfied by the evolution of biological N(2) fixation, possibly utilizing only Fe. Trace O(2) in late Archean environments, and the eventual 'Great Oxidation Event' c. 2.3 Ga, mobilized metals such as Mo, enabling the evolution of Mo (or V)-based N(2) fixation and the Mo-dependent enzymes for NO(3)(-) assimilation and denitrification by prokaryotes. However, the subsequent onset of deep-sea euxinia, an increasingly-accepted idea, may have kept ocean Mo inventories low and depressed Fe, limiting the rate of N(2) fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic NO(3)(-) assimilation. Thorough ocean oxygenation in the Neoproterozoic led to Mo-rich oceans, possibly contributing to the proliferation of eukaryotes and thus the Cambrian explosion of metazoan life. These ideas can be tested by more intensive study of the metal requirements in N assimilation and the biological strategies for metal uptake, regulation, and storage.
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Affiliation(s)
- J B Glass
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA.
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92
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Eierhoff D, Tung WC, Hammerschmidt A, Krebs B. Molybdenum complexes with O,N,S donor ligands as models for active sites in oxotransferases and hydroxylases. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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93
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Affiliation(s)
- Maria João Romão
- REQUIMTE-CQFB, Departamento de Química, FCT-Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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94
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Majumdar A, Pal K, Sarkar S. Necessity of fine tuning in Mo(iv) bis(dithiolene) complexes to warrant nitrate reduction. Dalton Trans 2009:1927-38. [DOI: 10.1039/b815436h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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95
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Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico). Extremophiles 2008; 13:169-78. [DOI: 10.1007/s00792-008-0207-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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96
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Pal K, Sarkar S. The Role of Axial Ligation in Nitrate Reductase: A Model Study by DFT Calculations on the Mechanism of Nitrate Reduction. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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97
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Fourmond V, Burlat B, Dementin S, Arnoux P, Sabaty M, Boiry S, Guigliarelli B, Bertrand P, Pignol D, Léger C. Major Mo(V) EPR Signature of Rhodobacter sphaeroides Periplasmic Nitrate Reductase Arising from a Dead-End Species That Activates upon Reduction. Relation to Other Molybdoenzymes from the DMSO Reductase Family. J Phys Chem B 2008; 112:15478-86. [DOI: 10.1021/jp807092y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent Fourmond
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Bénédicte Burlat
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Sébastien Dementin
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Pascal Arnoux
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Monique Sabaty
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Séverine Boiry
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Patrick Bertrand
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - David Pignol
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Christophe Léger
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
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Neumann M, Leimkühler S. Heavy metal ions inhibit molybdoenzyme activity by binding to the dithiolene moiety of molybdopterin in Escherichia coli. FEBS J 2008; 275:5678-89. [DOI: 10.1111/j.1742-4658.2008.06694.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rothery RA, Workun GJ, Weiner JH. The prokaryotic complex iron–sulfur molybdoenzyme family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1897-929. [DOI: 10.1016/j.bbamem.2007.09.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2007] [Revised: 08/17/2007] [Accepted: 09/02/2007] [Indexed: 10/22/2022]
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Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617. J Biol Inorg Chem 2008; 13:1321-33. [PMID: 18704520 DOI: 10.1007/s00775-008-0416-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Accepted: 08/02/2008] [Indexed: 10/21/2022]
Abstract
Membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617 can be solubilized in either of two ways that will ultimately determine the presence or absence of the small (Iota) subunit. The enzyme complex (NarGHI) is composed of three subunits with molecular masses of 130, 65, and 20 kDa. This enzyme contains approximately 14 Fe, 0.8 Mo, and 1.3 molybdopterin guanine dinucleotides per enzyme molecule. Curiously, one heme b and 0.4 heme c per enzyme molecule have been detected. These hemes were potentiometrically characterized by optical spectroscopy at pH 7.6 and two noninteracting species were identified with respective midpoint potentials at Em=+197 mV (heme c) and -4.5 mV (heme b). Variable-temperature (4-120 K) X-band electron paramagnetic resonance (EPR) studies performed on both as-isolated and dithionite-reduced nitrate reductase showed, respectively, an EPR signal characteristic of a [3Fe-4S]+ cluster and overlapping signals associated with at least three types of [4Fe-4S]+ centers. EPR of the as-isolated enzyme shows two distinct pH-dependent Mo(V) signals with hyperfine coupling to a solvent-exchangeable proton. These signals, called "low-pH" and "high-pH," changed to a pH-independent Mo(V) signal upon nitrate or nitrite addition. Nitrate addition to dithionite-reduced samples at pH 6 and 7.6 yields some of the EPR signals described above and a new rhombic signal that has no hyperfine structure. The relationship between the distinct EPR-active Mo(V) species and their plausible structures is discussed on the basis of the structural information available to date for closely related membrane-bound nitrate reductases.
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