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Andrés CMC, Pérez de la Lastra JM, Andrés Juan C, Plou FJ, Pérez-Lebeña E. Superoxide Anion Chemistry-Its Role at the Core of the Innate Immunity. Int J Mol Sci 2023; 24. [PMID: 36768162 DOI: 10.3390/ijms24031841] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Classically, superoxide anion O2•- and reactive oxygen species ROS play a dual role. At the physiological balance level, they are a by-product of O2 reduction, necessary for cell signalling, and at the pathological level they are considered harmful, as they can induce disease and apoptosis, necrosis, ferroptosis, pyroptosis and autophagic cell death. This revision focuses on understanding the main characteristics of the superoxide O2•-, its generation pathways, the biomolecules it oxidizes and how it may contribute to their modification and toxicity. The role of superoxide dismutase, the enzyme responsible for the removal of most of the superoxide produced in living organisms, is studied. At the same time, the toxicity induced by superoxide and derived radicals is beneficial in the oxidative death of microbial pathogens, which are subsequently engulfed by specialized immune cells, such as neutrophils or macrophages, during the activation of innate immunity. Ultimately, this review describes in some depth the chemistry related to O2•- and how it is harnessed by the innate immune system to produce lysis of microbial agents.
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Desbois A, Valton J, Moreau Y, Torelli S, Nivière V. Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies. Phys Chem Chem Phys 2021; 23:4636-4645. [PMID: 33527107 DOI: 10.1039/d0cp03898a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superoxide reductases (SORs) are mononuclear non-heme iron enzymes involved in superoxide radical detoxification in some microorganisms. Their atypical active site is made of an iron atom pentacoordinated by four equatorial nitrogen atoms from histidine residues and one axial sulfur atom from a cysteinate residue, which plays a central role in catalysis. In most SORs, the residue immediately following the cysteinate ligand is an asparagine, which belongs to the second coordination sphere and is expected to have a critical influence on the properties of the active site. In this work, in order to investigate the role of this asparagine residue in the Desulfoarculus baarsii enzyme (Asn117), we carried out, in comparison with the wild-type enzyme, absorption and resonance Raman (RR) studies on a SOR mutant in which Asn117 was changed into an alanine. RR analysis was developed in order to assign the different bands using excitation in the (Cys116)-S-→ Fe3+ charge transfer band. By investigating the correlation between the (Cys116)-S-→ Fe3+ charge transfer band maximum with the frequency of each RR band in different SOR forms, we assessed the contribution of the ν(Fe-S) vibration among the different RR bands. The data showed that Asn117, by making hydrogen bond interactions with Lys74 and Tyr76, allows a rigidification of the backbone of the Cys116 ligand, as well as that of the neighboring residues Ile118 and His119. Such a structural role of Asn117 has a deep impact on the S-Fe bond. It results in a tight control of the H-bond distance between the Ile118 and His119 NH peptidic moiety with the cysteine sulfur ligand, which in turn enables fine-tuning of the S-Fe bond strength, an essential property for the SOR active site. This study illustrates the intricate roles of second coordination sphere residues to adjust the ligand to metal bond properties in the active site of metalloenzymes.
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Affiliation(s)
- Alain Desbois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette Cedex, France
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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4
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Abstract
Using superoxide reductase as a model system, a computational approach reveals how histidine tautomerism tunes the redox properties of metalloenzymes to enable their catalytic function. Inspired by these experimentally inaccessible insights, non-canonical histidine congeners are introduced as new versatile tools for the rational engineering of biological transition metal sites.
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Affiliation(s)
- Marius Horch
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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6
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Hölzl SM, Altmann PJ, Kück JW, Kühn FE. Speciation in iron epoxidation catalysis: A perspective on the discovery and role of non-heme iron(III)-hydroperoxo species in iron-catalyzed oxidation reactions. Coord Chem Rev 2017; 352:517-36. [DOI: 10.1016/j.ccr.2017.09.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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David R, Jamet H, Nivière V, Moreau Y, Milet A. Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study. J Chem Theory Comput 2017; 13:2987-3004. [DOI: 10.1021/acs.jctc.7b00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rolf David
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Hélène Jamet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
| | - Vincent Nivière
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/BioCat, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Yohann Moreau
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Anne Milet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
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8
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Horch M, Utesch T, Hildebrandt P, Mroginski MA, Zebger I. Domain motions and electron transfer dynamics in 2Fe-superoxide reductase. Phys Chem Chem Phys 2016; 18:23053-66. [DOI: 10.1039/c6cp03666j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical studies on 2Fe-superoxide reductase provide mechanistic insights into structural dynamics and electron transfer efficiencies.
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Affiliation(s)
- Marius Horch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Tillmann Utesch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Peter Hildebrandt
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | | | - Ingo Zebger
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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9
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Pinto AF, Romão CV, Pinto LC, Huber H, Saraiva LM, Todorovic S, Cabelli D, Teixeira M. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue. J Biol Inorg Chem 2015; 20:155-164. [PMID: 25476860 DOI: 10.1007/s00775-014-1222-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/26/2014] [Indexed: 01/12/2023]
Abstract
Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the -EKHVP- motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (-E23T24HVP-), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild-type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.
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Affiliation(s)
- Ana F Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177, Stockholm, Sweden
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Liliana C Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Harald Huber
- Lehrstuhl fuer Mikrobiologie, Universität Regensburg, 93053, Regensburg, Germany
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Diane Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.
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Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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11
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Horch M, Pinto AF, Utesch T, Mroginski MA, Romão CV, Teixeira M, Hildebrandt P, Zebger I. Reductive activation and structural rearrangement in superoxide reductase: a combined infrared spectroscopic and computational study. Phys Chem Chem Phys 2014; 16:14220-30. [DOI: 10.1039/c4cp00884g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local and global structural changes that enable reductive activation of superoxide reductase are revealed by a combined approach of infrared difference spectroscopy and computational methods.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - A. F. Pinto
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - T. Utesch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - M. A. Mroginski
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - C. V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - M. Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
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12
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Tremey E, Bonnot F, Moreau Y, Berthomieu C, Desbois A, Favaudon V, Blondin G, Houée-Levin C, Nivière V. Hydrogen bonding to the cysteine ligand of superoxide reductase: acid–base control of the reaction intermediates. J Biol Inorg Chem 2013; 18:815-30. [DOI: 10.1007/s00775-013-1025-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/15/2013] [Indexed: 12/26/2022]
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13
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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McDonald AR, Van Heuvelen KM, Guo Y, Li F, Bominaar EL, Münck E, Que L. Characterization of a thiolato iron(III) Peroxy dianion complex. Angew Chem Int Ed Engl 2012; 51:9132-6. [PMID: 22888066 PMCID: PMC3448492 DOI: 10.1002/anie.201203602] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/19/2012] [Indexed: 11/09/2022]
Abstract
Nucleophilic oxidant: The reaction between a thiolato iron(II) complex 1 and superoxide in aprotic solvent at -90 °C yields a novel thiolato iron(III) peroxide intermediate 2, which exhibits unusually high nucleophilic reactivity. Compound 2 is an isomer of the thiolato iron(II) superoxide intermediate that is invoked in the reaction between superoxide reductase and superoxide.
