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Hagen WR. Quantum Magnetism of the Iron Core in Ferritin Proteins-A Re-Evaluation of the Giant-Spin Model. Molecules 2024; 29:2254. [PMID: 38792115 PMCID: PMC11123763 DOI: 10.3390/molecules29102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The electron-electron, or zero-field interaction (ZFI) in the electron paramagnetic resonance (EPR) of high-spin transition ions in metalloproteins and coordination complexes, is commonly described by a simple spin Hamiltonian that is second-order in the spin S: H=D[Sz2-SS+1/3+E(Sx2-Sy2). Symmetry considerations, however, allow for fourth-order terms when S ≥ 2. In metalloprotein EPR studies, these terms have rarely been explored. Metal ions can cluster via non-metal bridges, as, for example, in iron-sulfur clusters, in which exchange interaction can result in higher system spin, and this would allow for sixth- and higher-order ZFI terms. For metalloproteins, these have thus far been completely ignored. Single-molecule magnets (SMMs) are multi-metal ion high spin complexes, in which the ZFI usually has a negative sign, thus affording a ground state level pair with maximal spin quantum number mS = ±S, giving rise to unusual magnetic properties at low temperatures. The description of EPR from SMMs is commonly cast in terms of the 'giant-spin model', which assumes a magnetically isolated system spin, and in which fourth-order, and recently, even sixth-order ZFI terms have been found to be required. A special version of the giant-spin model, adopted for scaling-up to system spins of order S ≈ 103-104, has been applied to the ubiquitous iron-storage protein ferritin, which has an internal core containing Fe3+ ions whose individual high spins couple in a way to create a superparamagnet at ambient temperature with very high system spin reminiscent to that of ferromagnetic nanoparticles. This scaled giant-spin model is critically evaluated; limitations and future possibilities are explicitly formulated.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Building 58, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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2
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Martins MC, Alves CM, Teixeira M, Folgosa F. The flavodiiron protein from Syntrophomonas wolfei has five domains and acts both as an NADH:O 2 or an NADH:H 2 O 2 oxidoreductase. FEBS J 2024; 291:1275-1294. [PMID: 38129989 DOI: 10.1111/febs.17040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/10/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Flavodiiron proteins (FDPs) are a family of enzymes with a significant role in O2 /H2 O2 and/or NO detoxification through the reduction of these species to H2 O or N2 O, respectively. All FDPs contain a minimal catalytic unit of two identical subunits, each one having a metallo-β-lactamase-like domain harboring the catalytic diiron site, and a flavodoxin-like domain. However, more complex and diverse arrangements in terms of domains are found in this family, of which the class H enzymes are among the most complex. One of such FDPs is encoded in the genome of the anaerobic bacterium Syntrophomonas wolfei subsp. wolfei str. Goettingen G311. Besides the core domains, this protein is predicted to have three additional ones after the flavodoxin core domain: two short-chain rubredoxins and a NAD(P)H:rubredoxin oxidoreductase-like domain. This enzyme, FDP_H, was produced and characterized and the presence of the predicted cofactors was investigated by a set of biochemical and spectroscopic methodologies. Syntrophomonas wolfei FDP_H exhibited a remarkable O2 reduction activity with a kcat = 52.0 ± 1.2 s-1 and a negligible NO reduction activity (~ 100 times lower than with O2 ), with NADH as an electron donor, that is, it is an oxygen-selective FDP. In addition, this enzyme showed the highest turnover value for H2 O2 reduction (kcat = 19.1 ± 2.2 s-1 ) ever observed among FDPs. Kinetic studies of site-directed mutants of iron-binding cysteines at the two rubredoxin domains demonstrated the essential role of these centers since their absence leads to a significant decrease or even abolishment of O2 and H2 O2 reduction activities.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Catarina M Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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3
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Moubarak S, Rippers Y, Elghobashi-Meinhardt N, Mroginski MA. Structural and electronic properties of the active site of [ZnFe] SulE. Front Mol Biosci 2022; 9:945415. [DOI: 10.3389/fmolb.2022.945415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The function of the recently isolated sulerythrin (SulE) has been investigated using a combination of structural and electronic analyses based on quantum mechanical calculations. In the SulE structure of Fushinobu et al. (2003), isolated from a strictly aerobic archaeon, Sulfolobus tokadaii, a dioxygen-containing species was tentatively included at the active site during crystallographic refinement although the substrate specificity of SulE remains unclear. Studies have suggested that a structurally related enzyme, rubrerythrin, functions as a hydrogen peroxide reductase. Since SulE is a truncated version of rubrerythrin, the enzymes are hypothesized to function similarly. Hence, using available X-ray crystallography data (1.7 Å), we constructed various models of SulE containing a ZnII–Fe active site, differing in the nature of the substrate specificity (O2, H2O2), the oxidation level and the spin state of the iron ion, and the protonation states of the coordinating glutamate residues. Also, the substrate H2O2 is modeled in two possible configurations, differing in the orientation of the hydrogen atoms. Overall, the optimized geometries with an O2 substrate do not show good agreement with the experimentally resolved geometry. In contrast, excellent agreement between crystal structure arrangement and optimized geometries is achieved considering a H2O2 substrate and FeII in both spin states, when Glu92 is protonated. These results suggest that the dioxo species detected at the [ZnFe] active site of sulerythrin is H2O2, rather than an O2 molecule in agreement with experimental data indicating that only the diferrous oxidation state of the dimetal site in rubrerythrin reacts rapidly with H2O2. Based on our computations, we proposed a possible reaction pathway for substrate binding at the ZnFeII site of SulE with a H2O2 substrate. In this reaction pathway, Fe or another electron donor, such as NAD(P)H, catalyzes the reduction of H2O2 to water at the zinc–iron site.
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Abdulaziz EN, Bell TA, Rashid B, Heacock ML, Begic T, Skinner OS, Yaseen MA, Chao LH, Mootha VK, Pierik AJ, Cracan V. A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. J Biol Chem 2022; 298:102210. [PMID: 35780837 PMCID: PMC9364112 DOI: 10.1016/j.jbc.2022.102210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from H2O-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: H2O-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD+ while simultaneously removing O2 from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX-like enzyme and instead harbors three paralogous genes (FDPF1-3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a "stand-alone" FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions.
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Affiliation(s)
- Evana N Abdulaziz
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tristan A Bell
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bazlur Rashid
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Mina L Heacock
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA
| | - Tarik Begic
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mohammad A Yaseen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Antonio J Pierik
- Faculty of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Valentin Cracan
- Redox Biology and Metabolism Laboratory, Scintillon Institute, San Diego, California, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.
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Caldas Nogueira ML, Pastore AJ, Davidson VL. Diversity of structures and functions of oxo-bridged non-heme diiron proteins. Arch Biochem Biophys 2021; 705:108917. [PMID: 33991497 PMCID: PMC8165033 DOI: 10.1016/j.abb.2021.108917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O2 or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.
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Affiliation(s)
- Maria Luiza Caldas Nogueira
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Anthony J Pastore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
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6
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Abstract
Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract. Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon.
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Capeness MJ, Imrie L, Mühlbauer LF, Le Bihan T, Horsfall LE. Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium. MICROBIOLOGY-SGM 2019; 165:1282-1294. [PMID: 31361216 PMCID: PMC7376266 DOI: 10.1099/mic.0.000840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. Desulfovibrio alaskensis is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of D. alaskensis in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of Desulfovibrio and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.
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Affiliation(s)
- Michael J Capeness
- Institute of Quantitative Biology, Biochemistry and Biotechnology/CSEC, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lisa Imrie
- EdinOmics, SynthSys, CH Waddington Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Lukas F Mühlbauer
- Institute of Quantitative Biology, Biochemistry and Biotechnology/CSEC, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Thierry Le Bihan
- Currently: Rapid Novor, Inc., Kitchener, Ontario N2G 4P3, Canada.,EdinOmics, SynthSys, CH Waddington Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Louise E Horsfall
- Institute of Quantitative Biology, Biochemistry and Biotechnology/CSEC, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
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Li Q, Wang J, Xing X, Hu W. Corrosion behavior of X65 steel in seawater containing sulfate reducing bacteria under aerobic conditions. Bioelectrochemistry 2018; 122:40-50. [DOI: 10.1016/j.bioelechem.2018.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/04/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
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9
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The multidomain flavodiiron protein from Clostridium difficile 630 is an NADH:oxygen oxidoreductase. Sci Rep 2018; 8:10164. [PMID: 29977056 PMCID: PMC6033852 DOI: 10.1038/s41598-018-28453-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Flavodiiron proteins (FDPs) are enzymes with a minimal core of two domains: a metallo-β-lactamase-like, harbouring a diiron center, and a flavodoxin, FMN containing, domains. FDPs are O2 or NO reducing enzymes; for many pathogens, they help mitigate the NO produced by the immune system of the host, and aid survival during fluctuating concentrations concentrations of oxygen. FDPs have a mosaic structure, being predicted to contain multiple extra domains. Clostridium difficile, a threatening human pathogen, encodes two FDPs: one with the two canonical domains, and another with a larger polypeptide chain of 843 amino acids, CD1623, with two extra domains, predicted to be a short-rubredoxin-like and an NAD(P)H:rubredoxin oxidoreductase. This multi-domain protein is the most complex FDP characterized thus far. Each of the predicted domains was characterized and the presence of the predicted cofactors confirmed by biochemical and spectroscopic analysis. Results show that this protein operates as a standalone FDP, receiving electrons directly from NADH, and reducing oxygen to water, precluding the need for extra partners. CD1623 displayed negligible NO reductase activity, and is thus considered an oxygen selective FDP, that may contribute to the survival of C. difficile in the human gut and in the environment.
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10
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Bryukhanov AL, Korneeva VA, Dinarieva TY, Karnachuk OV, Netrusov AI, Pimenov NV. Components of antioxidant systems in the cells of aerotolerant sulfate-reducing bacteria of the genus Desulfovibrio (strains A2 and TomC) isolated from metal mining waste. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716060047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Jacques A, Latour JM, Sénèque O. Peptide-based FeS4 complexes: the zinc ribbon fold is unsurpassed to stabilize both the FeII and FeIII states. Dalton Trans 2014; 43:3922-30. [DOI: 10.1039/c3dt53157k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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14
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part I. {Fe(SγCys)4} proteins. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Jacques A, Clémancey M, Blondin G, Fourmond V, Latour JM, Sénèque O. A cyclic peptide-based redox-active model of rubredoxin. Chem Commun (Camb) 2013; 49:2915-7. [DOI: 10.1039/c3cc40517f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Sato Y, Kameya M, Fushinobu S, Wakagi T, Arai H, Ishii M, Igarashi Y. A novel enzymatic system against oxidative stress in the thermophilic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus. PLoS One 2012; 7:e34825. [PMID: 22485188 PMCID: PMC3317640 DOI: 10.1371/journal.pone.0034825] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 03/06/2012] [Indexed: 11/19/2022] Open
Abstract
Rubrerythrin (Rbr) is a non-heme iron protein composed of two distinctive domains and functions as a peroxidase in anaerobic organisms. A novel Rbr-like protein, ferriperoxin (Fpx), was identified in Hydrogenobacter thermophilus and was found not to possess the rubredoxin-like domain that is present in typical Rbrs. Although this protein is widely distributed among aerobic organisms, its function remains unknown. In this study, Fpx exhibited ferredoxin:NADPH oxidoreductase (FNR)-dependent peroxidase activity and reduced both hydrogen peroxide (H(2)O(2)) and organic hydroperoxide in the presence of NADPH and FNR as electron donors. The calculated K(m) and V(max) values of Fpx for organic hydroperoxides were comparable to that for H(2)O(2), demonstrating a multiple reactivity of Fpx towards hydroperoxides. An fpx gene disruptant was unable to grow under aerobic conditions, whereas its growth profiles were comparable to those of the wild-type strain under anaerobic and microaerobic conditions, clearly indicating the indispensability of Fpx as an antioxidant of H. thermophilus in aerobic environments. Structural analysis suggested that domain-swapping occurs in Fpx, and this domain-swapped structure is well conserved among thermophiles, implying the importance of structural stability of domain-swapped conformation for thermal environments. In addition, Fpx was located on a deep branch of the phylogenetic tree of Rbr and Rbr-like proteins. This finding, taken together with the wide distribution of Fpx among Bacteria and Archaea, suggests that Fpx is an ancestral type of Rbr homolog that functions as an essential antioxidant and may be part of an ancestral peroxide-detoxification system.
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Affiliation(s)
- Yuya Sato
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Arai
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaharu Ishii
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Yasuo Igarashi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Barnett JP, Scanlan DJ, Blindauer CA. Fractionation and identification of metalloproteins from a marine cyanobacterium. Anal Bioanal Chem 2012; 402:3371-7. [DOI: 10.1007/s00216-011-5708-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 12/21/2011] [Accepted: 12/29/2011] [Indexed: 11/29/2022]
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18
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Dillard BD, Demick JM, Adams MWW, Lanzilotta WN. A cryo-crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus. J Biol Inorg Chem 2011; 16:949-59. [PMID: 21647777 DOI: 10.1007/s00775-011-0795-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/16/2011] [Indexed: 11/28/2022]
Abstract
High-resolution crystal structures of Pyrococcus furiosus rubrerythrin (PfRbr) in the resting (all-ferrous) state and at time points following exposure of the crystals to hydrogen peroxide are reported. This approach was possible because of the relativity slow turnover of PfRbr at room temperature. To this end, we were able to perform time-dependent peroxide treatment of the fully reduced enzyme, under strictly anaerobic conditions, in the crystalline state. In this work we demonstrate, for the first time, that turnover of a thermophilic rubrerythrin results in approximately 2-Å movement of one iron atom in the diiron site from a histidine to a carboxylate ligand. These results confirm that, despite the domain-swapped architecture, the hyperthermophilic rubrerythrins also utilize the classic combination of iron sites together with redox-dependent iron toggling to selectively reduce hydrogen peroxide over dioxygen. In addition, we have identified previously unobserved intermediates in the reaction cycle and observed structural changes that may explain the enzyme precipitation observed for the all-iron form of PfRbr upon oxidation to the all-ferric state.