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Affiliation(s)
- Aidan R. McDonald
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Katherine M. Van Heuvelen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Feifei Li
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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McDonald AR, Van Heuvelen KM, Guo Y, Li F, Bominaar EL, Münck E, Que L. Characterization of a Thiolato Iron(III) Peroxy Dianion Complex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Bonnot F, Molle T, Ménage S, Moreau Y, Duval S, Favaudon V, Houée-Levin C, Nivière V. Control of the Evolution of Iron Peroxide Intermediate in Superoxide Reductase from Desulfoarculus baarsii. Involvement of Lysine 48 in Protonation. J Am Chem Soc 2012; 134:5120-30. [DOI: 10.1021/ja209297n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florence Bonnot
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
| | - Thibaut Molle
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
| | - Stéphane Ménage
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
| | - Yohann Moreau
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
| | - Simon Duval
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
| | - Vincent Favaudon
- Institut Curie, Inserm U612, Bâtiment 110-112,
Centre Universitaire 91405
Orsay Cedex, France
| | - Chantal Houée-Levin
- Laboratoire
de Chimie Physique,
UMR8000 CNRS/Université Paris-Sud, Bâtiment 350, Centre Universitaire 91405 Orsay Cedex, France
| | - Vincent Nivière
- CEA, iRTSV, Laboratoire de Chimie et Biologie des Métaux,
F-38054 Grenoble,
France
- Université de Grenoble, F-38000 Grenoble, France
- CNRS, UMR 5249, F-38054
Grenoble, France
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Crawford JA, Li W, Pierce BS. Single turnover of substrate-bound ferric cysteine dioxygenase with superoxide anion: enzymatic reactivation, product formation, and a transient intermediate. Biochemistry 2011; 50:10241-53. [PMID: 21992268 DOI: 10.1021/bi2011724] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine dioxygenase (CDO) is a non-heme mononuclear iron enzyme that catalyzes the O(2)-dependent oxidation of L-cysteine (Cys) to produce cysteine sulfinic acid (CSA). In this study we demonstrate that the catalytic cycle of CDO can be "primed" by one electron through chemical oxidation to produce CDO with ferric iron in the active site (Fe(III)-CDO, termed 2). While catalytically inactive, the substrate-bound form of Fe(III)-CDO (2a) is more amenable to interrogation by UV-vis and EPR spectroscopy than the 'as-isolated' Fe(II)-CDO enzyme (1). Chemical-rescue experiments were performed in which superoxide (O(2)(•-)) anions were introduced to 2a to explore the possibility that a Fe(III)-superoxide species represents the first intermediate within the catalytic pathway of CDO. In principle, O(2)(•-) can serve as a suitable acceptor for the remaining 3-electrons necessary for CSA formation and regeneration of the active Fe(II)-CDO enzyme (1). Indeed, addition of O(2)(•-) to 2a resulted in the rapid formation of a transient species (termed 3a) observable at 565 nm by UV-vis spectroscopy. The subsequent decay of 3a is kinetically matched to CSA formation. Moreover, a signal attributed to 3a was also identified using parallel mode X-band EPR spectroscopy (g ~ 11). Spectroscopic simulations, observed temperature dependence, and the microwave power saturation behavior of 3a are consistent with a ground state S = 3 from a ferromagnetically coupled (J ~ -8 cm(-1)) high-spin ferric iron (S(A) = 5/2) with a bound radical (S(B) = 1/2), presumably O(2)(•-). Following treatment with O(2)(•-), the specific activity of recovered CDO increased to ~60% relative to untreated enzyme.
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Affiliation(s)
- Joshua A Crawford
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington, Arlington, Texas 76019, United States
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18
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Bonnot F, Duval S, Lombard M, Valton J, Houée-Levin C, Nivière V. Intermolecular electron transfer in two-iron superoxide reductase: a putative role for the desulforedoxin center as an electron donor to the iron active site. J Biol Inorg Chem 2011; 16:889-98. [PMID: 21590471 DOI: 10.1007/s00775-011-0788-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 04/19/2011] [Indexed: 10/18/2022]
Abstract
Superoxide reductase (SOR) is a superoxide detoxification system present in some microorganisms. Its active site consists of an unusual mononuclear iron center with an FeN4S1 coordination which catalyzes the one-electron reduction of superoxide to form hydrogen peroxide. Different classes of SORs have been described depending on the presence of an additional rubredoxin-like, desulforedoxin iron center, whose function has remained unknown until now. In this work, we investigated the mechanism of the reduction of the SOR iron active site using the NADPH:flavodoxin oxidoreductase from Escherichia coli, which was previously shown to efficiently transfer electrons to the Desulfoarculus baarsii SOR. When present, the additional rubredoxin-like iron center could function as an electronic relay between cellular reductases and the iron active site for superoxide reduction. This electron transfer was mainly intermolecular, between the rubredoxin-like iron center of one SOR and the iron active site of another SOR. These data provide the first experimental evidence for a possible role of the rubredoxin-like iron center in the superoxide detoxifying activity of SOR.
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Affiliation(s)
- Florence Bonnot
- Laboratoire de Chimie et Biologie des Métaux, iRTSV-CEA Grenoble/CNRS/Université Joseph Fourier, 17 Avenue des Martyrs, 38054, Grenoble Cedex 9, France
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Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F. SORGOdb: Superoxide Reductase Gene Ontology curated DataBase. BMC Microbiol 2011; 11:105. [PMID: 21575179 PMCID: PMC3116461 DOI: 10.1186/1471-2180-11-105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated. DESCRIPTION SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010). CONCLUSIONS SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.
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Affiliation(s)
- Céline Lucchetti-Miganeh
- CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France.
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Pinho FG, Pinto AF, Pinto LC, Huber H, Romão CV, Teixeira M, Matias PM, Bandeiras TM. Superoxide reductase from Nanoarchaeum equitans: expression, purification, crystallization and preliminary X-ray crystallographic analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:591-5. [PMID: 21543869 PMCID: PMC3087648 DOI: 10.1107/s1744309111009432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/11/2011] [Indexed: 11/10/2022]
Abstract
Superoxide reductases (SORs) are the most recent oxygen-detoxification system to be identified in anaerobic and microaerobic bacteria and archaea. SORs are metalloproteins that are characterized by their possession of a catalytic nonhaem iron centre in the ferrous form coordinated by four histidine ligands and one cysteine ligand. Ignicoccus hospitalis, a hyperthermophilic crenarchaeon, is the only organism known to date to serve as a host for Nanoarchaeum equitans, a nanosized hyperthermophilic archaeon isolated from a submarine hot vent which completely depends on the presence of and contact with I. hospitalis cells for growth to occur. Similarly to I. hospitalis, N. equitans has a neelaredoxin (a 1Fe-type SOR) that keeps toxic oxygen species under control, catalysing the one-electron reduction of superoxide to hydrogen peroxide. Blue crystals of recombinant N. equitans SOR in the oxidized form (12.7 kDa, 109 residues) were obtained using polyethylene glycol (PEG 2000 MME) as precipitant. These crystals diffracted to 1.9 Å resolution at 100 K and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 51.88, b = 82.01, c = 91.30 Å. Cell-content analysis suggested the presence of four monomers in the asymmetric unit. The Matthews coefficient (V(M)) was determined to be 1.9 Å(3) Da(-1), corresponding to an estimated solvent content of 36%. Self-rotation function and native Patterson calculations suggested a tetramer with 222 point-group symmetry, similar to other 1Fe-SORs. The three-dimensional structure will be determined by the molecular-replacement method.
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Affiliation(s)
- Filipa G. Pinho
- Instituto de Biologia Experimental e Tecnológica, Universidade Nova de Lisboa, Apartado 12, 2701-901 Oeiras, Portugal
| | - Ana F. Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Liliana C. Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Harald Huber
- Lehrstuhl für Mikrobiologie, Universität Regensburg, 93053 Regensburg, Germany
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Tiago M. Bandeiras
- Instituto de Biologia Experimental e Tecnológica, Universidade Nova de Lisboa, Apartado 12, 2701-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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Nam E, Alokolaro PE, Swartz RD, Gleaves MC, Pikul J, Kovacs JA. Investigation of the mechanism of formation of a thiolate-ligated Fe(III)-OOH. Inorg Chem 2011; 50:1592-602. [PMID: 21284379 DOI: 10.1021/ic101776m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic studies aimed at determining the most probable mechanism for the proton-dependent [Fe(II)(S(Me2)N(4)(tren))](+) (1) promoted reduction of superoxide via a thiolate-ligated hydroperoxo intermediate [Fe(III)(S(Me2)N(4)(tren))(OOH)](+) (2) are described. Rate laws are derived for three proposed mechanisms, and it is shown that they should conceivably be distinguishable by kinetics. For weak proton donors with pK(a(HA)) > pK(a(HO(2))) rates are shown to correlate with proton donor pK(a), and display first-order dependence on iron, and half-order dependence on superoxide and proton donor HA. Proton donors acidic enough to convert O(2)(-) to HO(2) (in tetrahydrofuran, THF), that is, those with pK(a(HA)) < pK(a(HO(2))), are shown to display first-order dependence on both superoxide and iron, and rates which are independent of proton donor concentration. Relative pK(a) values were determined in THF by measuring equilibrium ion pair acidity constants using established methods. Rates of hydroperoxo 2 formation displays no apparent deuterium isotope effect, and bases, such as methoxide, are shown to inhibit the formation of 2. Rate constants for p-substituted phenols are shown to correlate linearly with the Hammett substituent constants σ(-). Activation parameters ((ΔH(++) = 2.8 kcal/mol, ΔS(++) = -31 eu) are shown to be consistent with a low-barrier associative mechanism that does not involve extensive bond cleavage. Together, these data are shown to be most consistent with a mechanism involving the addition of HO(2) to 1 with concomitant oxidation of the metal ion, and reduction of superoxide (an "oxidative addition" of sorts), in the rate-determining step. Activation parameters for MeOH- (ΔH(++) = 13.2 kcal/mol and ΔS(++) = -24.3 eu), and acetic acid- (ΔH(++) = 8.3 kcal/mol and ΔS(++) = -34 eu) promoted release of H(2)O(2) to afford solvent-bound [Fe(III)(S(Me2)N(4)(tren))(OMe)](+) (3) and [Fe(III)(S(Me2)N(4)(tren))(O(H)Me)](+) (4), respectively, are shown to be more consistent with a reaction involving rate-limiting protonation of an Fe(III)-OOH, than with one involving rate-limiting O-O bond cleavage. The observed deuterium isotope effect (k(H)/k(D) = 3.1) is also consistent with this mechanism.
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Affiliation(s)
- Elaine Nam
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, USA
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Pieulle L, Stocker P, Vinay M, Nouailler M, Vita N, Brasseur G, Garcin E, Sebban-Kreuzer C, Dolla A. Study of the thiol/disulfide redox systems of the anaerobe Desulfovibrio vulgaris points out pyruvate:ferredoxin oxidoreductase as a new target for thioredoxin 1. J Biol Chem 2011; 286:7812-7821. [PMID: 21199874 DOI: 10.1074/jbc.m110.197988] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sulfate reducers have developed a multifaceted adaptative strategy to survive against oxidative stresses. Along with this oxidative stress response, we recently characterized an elegant reversible disulfide bond-dependent protective mechanism in the pyruvate:ferredoxin oxidoreductase (PFOR) of various Desulfovibrio species. Here, we searched for thiol redox systems involved in this mechanism. Using thiol fluorescent labeling, we show that glutathione is not the major thiol/disulfide balance-controlling compound in four different Desulfovibrio species and that no other plentiful low molecular weight thiol can be detected. Enzymatic analyses of two thioredoxins (Trxs) and three thioredoxin reductases allow us to propose the existence of two independent Trx systems in Desulfovibrio vulgaris Hildenborough (DvH). The TR1/Trx1 system corresponds to the typical bacterial Trx system. We measured a TR1 apparent K(m) value for Trx1 of 8.9 μM. Moreover, our results showed that activity of TR1 was NADPH-dependent. The second system named TR3/Trx3 corresponds to an unconventional Trx system as TR3 used preferentially NADH (K(m) for NADPH, 743 μM; K(m) for NADH, 5.6 μM), and Trx3 was unable to reduce insulin. The K(m) value of TR3 for Trx3 was 1.12 μM. In vitro experiments demonstrated that the TR1/Trx1 system was the only one able to reactivate the oxygen-protected form of Desulfovibrio africanus PFOR. Moreover, ex vivo pulldown assays using the mutant Trx1(C33S) as bait allowed us to capture PFOR from the DvH extract. Altogether, these data demonstrate that PFOR is a new target for Trx1, which is probably involved in the protective switch mechanism of the enzyme.