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Affiliation(s)
- Bret D Dillard
- Department of Biochemistry and Molecular Biology, The Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
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19
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Pinto AF, Todorovic S, Hildebrandt P, Yamazaki M, Amano F, Igimi S, Romão CV, Teixeira M. Desulforubrerythrin from Campylobacter jejuni, a novel multidomain protein. J Biol Inorg Chem 2010; 16:501-10. [PMID: 21170562 DOI: 10.1007/s00775-010-0749-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
A novel multidomain metalloprotein from Campylobacter jejuni was overexpressed in Escherichia coli, purified, and extensively characterized. This protein is isolated as a homotetramer of 24-kDa monomers. According to the amino acid sequence, each monomer was predicted to contain three structural domains: an N-terminal desulforedoxin-like domain, followed by a four-helix bundle domain harboring a non-sulfur μ-oxo diiron center, and a rubredoxin-like domain at the C-terminus. The three predicted iron sites were shown to be present and were studied by a combination of UV-vis, EPR, and resonance Raman spectroscopies, which allowed the determination of the electronic and redox properties of each site. The protein contains two FeCys(4) centers with reduction potentials of +240 mV (desulforedoxin-like center) and +185 mV (rubredoxin-like center). These centers are in the high-spin configuration in the as-isolated ferric form. The protein further accommodates a μ-oxo-bridged diiron site with reduction potentials of +270 and +235 mV for the two sequential redox transitions. The protein is rapidly reoxidized by hydrogen peroxide and has a significant NADH-linked hydrogen peroxide reductase activity of 1.8 μmol H(2)O(2) min(-1) mg(-1). Owing to its building blocks and its homology to the rubrerythrin family, the protein is named desulforubrerythrin. It represents a novel example of the large diversity of the organization of domains exhibited by this enzyme family.
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Affiliation(s)
- Ana F Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
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20
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Calusinska M, Happe T, Joris B, Wilmotte A. The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. MICROBIOLOGY-SGM 2010; 156:1575-1588. [PMID: 20395274 DOI: 10.1099/mic.0.032771-0] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Among the large variety of micro-organisms capable of fermentative hydrogen production, strict anaerobes such as members of the genus Clostridium are the most widely studied. They can produce hydrogen by a reversible reduction of protons accumulated during fermentation to dihydrogen, a reaction which is catalysed by hydrogenases. Sequenced genomes provide completely new insights into the diversity of clostridial hydrogenases. Building on previous reports, we found that [FeFe] hydrogenases are not a homogeneous group of enzymes, but exist in multiple forms with different modular structures and are especially abundant in members of the genus Clostridium. This unusual diversity seems to support the central role of hydrogenases in cell metabolism. In particular, the presence of multiple putative operons encoding multisubunit [FeFe] hydrogenases highlights the fact that hydrogen metabolism is very complex in this genus. In contrast with [FeFe] hydrogenases, their [NiFe] hydrogenase counterparts, widely represented in other bacteria and archaea, are found in only a few clostridial species. Surprisingly, a heteromultimeric Ech hydrogenase, known to be an energy-converting [NiFe] hydrogenase and previously described only in methanogenic archaea and some sulfur-reducing bacteria, was found to be encoded by the genomes of four cellulolytic strains: Clostridum cellulolyticum, Clostridum papyrosolvens, Clostridum thermocellum and Clostridum phytofermentans.
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Affiliation(s)
- Magdalena Calusinska
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
| | - Thomas Happe
- Lehrstuhl für Biochemie der Pflanzen, AG, Photobiotechnologie, Ruhr - Universität Bochum, 44780 Bochum, Germany
| | - Bernard Joris
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
| | - Annick Wilmotte
- Center for Protein Engineering, University of Liège, Allée de la Chimie 3, B4000 Liège, Belgium
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21
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Wan Y, Zhang D, Liu H, Li Y, Hou B. Influence of sulphate-reducing bacteria on environmental parameters and marine corrosion behavior of Q235 steel in aerobic conditions. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2009.10.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Bevers LE, Hagen WR. One- and two-electron reduction of molybdate reversibly bound to the archaeal tungstate/molybdate transporter WtpA. Dalton Trans 2009:8168-70. [DOI: 10.1039/b914697k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Brioukhanov AL. Nonheme iron proteins as an alternative system of antioxidant defense in the cells of strictly anaerobic microorganisms: A review. APPL BIOCHEM MICRO+ 2008. [DOI: 10.1134/s0003683808040017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Pereira PM, He Q, Xavier AV, Zhou J, Pereira IAC, Louro RO. Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions. Arch Microbiol 2007; 189:451-61. [PMID: 18060664 DOI: 10.1007/s00203-007-0335-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 11/16/2007] [Accepted: 11/20/2007] [Indexed: 12/31/2022]
Abstract
Sulfate-reducing bacteria (SRB) are anaerobes readily found in oxic-anoxic interfaces. Multiple defense pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that SRB are likely to encounter in natural habitats, and the global transcriptomic response was determined. Three hundred and seven genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism was up-regulated, involving the [NiFeSe] hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defense response concentrated on damage repair by metal-free enzymes. These data, together with the down-regulation of the ferric uptake regulator operon, which restricts the availability of iron, and the lack of response of the peroxide-sensing regulator operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.