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Affiliation(s)
- Laetitia Pieulle
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and.
| | - Pierre Stocker
- the Equipe Biosciences iSm2, UMR6263, Case 342, FST Université Paul Cézanne, St. Jérome, 13397 Marseille Cedex 20, France
| | - Manon Vinay
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Matthieu Nouailler
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Nicolas Vita
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Gaël Brasseur
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Edwige Garcin
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Corinne Sebban-Kreuzer
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Alain Dolla
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
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Sit PHL, Migliore A, Ho MH, Klein ML. Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron−Dioxygen Intermediates and Proton Transfer in Superoxide Reductase. J Chem Theory Comput 2010; 6:2896-909. [DOI: 10.1021/ct900599q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick H.-L. Sit
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Agostino Migliore
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Ming-Hsun Ho
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
| | - Michael L. Klein
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19130
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Bandeiras TM, Romão CV, Rodrigues JV, Teixeira M, Matias PM. Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:316-9. [PMID: 20208170 PMCID: PMC2833046 DOI: 10.1107/s1744309110000916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 01/07/2010] [Indexed: 11/10/2022]
Abstract
Neelaredoxins are a type of superoxide reductase (SOR), which are blue 14 kDa metalloproteins with a catalytic nonhaem iron centre coordinated by four histidines and one cysteine in the ferrous form. Anaerobic organisms such as Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, have developed defence mechanisms against toxic oxygen species in which superoxide reductases play a key role. SOR is responsible for scavenging toxic superoxide anion radicals (O(2)(*-)), catalysing the one-electron reduction of superoxide to hydrogen peroxide. Crystals of recombinant A. fulgidus neelaredoxin in the oxidized form (13.7 kDa, 125 residues) were obtained using polyethylene glycol and ammonium sulfate. These crystals diffracted to 1.9 A resolution and belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 75.72, c = 185.44 A. Cell-content analysis indicated the presence of a tetramer in the asymmetric unit, with a Matthews coefficient (V(M)) of 2.36 A(3) Da(-1) and an estimated solvent content of 48%. The three-dimensional structure was determined by the MAD method and is currently under refinement.
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Affiliation(s)
- Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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Bonnot F, Houée-Levin C, Favaudon V, Nivière V. Photochemical processes observed during the reaction of superoxide reductase from Desulfoarculus baarsii with superoxide: re-evaluation of the reaction mechanism. Biochim Biophys Acta 2009; 1804:762-7. [PMID: 19962458 DOI: 10.1016/j.bbapap.2009.11.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 10/30/2009] [Accepted: 11/23/2009] [Indexed: 11/24/2022]
Abstract
Superoxide reductase SOR is an enzyme involved in superoxide detoxification in some microorganisms. Its active site consists of a non-heme ferrous center in an unusual [Fe(NHis)(4) (SCys)(1)] square pyramidal pentacoordination that efficiently reduces superoxide into hydrogen peroxide. In previous works, the reaction mechanism of the SOR from Desulfoarculus baarsii enzyme, studied by pulse radiolysis, was shown to involve the formation of two reaction intermediates T1 and T2. However, the absorption spectrum of T2 was reported with an unusual sharp band at 625 nm, very different from that reported for other SORs. In this work, we show that the sharp band at 625 nm observed by pulse radiolysis reflects the presence of photochemical processes that occurs at the level of the transient species formed during the reaction of SOR with superoxide. These processes do not change the stoichiometry of the global reaction. These data highlight remarkable photochemical properties for these reaction intermediates, not previously suspected for iron-peroxide species formed in the SOR active site. We have reinvestigated the reaction mechanism of the SOR from D. baarsii by pulse radiolysis in the absence of these photochemical processes. The T1 and T2 intermediates now appear to have absorption spectra similar to those reported for the Archaeoglobus fulgidus SOR enzymes. Although for some enzymes of the family only one transient was reported, on the whole, the reaction mechanisms of the different SORs studied so far seem very similar, which is in agreement with the strong sequence and structure homologies of their active sites.
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Affiliation(s)
- Florence Bonnot
- Laboratoire de Chimie et Biologie des Métaux, CEA iRTSV, CNRS, Université Joseph Fourier, UMR 5249, 38054 Grenoble Cedex 9, France
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Pinto AF, Rodrigues JV, Teixeira M. Reductive elimination of superoxide: Structure and mechanism of superoxide reductases. Biochim Biophys Acta 2009; 1804:285-97. [PMID: 19857607 DOI: 10.1016/j.bbapap.2009.10.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 10/12/2009] [Accepted: 10/14/2009] [Indexed: 10/20/2022]
Abstract
Superoxide anion is among the deleterious reactive oxygen species, towards which all organisms have specialized detoxifying enzymes. For quite a long time, superoxide elimination was thought to occur through its dismutation, catalyzed by Fe, Cu, and Mn or, as more recently discovered, by Ni-containing enzymes. However, during the last decade, a novel type of enzyme was established that eliminates superoxide through its reduction: the superoxide reductases, which are spread among anaerobic and facultative microorganisms, from the three life kingdoms. These enzymes share the same unique catalytic site, an iron ion bound to four histidines and a cysteine that, in its reduced form, reacts with superoxide anion with a diffusion-limited second order rate constant of approximately 10(9) M(-1) s(-1). In this review, the properties of these enzymes will be thoroughly discussed.
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Affiliation(s)
- Ana Filipa Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
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Todorovic S, Rodrigues JV, Pinto AF, Thomsen C, Hildebrandt P, Teixeira M, Murgida DH. Resonance Raman study of the superoxide reductase from Archaeoglobus fulgidus, E12 mutants and a ‘natural variant’. Phys Chem Chem Phys 2009; 11:1809-15. [DOI: 10.1039/b815489a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moura I, Pauleta SR, Moura JJG. Enzymatic activity mastered by altering metal coordination spheres. J Biol Inorg Chem 2008; 13:1185-95. [PMID: 18719950 DOI: 10.1007/s00775-008-0414-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion.
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Affiliation(s)
- Isabel Moura
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rodrigues JV, Victor BL, Huber H, Saraiva LM, Soares CM, Cabelli DE, Teixeira M. Superoxide reduction by Nanoarchaeum equitans neelaredoxin, an enzyme lacking the highly conserved glutamate iron ligand. J Biol Inorg Chem 2007; 13:219-28. [PMID: 17968598 DOI: 10.1007/s00775-007-0313-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 10/15/2007] [Indexed: 10/22/2022]
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Kitagawa T, Dey A, Lugo-Mas P, Benedict JB, Kaminsky W, Solomon E, Kovacs JA. A functional model for the cysteinate-ligated non-heme iron enzyme superoxide reductase (SOR). J Am Chem Soc 2007; 128:14448-9. [PMID: 17090014 PMCID: PMC2532059 DOI: 10.1021/ja064870d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Superoxide reductases (SORs) are cysteine-ligated, non-heme iron enzymes that reduce toxic superoxide radicals (O2-). The functional role of the trans cysteinate, as well as the mechanism by which SOR reduces O2-, is unknown. Herein is described a rare example of a functional metalloenzyme analogue, which catalytically reduces superoxide in a proton-dependent mechanism, via a trans thiolate-ligated iron-peroxo intermediate, the first example of its type. Acetic-acid-promoted H2O2 release, followed by Cp2Co reduction, regenerates the active Fe(II) catalyst. The thiolate ligand and its trans positioning relative to the substrate are shown to contribute significantly to the catalyst's function, by lowering the redox potential, changing the spin state, and dramatically lowering the nuFe-O stretching frequency well-below that of any other reported iron-peroxo, while leaving nuO-O high, so as to favor superoxide reduction and Fe-O, as opposed to O-O, bond cleavage. Thus we provide critical insight into the relationship between the SOR structure and its function, as well as important benchmark parameters for characterizing highly unstable thiolate-ligated iron-peroxo intermediates.
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Dey A, Jenney FE, Adams MWW, Johnson MK, Hodgson KO, Hedman B, Solomon EI. Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity. J Am Chem Soc 2007; 129:12418-31. [PMID: 17887751 PMCID: PMC2533108 DOI: 10.1021/ja064167p] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Francis E. Jenney
- Department of Chemistry and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | - Michael W. W. Adams
- Department of Chemistry and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | - Michael K. Johnson
- Department of Chemistry and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, CA 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, CA 94025
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, CA 94025
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33
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Abstract
Toxic superoxide radicals, generated via adventitious reduction of dioxygen, have been implicated in a number of disease states. The cysteinate-ligated non-heme iron enzyme superoxide reductase (SOR) degrades superoxide via reduction. Biomimetic analogues which provide insight into why nature utilizes a trans-thiolate to promote SOR function are described. Spectroscopic and/or structural characterization of the first examples of thiolate-ligated Fe (III)-peroxo complexes provides important benchmark parameters for the identification of biological intermediates. Oxidative addition of superoxide is favored by low redox potentials. The trans influence of the thiolate appears to significantly weaken the Fe-O peroxo bond, favoring proton-induced release of H 2O 2 from a high-spin Fe(III)-OOH complex.
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Affiliation(s)
- Julie A Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, USA
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Affiliation(s)
- Alice S. Pereira
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
| | - Pedro Tavares
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
| | - Filipe Folgosa
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
| | - Rui M. Almeida
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
| | - Isabel Moura
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
| | - José J. G. Moura
- Requimte, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829‐516 Caparica, Portugal, Fax: +351‐21‐2948550
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35
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Mathé C, Weill CO, Mattioli TA, Berthomieu C, Houée-Levin C, Tremey E, Nivière V. Assessing the role of the active-site cysteine ligand in the superoxide reductase from Desulfoarculus baarsii. J Biol Chem 2007; 282:22207-16. [PMID: 17545670 DOI: 10.1074/jbc.m700279200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of O(2)(.) to H(2)O(2), providing an antioxidant defense in some bacteria. Its active site consists of an unusual non-heme Fe(2+) center in a [His(4) Cys(1)] square pyramidal pentacoordination. In this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. Previous Fourier transform infrared spectroscopy studies on the enzyme from Desulfoarculus baarsii revealed that a protonated carboxylate group, proposed to be the side chain of Glu(114), is in interaction with the cysteine ligand. In this work, using pulse radiolysis, Fourier transform infrared, and resonance Raman spectroscopies, we have investigated to what extent the presence of this Glu(114) carboxylic lateral chain affects the strength of the S-Fe bond and the reaction of the iron active site with superoxide. The E114A mutant shows significantly modified pulse radiolysis kinetics for the protonation process of the first reaction intermediate. Resonance Raman spectroscopy demonstrates that the E114A mutation results in both a strengthening of the S-Fe bond and an increase in the extent of freeze-trapping of a Fe-peroxo species after treatment with H(2)O(2) by a specific strengthening of the Fe-O bond. A fine tuning of the strength of the S-Fe bond by the presence of Glu(114) appears to be an essential factor for both the strength of the Fe-O bond and the pK(a) value of the Fe(3+)-peroxo intermediate species to form the reaction product H(2)O(2).
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Chimie et Biologie des Métaux, iRTSV-CEA Grenoble/CNRS/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
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36
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Abstract
The iron(II) complex of a tetradentate bispidine ligand with two tertiary amines and two pyridine groups (L = dimethyl [3,7-dimethyl-9,9'-dihydroxy-2,4-di-(2-pyridyl)-3,7-diazabicyclo nonan-1,5-dicaboxylate]) is oxidized with tert-butyl hydroperoxide to the corresponding end-on tert-butylperoxo complex [Fe(III)(L)(OOtBu)(X)]n+ (X = solvent, anion). UV-vis, resonance Raman, and EPR spectroscopy, as a function of the solvent, show that this is a spin-crossover compound. The experimentally observed Raman vibrations for both low-spin and high-spin isomers are in good agreement with those computed by DFT.
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Affiliation(s)
- Jochen Bautz
- Anorganisch-Chemisches Institut,Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
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37
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Katona G, Carpentier P, Nivière V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D. Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme. Science 2007; 316:449-53. [PMID: 17446401 DOI: 10.1126/science.1138885] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.