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Affiliation(s)
- Patrícia M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Lisbon, Portugal
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25
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Kawasaki S, Ono M, Watamura Y, Sakai Y, Satoh T, Arai T, Satoh J, Niimura Y. An O2-inducible rubrerythrin-like protein, rubperoxin, is functional as a H2O2 reductase in an obligatory anaerobe Clostridium acetobutylicum. FEBS Lett 2007; 581:2460-4. [PMID: 17485086 DOI: 10.1016/j.febslet.2007.04.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 04/15/2007] [Accepted: 04/16/2007] [Indexed: 11/21/2022]
Abstract
Clostridium acetobutylicum, an obligatory anaerobe, is able to grow microoxically with the accumulation of two functionally unknown O2-induced proteins identified by two-dimensional electrophoresis. One was determined to be a novel type rubrerythrin-like protein, named rubperoxin (Rpr) in this study, that conserves one rubredoxin-type Fe(SCys)(4) site per polypeptide in the N-terminus. Recombinant rubperoxin expressed in E. coli purified in its oxidized form is a dimer with optical absorption maxima at 492, 377, and 277nm. Reduced rubperoxin is rapidly and fully oxidized by a half molar ratio of H2O2 per mole protein, and slowly oxidized by t-butyl hydroperoxide and O2. Cell-free extracts from microoxically grown cells efficiently reduce rubperoxin when NAD(P)H is used as the electron donor (preferentially reduced by NADH). These results strongly suggest that rubperoxin is involved in NAD(P)H-dependent H2O2 detoxification in vivo.
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Affiliation(s)
- Shinji Kawasaki
- Department of Biosciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.
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26
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Dolla A, Fournier M, Dermoun Z. Oxygen defense in sulfate-reducing bacteria. J Biotechnol 2006; 126:87-100. [PMID: 16713001 DOI: 10.1016/j.jbiotec.2006.03.041] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 02/27/2006] [Accepted: 03/29/2006] [Indexed: 11/24/2022]
Abstract
Sulfate-reducing bacteria (SRB) are strict anaerobes that are often found in biotopes where oxic conditions can temporarily exist. The bacteria have developed several defense strategies in order to survive exposure to oxygen. These strategies includes peculiar behaviors in the presence of oxygen, like aggregation or aerotaxis, and enzymatic systems dedicated to the reduction and the elimination of oxygen and its reactive species. Sulfate-reducing bacteria, and specially Desulfovibrio species, possess a variety of enzymes acting together to achieve an efficient defense against oxidative stress. The function and occurrence of these enzymatic systems are described.
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Affiliation(s)
- Alain Dolla
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS - 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.
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27
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Kurtz DM. Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin. J Inorg Biochem 2006; 100:679-93. [PMID: 16504301 DOI: 10.1016/j.jinorgbio.2005.12.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
The Fenton or Fenton-type reaction between aqueous ferrous ion and hydrogen peroxide generates a highly oxidizing species, most often formulated as hydroxyl radical or ferryl ([Fe(IV)O](2+)). Intracellular Fenton-type chemistry can be lethal if not controlled. Nature has, therefore, evolved enzymes to scavenge superoxide and hydrogen peroxide, the reduced dioxygen species that initiate intracellular Fenton-type chemistry. Two such enzymes found predominantly in air-sensitive bacteria and archaea, superoxide reductase (SOR) and rubrerythrin (Rbr), functioning as a peroxidase (hydrogen peroxide reductase), contain non-heme iron. The iron coordination spheres in these enzymes contain five or six protein ligands from His and Glu residues, and, in the case of SOR, a Cys residue. SOR contains a mononuclear active site that is designed to protonate and rapidly expel peroxide generated as a product of the enzymatic reaction. The ferrous SOR reacts adventitiously but relatively slowly (several seconds to a few minutes) with exogenous hydrogen peroxide, presumably in a Fenton-type reaction. The diferrous active site of Rbr reacts more rapidly with hydrogen peroxide but can divert Fenton-type reactions towards the two-electron reduction of hydrogen peroxide to water. Proximal aromatic residues may function as radical sinks for Fenton-generated oxidants. Fenton-initiated damage to these iron active sites may become apparent only under extremely oxidizing intracellular conditions.
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Affiliation(s)
- Donald M Kurtz
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA.
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28
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Abstract
Molecular paramagnetism pervades the bioinorganic chemistry of V, Mn, Fe, Co, Ni, Cu, Mo, W, and of a number of non-biological transition elements. To date we can look back at half a century of fruitful EPR studies on metalloproteins, and against this background evaluate the significance of modern EPR spectroscopy from the perspective of a biochemist, making a distinction between conventional continuous wave X-band spectroscopy as a reliable work horse with broad, established applicability even on crude preparations, vs. a diffuse set of "advanced EPR" technologies whose practical application typically calls for narrowly focused research hypotheses and very high quality samples. The type of knowledge on metalloproteins that is readily obtainable with EPR spectroscopy, is explained with illustrative examples, as is the relation between experimental complexity and the spin value of the system.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands.
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29
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Iyer RB, Silaghi-Dumitrescu R, Kurtz DM, Lanzilotta WN. High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins. J Biol Inorg Chem 2005; 10:407-16. [PMID: 15895271 DOI: 10.1007/s00775-005-0650-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Accepted: 04/13/2005] [Indexed: 10/25/2022]
Abstract
High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-A movement of one iron (Fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([Fe2(II),Fe1(III)]) to diferrous states, even at cryogenic temperatures. This Glu<-->His ligand "toggling" of one iron, which also occurs in DvRbr, thus, appears to be a characteristic feature of Rbr-type diiron sites. Unique features of DvNgr revealed by these structures include redox-induced flipping of a peptide carbonyl that reversibly forms a hydrogen bond to the histidine ligand to Fe1 of the diiron site, an intra-subunit proximal orientation of the rubredoxin-(Rub)-like and diiron domains, and an electron transfer pathway consisting of six covalent and two hydrogen bonds connecting the Rub-like iron with Fe2 of the diiron site. This pathway can account for DvNgr's relatively rapid peroxidase turnover. The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen.
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Affiliation(s)
- Ramesh B Iyer
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
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30
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Jin S, Kurtz DM, Liu ZJ, Rose J, Wang BC. Displacement of iron by zinc at the diiron site of Desulfovibrio vulgaris rubrerythrin: X-ray crystal structure and anomalous scattering analysis. J Inorg Biochem 2005; 98:786-96. [PMID: 15134924 DOI: 10.1016/j.jinorgbio.2004.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 01/09/2004] [Accepted: 01/15/2004] [Indexed: 10/26/2022]
Abstract
X-ray crystal structures of recombinant Desulfovibrio (D.) vulgaris rubrerythrin (Rbr) have shown a diiron site, whereas the crystal structure of Rbr "as-isolated" from D. vulgaris was reported to contain a mixed Zn,Fe binuclear site. To investigate the possibility that zinc had displaced iron during isolation or crystallization of the "as-isolated" D. vulgaris Rbr, the X-ray crystal structure of recombinant D. vulgaris all-iron Rbr that had been incubated with excess zinc sulfate prior to crystallization, yielding a protein labeled Zn,FeRbr, was solved. Analysis of the anomalous scattering data obtained at two different wavelengths showed that zinc had displaced a significant proportion of iron from both iron centers of the diiron site, and that no iron had been displaced from the [Fe(SCys)(4)] site. UV-visible absorption spectra of the redissolved Zn,FeRbr crystals showed 30-40% retention of oxo-bridged diferric sites, and the redissolved crystals had 37% of the peroxidase specific activity of the starting all-iron Rbr, which, together with the crystallographic results, indicate a predominant mixture of Fe1,Fe2 and Zn1,Zn2 sites. The structure of the Zn(Fe)1,Fe(Zn)2 binuclear site in the Zn,FeRbr crystals was very similar to that of the Zn,Fe binuclear site reported for the "as-isolated" D. vulgaris Rbr, including tetrahedral four-coordination at the Zn(Fe)1 site. The diiron sites in the recombinant Zn,FeRbr crystals were likely at least partially reduced during synchrotron irradiation. Our results suggest that the mixed-metal binuclear site reported for the "as-isolated" D. vulgaris Rbr could be due to displacement of iron from a native diiron site by adventitious zinc during isolation and/or crystallization, and that reduced diiron and dizinc sites can adopt very similar structures in Rbr.