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Affiliation(s)
- Gergely Katona
- Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France
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38
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Jensen MP, Payeras AMI, Fiedler AT, Costas M, Kaizer J, Stubna A, Münck E, Que L. Kinetic analysis of the conversion of nonheme (alkylperoxo)iron(III) species to iron(IV) complexes. Inorg Chem 2007; 46:2398-408. [PMID: 17326618 PMCID: PMC2526350 DOI: 10.1021/ic0607787] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Low-spin mononuclear (alkylperoxo)iron(III) complexes decompose by peroxide O-O bond homolysis to form iron(IV) species. We examined the kinetics of previously reported homolysis reactions for (alkylperoxo)iron(III) intermediates supported by TPA (tris(2-pyridylmethyl)amine) in CH3CN solution and promoted by pyridine N-oxide, and by BPMCN (N,N-bis(2-pyridylmethyl)-N,N-dimethyl-trans-1,2-diaminocyclohexane) in its cis-beta configuration in CH3CN and CH2Cl2, as well as for the previously unreported chemistry of TPA and 5-Me3TPA intermediates in acetone. Each of these reactions forms an oxoiron(IV) complex, except for the beta-BPMCN reaction in CH2Cl2 that yields a novel (hydroxo)(alkylperoxo)iron(IV) product. Temperature-dependent rate measurements suggest a common reaction trajectory for each of these reactions and verify previous theoretical estimates of a ca. 60 kJ/mol enthalpic barrier to homolysis. However, both the tetradentate supporting ligand and exogenous ligands in the sixth octahedral coordination site significantly perturb the homolyses, such that observed rates can vary over 2 orders of magnitude at a given temperature. This is manifested as a compensation effect in which increasing activation enthalpy is offset by increasingly favorable activation entropy. Moreover, the applied kinetic model is consistent with geometric isomerism in the low-spin (alkylperoxo)iron(III) intermediates, wherein the alkylperoxo ligand is coordinated in either of the inequivalent cis sites afforded by the nonheme ligands.
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39
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Gosiewska S, van Faassen EE, Permentier HP, Bruins AP, van Koten G, Gebbink RJMK. Characterization and alkane oxidation activity of a diastereopure seven-coordinate iron(iii) alkylperoxo complex. Dalton Trans 2007:3365-8. [PMID: 17664972 DOI: 10.1039/b706604j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectroscopic characterization and alkane oxidation studies of a diastereopure seven-coordinate high-spin iron(iii) alkylperoxo complex based on the chiral N,N',N-bis(l-prolinate)pyridine ligand Py(ProMe)(2) () are reported.
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Affiliation(s)
- Silvia Gosiewska
- Organic Chemistry and Catalysis, Utrecht University, Padualaan 8, 3584, CH Utrecht, The Netherlands
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40
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Affiliation(s)
- Lisa M. Brines
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA, Fax: +1‐206‐685‐8665
| | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA, Fax: +1‐206‐685‐8665
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41
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Rodrigues JV, Saraiva LM, Abreu IA, Teixeira M, Cabelli DE. Superoxide reduction by Archaeoglobus fulgidus desulfoferrodoxin: comparison with neelaredoxin. J Biol Inorg Chem 2006; 12:248-56. [PMID: 17066300 DOI: 10.1007/s00775-006-0182-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 10/04/2006] [Indexed: 10/24/2022]
Abstract
Superoxide reductases (SORs) are non-heme iron-containing enzymes that remove superoxide by reducing it to hydrogen peroxide. The active center of SORs consists of a ferrous ion coordinated by four histidines and one cysteine in a square-pyramidal geometry. In the 2Fe-SOR, a distinct family of SORs, there is an additional desulforedoxin-like site that does not appear to be involved in SOR activity. Our previous studies on recombinant Archaeoglobus fulgidus neelaredoxin (1Fe-SOR) have shown that the reaction with superoxide involves the formation of a transient ferric form that, upon protonation, decays to yield an Fe(3+)-OH species, followed by binding of glutamate to the ferric ion via replacement of hydroxide (Rodrigues et al. in Biochemistry 45:9266-9278, 2006). Here, we report the characterization of recombinant desulfoferrodoxin from the same organism, which is a member of the 2Fe-SOR family, and show that the steps involved in the superoxide reduction are similar in both families of SOR. The electron donation to the SOR from its redox partner, rubredoxin, is also presented here.
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Affiliation(s)
- João V Rodrigues
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República (EAN), 2784-505, Oeiras, Portugal
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42
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Molina-Heredia FP, Houée-Levin C, Berthomieu C, Touati D, Tremey E, Favaudon V, Adam V, Nivière V. Detoxification of superoxide without production of H2O2: antioxidant activity of superoxide reductase complexed with ferrocyanide. Proc Natl Acad Sci U S A 2006; 103:14750-5. [PMID: 17001016 PMCID: PMC1595423 DOI: 10.1073/pnas.0510828103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The superoxide radical O(2)(-.) is a toxic by-product of oxygen metabolism. Two O(2)(-.) detoxifying enzymes have been described so far, superoxide dismutase and superoxide reductase (SOR), both forming H2O2 as a reaction product. Recently, the SOR active site, a ferrous iron in a [Fe(2+) (N-His)(4) (S-Cys)] pentacoordination, was shown to have the ability to form a complex with the organometallic compound ferrocyanide. Here, we have investigated in detail the reactivity of the SOR-ferrocyanide complex with O(2)(-.) by pulse and gamma-ray radiolysis, infrared, and UV-visible spectroscopies. The complex reacts very efficiently with O(2)(-.). However, the presence of the ferrocyanide adduct markedly modifies the reaction mechanism of SOR, with the formation of transient intermediates different from those observed for SOR alone. A one-electron redox chemistry appears to be carried out by the ferrocyanide moiety of the complex, whereas the SOR iron site remains in the reduced state. Surprisingly, the toxic H2O2 species is no longer the reaction product. Accordingly, in vivo experiments showed that formation of the SOR-ferrocyanide complex increased the antioxidant capabilities of SOR expressed in an Escherichia coli sodA sodB recA mutant strain. Altogether, these data describe an unprecedented O(2)(-.) detoxification activity, catalyzed by the SOR-ferrocyanide complex, which does not conduct to the production of the toxic H2O2 species.
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Affiliation(s)
- Fernando P. Molina-Heredia
- *Département de Réponse et Dynamique Cellulaires/Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, Unité Mixte de Recherche (UMR) 5047, Commissariat à l’Energie Atomique (CEA)/Centre National de la Recherche Scientifique (CNRS)/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Chantal Houée-Levin
- Laboratoire de Chimie Physique, UMR 8000, CNRS/Université Paris-Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Catherine Berthomieu
- Département d’Ecophysiologie Végétale et Microbiologie/Laboratoire des Interactions Proteine Metal, UMR 6191, CEA-Cadarache, 13108 Saint Paul-lez-Durance, France
| | - Danièle Touati
- Institut Jacques Monod, CNRS/Universités Paris 6 et Paris 7, 2 Place Jussieu, 75251 Paris Cedex 5, France
| | - Emilie Tremey
- *Département de Réponse et Dynamique Cellulaires/Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, Unité Mixte de Recherche (UMR) 5047, Commissariat à l’Energie Atomique (CEA)/Centre National de la Recherche Scientifique (CNRS)/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Vincent Favaudon
- Institut National de la Santé et de la Recherche Médicale Unité 612 and Institut Curie, Bâtiment 110–112, 91405 Orsay Cedex, France; and
| | - Virgile Adam
- **European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - Vincent Nivière
- *Département de Réponse et Dynamique Cellulaires/Laboratoire de Chimie et Biochimie des Centres Redox Biologiques, Unité Mixte de Recherche (UMR) 5047, Commissariat à l’Energie Atomique (CEA)/Centre National de la Recherche Scientifique (CNRS)/Université Joseph Fourier, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
- To whom correspondence should be addressed. E-mail:
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43
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Santos-Silva T, Trincão J, Carvalho AL, Bonifácio C, Auchère F, Raleiras P, Moura I, Moura JJG, Romão MJ. The first crystal structure of class III superoxide reductase from Treponema pallidum. J Biol Inorg Chem 2006; 11:548-58. [PMID: 16791639 DOI: 10.1007/s00775-006-0104-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 03/20/2006] [Indexed: 12/01/2022]
Abstract
Superoxide reductase (SOR) is a metalloprotein containing a non-heme iron centre, responsible for the scavenging of superoxide radicals in the cell. The crystal structure of Treponema pallidum (Tp) SOR was determined using soft X-rays and synchrotron radiation. Crystals of the oxidized form were obtained using poly(ethylene glycol) and MgCl2 and diffracted beyond 1.55 A resolution. The overall architecture is very similar to that of other known SORs but TpSOR contains an N-terminal domain in which the desulforedoxin-type Fe centre, found in other SORs, is absent. This domain conserves the beta-barrel topology with an overall arrangement very similar to that of other SOR proteins where the centre is present. The absence of the iron ion and its ligands, however, causes a decrease in the cohesion of the domain and some disorder is observed, particularly in the region where the metal would be harboured. The C-terminal domain exhibits the characteristic immunoglobulin-like fold and harbours the Fe(His)4(Cys) active site. The five ligands of the iron centre are well conserved despite some disorder observed for one of the four molecules in the asymmetric unit. The participation of a glutamate as the sixth ligand of some of the iron centres in Pyrococcus furiosus SOR was not observed in TpSOR. A possible explanation is that either X-ray photoreduction occurred or there was a mixture of redox states at the start of data collection. In agreement with earlier proposals, details in the TpSOR structure also suggest that Lys49 might be involved in attraction of superoxide to the active site.
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Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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44
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Clay MD, Yang TC, Jenney FE, Kung IY, Cosper CA, Krishnan R, Kurtz DM, Adams MW, Hoffman BM, Johnson MK. Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies. Biochemistry 2006; 45:427-38. [PMID: 16401073 PMCID: PMC2531258 DOI: 10.1021/bi052034v] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Brian M. Hoffman
- Corresponding authors: BMH: Department of Chemistry, Northwestern University, Evanston, IL 60208; Tel.: 847−491−3104, E-mail: . M.K.J.: Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Tel.: 706−542−9378; Fax: 706−542−2353, E-mail:
| | - Michael K. Johnson
- Corresponding authors: BMH: Department of Chemistry, Northwestern University, Evanston, IL 60208; Tel.: 847−491−3104, E-mail: . M.K.J.: Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Tel.: 706−542−9378; Fax: 706−542−2353, E-mail:
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45
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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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46
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Mathé C, Nivière V, Houée-Levin C, Mattioli TA. Fe3+–η2–peroxo species in superoxide reductase from Treponema pallidum. Comparison with Desulfoarculus baarsii. Biophys Chem 2006; 119:38-48. [PMID: 16084640 DOI: 10.1016/j.bpc.2005.06.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 06/29/2005] [Accepted: 06/29/2005] [Indexed: 11/16/2022]
Abstract
Superoxide reductases (SORs) are superoxide (O2-)-detoxifying enzymes that catalyse the reduction of O2- into hydrogen peroxide. Three different classes of SOR have been reported on the basis of the presence or not of an additional N-terminal domain. They all share a similar active site, with an unusual non-heme Fe atom coordinated by four equatorial histidines and one axial cysteine residues. Crucial catalytic reaction intermediates of SOR are purported to be Fe(3+)-(hydro)peroxo species. Using resonance Raman spectroscopy, we compared the vibrational properties of the Fe3+ active site of two different classes of SOR, from Desulfoarculus baarsii and Treponema pallidum, along with their ferrocyanide and their peroxo complexes. In both species, rapid treatment with H2O2 results in the stabilization of a side-on high spin Fe(3+)-(eta(2)-OO) peroxo species. Comparison of these two peroxo species reveals significant differences in vibrational frequencies and bond strengths of the Fe-O2 (weaker) and O-O (stronger) bonds for the T. pallidum enzyme. Thus, the two peroxo adducts in these two SORs have different stabilities which are also seen to be correlated with differences in the Fe-S coordination strengths as gauged by the Fe-S vibrational frequencies. This was interpreted from structural variations in the two active sites, resulting in differences in the electron donating properties of the trans cysteine ligand. Our results suggest that the structural differences observed in the active site of different classes of SORs should be a determining factor for the rate of release of the iron-peroxo intermediate during enzymatic turnover.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Biophysique du Stress Oxydant, SBE and CNRS URA 2096, Département de Biologie Joliot Curie, CEA Saclay, 91191 Gif-sur-Yvette cedex, France
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47
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Mathé C, Nivière V, Mattioli TA. Fe3+-Hydroxide Ligation in the Superoxide Reductase from Desulfoarculus baarsii Is Associated with pH Dependent Spectral Changes. J Am Chem Soc 2005; 127:16436-41. [PMID: 16305229 DOI: 10.1021/ja053808y] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide reductase (SOR) catalyzes the reduction of O2*- to H2O2. Its active site consists of a non-heme Fe2+ center in an unusual square-pyramidal [His4 Cys] coordination. Like many SORs, the electronic absorption band corresponding to the oxidized active site of the SOR from Desulfoarculus baarsii exhibits a pH-dependent alkaline transition changing from ca. 644 to 560 nm as the pH increases and with an apparent pKa of 9.0. Variants in which the conserved amino acids glutamate 47 and lysine 48 were replaced by the neutral residues alanine (E47A) and isoleucine (K48I), respectively, exhibited the same alkaline transition but at lower apparent pKa values of 6.7 and 7.6, respectively. Previous work [Nivière, V.; Asso, M.; Weill, C. O.; Lombard, M.; Guigliarelli, B.; Favaudon, V.; Houée-Levin, C. Biochemistry 2004, 43, 808-818] has shown that this alkaline transition is associated with the protonation/deprotonation of an unidentified base, B-, which is neither E47 nor K48. In this work, we show by resonance Raman spectroscopy that at basic pH a high-spin Fe3+-OH species is formed at the active site. The presence of the HO- ligand was directly associated with an absorption band maximum at 560 nm, whereas upon protonation, the band shifts to 644 nm. With respect to our previous work, B- can be identified with this high-spin Fe3+-OH species, which upon protonation results in a water molecule at the active site. Implications for the SOR catalytic cycle are proposed.