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Affiliation(s)
- Shi Jin
- Department of Chemistry, Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
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31
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Weinberg MV, Jenney FE, Cui X, Adams MWW. Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase. J Bacteriol 2004; 186:7888-95. [PMID: 15547260 PMCID: PMC529063 DOI: 10.1128/jb.186.23.7888-7895.2004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrerythrin was purified by multistep chromatography under anaerobic, reducing conditions from the hyperthermophilic archaeon Pyrococcus furiosus. It is a homodimer with a molecular mass of 39.2 kDa and contains 2.9 +/- 0.2 iron atoms per subunit. The purified protein had peroxidase activity at 85 degrees C using hydrogen peroxide with reduced P. furiosus rubredoxin as the electron donor. The specific activity was 36 micromol of rubredoxin oxidized/min/mg with apparent K(m) values of 35 and 70 microM for hydrogen peroxide and rubredoxin, respectively. When rubrerythrin was combined with rubredoxin and P. furiosus NADH:rubredoxin oxidoreductase, the complete system used NADH as the electron donor to reduce hydrogen peroxide with a specific activity of 7.0 micromol of H(2)O(2) reduced/min/mg of rubrerythrin at 85 degrees C. Strangely, as-purified (reduced) rubrerythrin precipitated when oxidized by either hydrogen peroxide, air, or ferricyanide. The gene (PF1283) encoding rubrerythrin was expressed in Escherichia coli grown in medium with various metal contents. The purified recombinant proteins each contained approximately three metal atoms/subunit, ranging from 0.4 Fe plus 2.2 Zn to 1.9 Fe plus 1.2 Zn, where the metal content of the protein depended on the metal content of the E. coli growth medium. The peroxidase activities of the recombinant forms were proportional to the iron content. P. furiosus rubrerythrin is the first to be characterized from a hyperthermophile or from an archaeon, and the results are the first demonstration that this protein functions in an NADH-dependent, hydrogen peroxide:rubredoxin oxidoreductase system. Rubrerythrin is proposed to play a role in the recently defined anaerobic detoxification pathway for reactive oxygen species.
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Affiliation(s)
- Michael V Weinberg
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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32
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Fournier M, Zhang Y, Wildschut JD, Dolla A, Voordouw JK, Schriemer DC, Voordouw G. Function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris hildenborough. J Bacteriol 2003; 185:71-9. [PMID: 12486042 PMCID: PMC141827 DOI: 10.1128/jb.185.1.71-79.2003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two mutant strains of Desulfovibrio vulgaris Hildenborough lacking either the sod gene for periplasmic superoxide dismutase or the rbr gene for rubrerythrin, a cytoplasmic hydrogen peroxide (H(2)O(2)) reductase, were constructed. Their resistance to oxidative stress was compared to that of the wild-type and of a sor mutant lacking the gene for the cytoplasmic superoxide reductase. The sor mutant was more sensitive to exposure to air or to internally or externally generated superoxide than was the sod mutant, which was in turn more sensitive than the wild-type strain. No obvious oxidative stress phenotype was found for the rbr mutant, indicating that H(2)O(2) resistance may also be conferred by two other rbr genes in the D. vulgaris genome. Inhibition of Sod activity by azide and H(2)O(2), but not by cyanide, indicated it to be an iron-containing Sod. The positions of Fe-Sod and Sor were mapped by two-dimensional gel electrophoresis (2DE). A strong decrease of Sor in continuously aerated cells, indicated by 2DE, may be a critical factor in causing cell death of D. vulgaris. Thus, Sor plays a key role in oxygen defense of D. vulgaris under fully aerobic conditions, when superoxide is generated mostly in the cytoplasm. Fe-Sod may be more important under microaerophilic conditions, when the periplasm contains oxygen-sensitive, superoxide-producing targets.
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Affiliation(s)
- Marjorie Fournier
- Department of Biological Sciences. Department of Biochemistry and Molecular Biology, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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33
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Sztukowska M, Bugno M, Potempa J, Travis J, Kurtz DM. Role of rubrerythrin in the oxidative stress response of Porphyromonas gingivalis. Mol Microbiol 2002; 44:479-88. [PMID: 11972784 DOI: 10.1046/j.1365-2958.2002.02892.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rubrerythrins are non-haem iron proteins that have been implicated in oxidative stress protection in anaerobic bacteria and archaea. However, up to now, this role has not been confirmed directly by inactivation of a rubrerythrin gene. Here we report generation of an rbr- mutant of Porphyromonas gingivalis, an obligately anaerobic gingival pathogenic bacterium. Characterization of the rbr- strain clearly showed that P. gingivalis produces a rubrerythrin-like protein that is absent in the rbr- strain, and that the P. gingivalis rbr- strain is more dioxygen- and hydrogen peroxide-sensitive than the wild type. The latter conclusion is based on two independent results, namely, deeper no-growth zones upon diffusion of the oxidants through soft agar culture tubes and growth impairment of liquid cultures exposed to the oxidants. A same-site rbr+ revertant showed increased hydrogen peroxide and dioxygen resistance relative to the rbr- strain. Transcription of the P. gingivalis rubrerythrin gene is induced above its constitutive anaerobic level in response to dioxygen or hydrogen peroxide exposures. Purified rubrerythrins from other organisms have been shown to catalyse reduction of hydrogen peroxide, while showing relatively sluggish reaction with dioxygen and little or no catalase or superoxide dismutase activities. Porphyromonas gingivalis contains a superoxide dismutase but lacks catalase and haem peroxidases. We therefore suggest that rubrerythrin provides oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide.
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Affiliation(s)
- Maryta Sztukowska
- Institute of Molecular Biology, Jagiellonian University, 31-120 Krakow, Poland
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34
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Coulter ED, Kurtz DM. A role for rubredoxin in oxidative stress protection in Desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase. Arch Biochem Biophys 2001; 394:76-86. [PMID: 11566030 DOI: 10.1006/abbi.2001.2531] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Desulfovibrio vulgaris rubredoxin, which contains a single [Fe(SCys)4] site, is shown to be a catalytically competent electron donor to two enzymes from the same organism, namely, rubrerythrin and two-iron superoxide reductase (a.k.a. rubredoxin oxidoreductase or desulfoferrodoxin). These two enzymes have been implicated in catalytic reduction of hydrogen peroxide and superoxide, respectively, during periods of oxidative stress in D. vulgaris, but their proximal electron donors had not been characterized. We further demonstrate the incorrectness of a previous report that rubredoxin is not an electron donor to the superoxide reductase and describe convenient assays for demonstrating the catalytic competence of all three proteins in their respective functions. Rubrerythrin is shown to be an efficient rubredoxin peroxidase in which the rubedoxin:hydrogen peroxide redox stoichiometry is 2:1 mol:mol. Using spinach ferredoxin-NADP+ oxidoreductase (FNR) as an artificial, but proficient, NADPH:rubredoxin reductase, rubredoxin was further found to catalyze rapid and complete reduction of all Fe3+ to Fe2+ in rubrerythrin by NADPH under anaerobic conditions. The combined system, FNR/rubredoxin/rubrerythrin, was shown to function as a catalytically competent NADPH peroxidase. Another small rubredoxin-like D. vulgaris protein, Rdl, could not substitute for rubredoxin as a peroxidase substrate of rubrerythrin. Similarly, D. vulgaris rubredoxin was demonstrated to efficiently catalyze reduction of D. vulgaris two-iron superoxide reductase and, when combined with FNR, to function as an NADPH:superoxide oxidoreductase. We suggest that, during periods of oxidative stress, rubredoxin could divert electron flow from the electron transport chain of D. vulgaris to rubrerythrin and superoxide reductase, thereby simultaneously protecting autoxidizable redox enzymes and lowering intracellular hydrogen peroxide and superoxide levels.
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Affiliation(s)
- E D Coulter
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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Das A, Coulter ED, Kurtz DM, Ljungdahl LG. Five-gene cluster in Clostridium thermoaceticum consisting of two divergent operons encoding rubredoxin oxidoreductase- rubredoxin and rubrerythrin-type A flavoprotein- high-molecular-weight rubredoxin. J Bacteriol 2001; 183:1560-7. [PMID: 11160086 PMCID: PMC95040 DOI: 10.1128/jb.183.5.1560-1567.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A five-gene cluster encoding four nonheme iron proteins and a flavoprotein from the thermophilic anaerobic bacterium Clostridium thermoaceticum (Moorella thermoacetica) was cloned and sequenced. Based on analysis of deduced amino acid sequences, the genes were identified as rub (rubredoxin), rbo (rubredoxin oxidoreductase), rbr (rubrerythrin), fprA (type A flavoprotein), and a gene referred to as hrb (high-molecular-weight rubredoxin). Northern blot analysis demonstrated that the five-gene cluster is organized as two subclusters, consisting of two divergently transcribed operons, rbr-fprA-hrb and rbo-rub. The rbr, fprA, and rub genes were expressed in Escherichia coli, and their encoded recombinant proteins were purified. The molecular masses, UV-visible absorption spectra, and cofactor contents of the recombinant rubrerythrin, rubredoxin, and type A flavoprotein were similar to those of respective homologs from other microorganisms. Antibodies raised against Desulfovibrio vulgaris Rbr reacted with both native and recombinant Rbr from C. thermoaceticum, indicating that this protein was expressed in the native organism. Since Rbr and Rbo have been recently implicated in oxidative stress protection in several anaerobic bacteria and archaea, we suggest a similar function of these proteins in oxygen tolerance of C. thermoaceticum.
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Affiliation(s)
- A Das
- Center for Biological Resource Recovery and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA
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36
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Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM. Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system. J Bacteriol 2001; 183:101-8. [PMID: 11114906 PMCID: PMC94855 DOI: 10.1128/jb.183.1.101-108.2001] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2000] [Accepted: 10/11/2000] [Indexed: 11/20/2022] Open
Abstract
Evidence is presented for an alternative to the superoxide dismutase (SOD)-catalase oxidative stress defense system in Desulfovibrio vulgaris (strain Hildenborough). This alternative system consists of the nonheme iron proteins, rubrerythrin (Rbr) and rubredoxin oxidoreductase (Rbo), the product of the rbo gene (also called desulfoferrodoxin). A Deltarbo strain of D. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. Unlike Rbo, expression of plasmid-borne Rbr failed to restore the aerobic growth of a SOD-deficient strain of Escherichia coli. Conversely, plasmid-borne expression of two different Rbrs from D. vulgaris increased the viability of a catalase-deficient strain of E. coli that had been exposed to hydrogen peroxide whereas Rbo actually decreased the viability. A previously undescribed D. vulgaris gene was found to encode a protein having 50% sequence identity to that of E. coli Fe-SOD. This gene also encoded an extended N-terminal sequence with high homologies to export signal peptides of periplasmic redox proteins. The SOD activity of D. vulgaris is not affected by the absence of Rbo and is concentrated in the periplasmic fraction of cell extracts. These results are consistent with a superoxide reductase rather than SOD activity of Rbo and with a peroxidase activity of Rbr. A joint role for Rbo and Rbr as a novel cytoplasmic oxidative stress protection system in D. vulgaris and other anaerobic microorganisms is proposed.
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Affiliation(s)
- H L Lumppio
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Archer M, Carvalho AL, Teixeira S, Moura I, Moura JJ, Rusnak F, Romão MJ. Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein. Protein Sci 1999; 8:1536-45. [PMID: 10422844 PMCID: PMC2144384 DOI: 10.1110/ps.8.7.1536] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Desulforedoxin (Dx), isolated from the sulfate reducing bacterium Desulfovibrio gigas, is a small homodimeric (2 x 36 amino acids) protein. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulfur atoms, a metal center similar to that found in rubredoxin (Rd) type proteins. The simplicity of the active center in Dx and the possibility of replacing the iron by other metals make this protein an attractive case for the crystallographic analysis of metal-substituted derivatives. This study extends the relevance of Dx to the bioinorganic chemistry field and is important to obtain model compounds that can mimic the four sulfur coordination of metals in biology. Metal replacement experiments were carried out by reconstituting the apoprotein with In3+, Ga3+, Cd2+, Hg2+, and Ni2+ salts. The In3+ and Ga3+ derivatives are isomorphous with the iron native protein; whereas Cd2+, Hg2+, and Ni2+ substituted Dx crystallized under different experimental conditions, yielding two additional crystal morphologies; their structures were determined by the molecular replacement method. A comparison of the three-dimensional structures for all metal derivatives shows that the overall secondary and tertiary structures are maintained, while some differences in metal coordination geometry occur, namely, bond lengths and angles of the metal with the sulfur ligands. These data are discussed in terms of the entatic state theory.