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Affiliation(s)
- Christelle Mathé
- Laboratoire de Biophysique du Stress Oxydant, SBE/DBJC and CNRS URA 2096, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
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48
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Abstract
Superoxide reduction by thiolate-ligated [FeII(SMe2N4(tren))]+ (1) involves two proton-dependent steps and a single peroxide intermediate, [FeIII(SMe2N4(tren))(OOH)]+ (2). An external proton donor is required, ruling out mechanisms involving H+ or H-atom abstraction from the ligand N-H. The initial protonation step affording 2 occurs with fairly basic proton donors (EtOH, MeOH, NH4+) in THF. More acidic proton donors are required to cleave the Fe-O(peroxide) bond in MeOH, and this occurs via a dissociative mechanism. Reaction rates are dependent on the pKa of the proton donor, and a common [FeIII(SMe2N4(tren))(MeOH)]2+ (3) intermediate is involved. Acetic acid releases H2O2 from 2 under pseudo-first-order conditions ([HOAc] = 138 mM, [2] = 0.49 mM) with a rate constant of 8.2 x 10(-4) s(-1) at -78 degrees C in MeOH. Reduction of 3 with Cp2Co regenerates the active catalyst 1.
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Rohde JU, Torelli S, Shan X, Lim MH, Klinker EJ, Kaizer J, Chen K, Nam W, Que L. Structural insights into nonheme alkylperoxoiron(III) and oxoiron(IV) intermediates by X-ray absorption spectroscopy. J Am Chem Soc 2005; 126:16750-61. [PMID: 15612713 DOI: 10.1021/ja047667w] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transient mononuclear low-spin alkylperoxoiron(III) and oxoiron(IV) complexes that are relevant to the activation of dioxygen by nonheme iron enzymes have been generated from synthetic iron(II) complexes of neutral tetradentate (TPA) and pentadentate (N4Py, Bn-TPEN) ligands and structurally characterized by means of Fe K-edge X-ray absorption spectroscopy (XAS). Notable features obtained from fits of the EXAFS region are Fe-O bond lengths of 1.78 A for the alkylperoxoiron(III) intermediates and 1.65-1.68 A for the oxoiron(IV) intermediates, reflecting different strengths in the Fe-O pi interactions. These differences are also observed in the intensities of the 1s-to-3d transitions in the XANES region, which increase from 4 units for the nearly octahedral iron(II) precursor to 9-15 units for the alkylperoxoiron(III) intermediates to 25-29 units for the oxoiron(IV) species.
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Affiliation(s)
- Jan-Uwe Rohde
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Theisen RM, Shearer J, Kaminsky W, Kovacs JA. Steric and electronic control over the reactivity of a thiolate-ligated Fe(II) complex with dioxygen and superoxide: reversible mu-oxo dimer formation. Inorg Chem 2004; 43:7682-90. [PMID: 15554633 PMCID: PMC4485619 DOI: 10.1021/ic0491884] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reactivity between a thiolate-ligated five-coordinate complex [FeII(SMe2N4(tren))]+ (1) and dioxygen is examined in order to determine if O2 activation, resembling that of the metalloenzyme cytochrome P450, can be promoted even when O2 binds cis, as opposed to trans, to a thiolate. Previous work in our group showed that [FeII(SMe2N4(tren))]+ (1) reacts readily with superoxide (O2-) in the presence of a proton source to afford H2O2 via an Fe(III)-OOH intermediate, thus providing a biomimetic model for the metalloenzyme superoxide reductase (SOR). Addition of O2 to 1 affords binuclear mu-oxo-bridged [FeIII(SMe2N4(tren))]2(mu2-O)(PF6)2.3MeCN (3). At low temperatures, in protic solvents, an intermediate is detected, the details of which will be the subject of a separate paper. Although the thiolate ligand does not appear to perturb the metrical parameters of the unsupported mu-oxo bridge (Fe-O= 1.807(8) A, and Fe-O-Fe= 155.3(5) degrees fall in the usual range), it decreases the magnetic coupling between the irons (J=-28 cm(-1)) and creates a rather basic oxo site. Protonation of this oxo using strong (HBF4, HCl) or weak (HOAc, NH4PF6, LutNHCl) acids results in bridge cleavage to cleanly afford the corresponding monomeric anion-ligated (OAc- (6), or Cl- (7)) or solvent-ligated (MeCN (4)) derivatives. Addition of OH- converts [FeIII(SMe2N4(tren))(MeCN2+ (4) back to mu-oxo 3. Thus, mu-oxo bridge cleavage is reversible. The protonated mu-hydroxo-bridged intermediate is not observed. In an attempt to prevent mu-oxo dimer formation, and facilitate the observation of O2-bound intermediates, a bulkier tertiary amine ligand, tren-Et4= N-(2-amino-ethyl)-N-(2-diethylamino-ethyl)-N',N'-diethyl-ethane-1,2-diamine, and the corresponding [FeII(SMe2N4(tren-Et4))]+ (5) complex was synthesized and structurally characterized. Steric repulsive interactions create unusually long FeII-N(3,4) amine bonds in 5 (mean distance=2.219(1) A). The [(tren-Et4)N4SMe2]1- ligand is unable to accommodate iron in the +3 oxidation state, and consequently, in contrast to most thiolate-ligated Fe(II) complexes, [FeII(SMe2N4(tren-Et4))]+ (5) does not readily react with O2. Oxidation of 5 is irreversible, and the potential (Epa=+410 mV (vs SCE)) is anodically shifted relative to 1 (E1/2=-100 mV (vs SCE)).
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Affiliation(s)
- Roslyn M. Theisen
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700
| | - Jason Shearer
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700
| | | | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700
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