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Affiliation(s)
- M Archer
- Departamento de Química, Centro de Química Fina e Biotechnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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39
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Romão CV, Liu MY, Le Gall J, Gomes CM, Braga V, Pacheco I, Xavier AV, Teixeira M. The superoxide dismutase activity of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:438-43. [PMID: 10215854 DOI: 10.1046/j.1432-1327.1999.00278.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Desulfoferrodoxin (Dfx), a small iron protein containing two mononuclear iron centres (designated centre I and II), was shown to complement superoxide dismutase (SOD) deficient mutants of Escherichia coli [Pianzzola, M.J., Soubes M. & Touati, D. (1996) J. Bacteriol. 178, 6736-6742]. Furthermore, neelaredoxin, a protein from Desulfovibrio gigas containing an iron site similar to centre II of Dfx, was recently shown to have a significant SOD activity [Silva, G., Oliveira, S., Gomes, C.M., Pacheco, I., Liu, M.Y., Xavier, A.V., Teixeira, M., Le Gall, J. & Rodrigues-Pousada, C. (1999) Eur. J. Biochem. 259, 235-243]. Thus, the SOD activity of Dfx isolated from the sulphate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 was studied. The protein exhibits a SOD activity of 70 U x mg-1, which increases approximately 2.5-fold upon incubation with cyanide. Cyanide binds specifically to Dfx centre II, yielding a low-spin iron species with g-values at 2.27 (g perpendicular) and 1.96 (g parallel). Upon reaction of fully oxidized Dfx with the superoxide generating system xanthine/xanthine oxidase, Dfx centres I and II become partially reduced, suggesting that Dfx operates by a redox cycling mechanism, similar to those proposed for other SODs. Evidence for another SOD in D. desulfuricans is also presented - this enzyme is inhibited by cyanide, and N-terminal sequence data strongly indicates that it is an analogue to Cu,Zn-SODs isolated from other sources. This is the first indication that a Cu-containing protein may be present in a sulphate-reducing bacterium.
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Affiliation(s)
- C V Romão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Partugal
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40
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Abstract
P. S. Alban et al. (J. Appl. Microbiol. (1998) 85, 875-882) reported that a mutant H2O2-resistant strain of Spirullum (S.) volutans showed constitutive overexpression of a protein whose amino acid sequence and molecular weight closely resembled that of a subunit of rubrerythrin, a non-heme iron protein with no known function. They also reported that the mutant strain, but not the wild-type, showed NADH peroxidase activity. Here we demonstrate that rubrerythrin and nigerythrin from Desulfovibrio vulgaris and rubrerythrin from Clostridium perfringens show NADH peroxidase activities in an in vitro system containing NADH, hydrogen peroxide, and a bacterial NADH oxidoreductase. The peroxidase specific activities of the rubrerythrins with the "classical" heme peroxidase substrate, o-dianisidine, are many orders of magnitude lower than that of horseradish peroxidase. These results are consistent with the phenotype of the H2O2-resistant strain of S. volutans. The reaction of reduced (i.e., all-ferrous) rubrerythrin with excess O2 takes several minutes, whereas the anaerobic reaction of reduced rubrerythrin with hydrogen peroxide is on the millisecond time scale and results in full oxidation of all iron centers to their ferric states. Rubrerythrins could, thus, function as the terminal components of NADH peroxidases in air-sensitive bacteria and archaea.
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Affiliation(s)
- E D Coulter
- Department of Chemistry, Center for Metalloenzyme Studies, University of Georgia, Athens 30602, USA
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41
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Simple and Complex Iron-Sulfur Proteins in Sulfate Reducing Bacteria. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60083-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Guigliarelli B, Bertrand P. Application of EPR Spectroscopy to the Structural and Functional Study of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Re-engineering the diiron site in rubrerythrin towards that in ribonucleotide reductase. Inorganica Chim Acta 1997. [DOI: 10.1016/s0020-1693(97)05662-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Lumppio HL, Shenvi NV, Garg RP, Summers AO, Kurtz DM. A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough). J Bacteriol 1997; 179:4607-15. [PMID: 9226272 PMCID: PMC179298 DOI: 10.1128/jb.179.14.4607-4615.1997] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Rubrerythrin is a nonheme iron protein of unknown function isolated from Desulfovibrio vulgaris (Hildenborough). We have sequenced a 3.3-kbp Sal1 fragment of D. vulgaris chromosomal DNA containing the rubrerythrin gene, rbr, identified additional open reading frames (ORFs) adjacent to rbr, and shown that these ORFs are part of a transcriptional unit containing rbr. One ORF, designated fur, lies just upstream of rbr and encodes a 128-amino-acid-residue protein which shows homology to Fur (ferric uptake regulatory) proteins from other purple bacteria. The other ORF, designated rdl, lies just downstream of rbr and encodes a 74-residue protein with significant sequence homology to rubredoxins but with a different number and spacing of cysteine residues. Overexpression of rdl in Escherichia coli yielded a protein, Rdl, which has spectroscopic properties and iron content consistent with one Fe3+(SCys)4 site per polypeptide but is clearly distinct from both rubrerythrin and a related protein, nigerythrin. Northern analysis indicated that fur, rbr, and rdl were each present on a transcript of 1.3 kb; i.e., these three genes are cotranscribed. Because D. vulgaris nigerythrin appears to be closely related to rubrerythrin, and its function is also unknown, we cloned and sequenced the gene encoding nigerythrin, ngr. The amino acid sequence of nigerythrin is 33% identical to that of rubrerythrin, and all residues which furnish iron ligands to both the FeS4 and diiron-oxo sites in rubrerythrin are conserved in nigerythrin. Despite the close resemblance of these two proteins, ngr was found to be no closer than 7 kb to rbr on the D. vulgaris chromosome, and Northern analysis showed that, in contrast to rbr, ngr is not cotranscribed with other genes. Possible redox-linked functions for rubrerythrin and nigerythrin in iron homeostasis are proposed.
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Affiliation(s)
- H L Lumppio
- Department of Microbiology and Center for Metalloenzyme Studies, University of Georgia, Athens 30602, USA
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45
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Pulver SC, Froland WA, Lipscomb JD, Solomon EI. Ligand Field Circular Dichroism and Magnetic Circular Dichroism Studies of Component B and Substrate Binding to the Hydroxylase Component of Methane Monooxygenase. J Am Chem Soc 1997. [DOI: 10.1021/ja962854i] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sabine Coates Pulver
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Wayne A. Froland
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Edward I. Solomon
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
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46
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Lehmann Y, Meile L, Teuber M. Rubrerythrin from Clostridium perfringens: cloning of the gene, purification of the protein, and characterization of its superoxide dismutase function. J Bacteriol 1996; 178:7152-8. [PMID: 8955396 PMCID: PMC178627 DOI: 10.1128/jb.178.24.7152-7158.1996] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The food-borne pathogen Clostridium perfringens, which is an obligate anaerobe, showed growth under conditions of oxidative stress. In protein extracts we looked for superoxide dismutase (SOD) activities which might scavenge highly toxic superoxide radicals evolving under such stress conditions. Using the classical assay to detect SOD activity on gels after electrophoresis of C. perfringens proteins, we obtained a pattern of three major bands indicating SOD activity. The protein representing the brightest band was purified by three chromatographic steps. On the basis of 20 amino acids determined from the N terminus of the protein, we designed a degenerate oligonucleotide probe to isolate the corresponding gene. We finally sequenced an open reading frame of 195 amino acids (molecular mass, 21,159 Da) with a strong homology to the Desulfovibrio vulgaris rubrerythrin; therefore, we assumed to have cloned a rubrerythrin gene from C. perfringens, and we named it rbr. The C-terminal region of the newly detected rubrerythrin from C. perfringens contains a characteristic non-heme, non-sulfur iron-binding site -Cys-X-X-Cys-(X)12-Cys-X-X-Cys- similar to that found in rubrerythrin from D. vulgaris. In addition, three -Glu-X-X-His- sequences could represent diiron binding domains. We observed SOD activity in extracts of Escherichia coli strains containing the recombinant rbr gene from C. perfringens. A biological function of rubrerythrin as SOD was confirmed with the functional complementation by the rbr gene of an E. coli mutant strain lacking SOD activity. We therefore suppose that rubrerythrin plays a role as a scavenger of oxygen radicals.
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Affiliation(s)
- Y Lehmann
- Laboratorium für Lebensmittel-Mikrobiologie, Institut für Lebensmittelwissenschaften, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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47
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Stephens PJ, Jollie DR, Warshel A. Protein Control of Redox Potentials of Ironminus signSulfur Proteins. Chem Rev 1996; 96:2491-2514. [PMID: 11848834 DOI: 10.1021/cr950045w] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. J. Stephens
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
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48
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deMaré F, Kurtz DM, Nordlund P. The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. NATURE STRUCTURAL BIOLOGY 1996; 3:539-46. [PMID: 8646540 DOI: 10.1038/nsb0696-539] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have determined the structure of rubrerythrin, a non-haem iron protein from the anaerobic sulphate-reducing bacterium, Desulfovibrio vulgaris (Hildenborough), by X-ray crystallography. The structure reveals a tetramer of two-domain subunits. Each subunit contains a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like FeS4 domain. The diiron-oxo site contains a larger number of carboxylate ligands and a higher degree of solvent exposure than do those in other diiron-oxo proteins. The four-helix bundle of rubrerythrin closely resembles those of the ferritin and bacterioferritin subunits, suggesting a relationship among these proteins-consistent with the recently demonstrated ferroxidase activity of rubrerythrin.
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Affiliation(s)
- F deMaré
- Department of Molecular Biology, Stockholm University, Sweden
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49
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Marritt SJ, Farrar JA, Breton JL, Hagen WR, Thomson AJ. Characterization of the prismane protein from Desulfovibrio vulgaris (Hildenborough) by low-temperature magnetic circular dichroic spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 232:501-5. [PMID: 7556199 DOI: 10.1111/j.1432-1033.1995.501zz.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The prismane protein of Desulfovibrio vulgaris (Hildenborough) contains a putative [6Fe-6S] cluster. This novel iron-sulfur cluster has been characterized here by magnetic circular dichroism (MCD) spectroscopy. Three paramagnetic redox states of the cluster, [6Fe-6S]5+, [6Fe-6S]4+ and [6Fe-6S]3+, each show a distinctive low-temperature MCD spectrum which is unlike that observed for any other iron-sulfur clusters. Magnetization data for the prismane protein in these three redox states indicate ground state spins that are in accordance with previous EPR assignments. For the protein as isolated, with the [6Fe-6S]5+ form of the cluster, magnetizations show an exceptionally steep initial slope that can be fit to a ground state of spin S = 9/2. For the semi-reduced protein, the cluster in the [6Fe-6S]4+ form, magnetizations show an initial slope characteristic for a ground state of spin S = 4. For the dithionite-reduced protein, with the [6Fe-6S]3+ form of the cluster, magnetizations are typical for a ground state of spin S = 1/2.
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Affiliation(s)
- S J Marritt
- Department of Biochemistry, Wageningen Agricultural University, The Netherlands
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50
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Gupta N, Bonomi F, Kurtz DM, Ravi N, Wang DL, Huynh BH. Recombinant Desulfovibrio vulgaris rubrerythrin. Isolation and characterization of the diiron domain. Biochemistry 1995; 34:3310-8. [PMID: 7880826 DOI: 10.1021/bi00010a021] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The gene encoding Desulfovibrio (D.) vulgaris rubrerythrin (Prickril, B. C., Kurtz, D. M., Jr., LeGall, J., & Voordouw, G. (1991) Biochemistry 30, 1118), a protein of unknown function containing both FeS4 and (mu-oxo)diiron sites, was cloned and overexpressed in Escherichia coli. Upon cell lysis, the overexpressed protein was found in an insoluble form deficient in iron. Iron was incorporated in vitro by dissolving the protein in 3 M guanidinium chloride, adding Fe(II) anaerobically and diluting the denaturant. This recombinant rubrerythrin was found to have properties very similar to those of rubrerythrin isolated from D. vulgaris, except that the recombinant rubrerythrin contained six rather than four (or five) iron atoms per 44 kDa homodimer. Analyses of UV-vis, Mössbauer, and EPR spectra showed that the six iron atoms in recombinant rubrerythrin are organized as two FeS4 and two (mu-oxo/hydroxo)diiron sites. In order to allow examination of the diiron sites in the absence of the FeS4 sites, a truncated gene encoding the N-terminal 152 residues of D. vulgaris rubrerythrin was also cloned and overexpressed as an insoluble protein in E. coli, and iron was incorporated by a procedure analogous to that for recombinant rubrerythrin. This so-called "chopped" rubrerythrin (CRr) was found to consist of an approximately 35 kDa homodimer containing four iron atoms. Spectroscopic characterization indicated that the four iron atoms in CRr are organized as two diiron sites, the majority of which closely resemble the (mu-oxo)diiron(III) sites in E. coli ribonucleotide reductase R2 protein, and a minor fraction of which resemble the mixed-valent diiron(II,III) site in methane monooxygenase hydroxylase.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- N Gupta
- Department of Chemistry, University of Georgia, Athens 30602
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