101
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Krewald V, Lassalle-Kaiser B, Boron TT, Pollock CJ, Kern J, Beckwith MA, Yachandra VK, Pecoraro VL, Yano J, Neese F, DeBeer S. The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy. Inorg Chem 2013; 52:12904-14. [PMID: 24161030 PMCID: PMC3911776 DOI: 10.1021/ic4008203] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.
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Affiliation(s)
- Vera Krewald
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Benedikt Lassalle-Kaiser
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thaddeus T. Boron
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christopher J. Pollock
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Jan Kern
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Martha A. Beckwith
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Vittal K. Yachandra
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Junko Yano
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Frank Neese
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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102
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Lassalle-Kaiser B, Boron TT, Krewald V, Kern J, Beckwith MA, Schroeder H, Alonso-Mori R, Nordlund D, Weng TC, Sokaras D, Neese F, Bergmann U, Yachandra VK, DeBeer S, Pecoraro VL, Yano J. Experimental and computational X-ray emission spectroscopy as a direct probe of protonation states in oxo-bridged Mn(IV) dimers relevant to redox-active metalloproteins. Inorg Chem 2013; 52:12915-22. [PMID: 24161081 PMCID: PMC3867288 DOI: 10.1021/ic400821g] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-μ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kβ emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kβ(2,5) peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kβ" peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated μ-oxo bridges dominate this spectral region. The energies of the Kβ" features differ by ~3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (μ-O)(μ-OH2) motif can be distinguished from a symmetric (μ-OH)2 one. The results reported here highlight the sensitivity of Kβ valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.
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Affiliation(s)
- Benedikt Lassalle-Kaiser
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thaddeus T. Boron
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vera Krewald
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Jan Kern
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Martha A. Beckwith
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Henning Schroeder
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Dennis Nordlund
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Tsu-Chien Weng
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Uwe Bergmann
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Vittal K. Yachandra
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Junko Yano
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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103
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Bihani SC, Chakravarty D, Ballal A. Purification, crystallization and preliminary crystallographic analysis of KatB, a manganese catalase from Anabaena PCC 7120. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1299-302. [PMID: 24192374 PMCID: PMC3818058 DOI: 10.1107/s1744309113028017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/11/2013] [Indexed: 11/11/2022]
Abstract
Catalases are enzymes that play an important role in the detoxification of hydrogen peroxide (H2O2) in aerobic organisms. Among catalases, haem-containing catalases are ubiquitously distributed and their enzymatic mechanism is very well understood. On the other hand, manganese catalases that contain a bimanganese core in the active site have been less well characterized and their mode of action is not fully understood. The genome of Anabaena PCC 7120 does not show the presence of a haem catalase-like gene; instead, two ORFs encoding manganese catalases (Mn-catalases) are present. Here, the crystallization and preliminary X-ray crystallographic analysis of KatB, one of the two Mn-catalases from Anabaena, are reported. KatB was crystallized using the hanging-drop vapour-diffusion method with PEG 400 as a precipitant and calcium acetate as an additive. Diffraction data were collected in-house on an Agilent SuperNova system using a microfocus sealed-tube X-ray source. The crystal diffracted to 2.2 Å resolution at 100 K. The tetragonal crystal belonged to space group P4(1)2(1)2 (or enantiomer), with unit-cell parameters a = b = 101.87, c = 138.86 Å. Preliminary X-ray diffraction analysis using the Matthews coefficient and self-rotation function suggests the presence of a trimer in the asymmetric unit.
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Affiliation(s)
- Subhash Chandra Bihani
- Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Dhiman Chakravarty
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400 085, India
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104
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Pandelia ME, Li N, Nørgaard H, Warui DM, Rajakovich LJ, Chang WC, Booker SJ, Krebs C, Bollinger JM. Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate. J Am Chem Soc 2013; 135:15801-12. [PMID: 23987523 PMCID: PMC3869994 DOI: 10.1021/ja405047b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or monounsaturated C(n) fatty aldehydes to formate and the corresponding C(n-1) alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 cosubstrate to the oxidation state of water and incorporates one O-atom from O2 into the formate coproduct. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2(III/III) complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2(III/III) center with resolved subsites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t(1/2) ~ 400 s at 5 °C) to produce a very modest yield of formate (<0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazinium methylsulfate ((MeO)PMS) to yield product, albeit at only ~50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or heterodinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2(III/III)-peroxyhemiacetal complex, which undergoes reductive O-O-bond cleavage, leading to C1-C2 radical fragmentation and formation of the alk(a/e)ne and formate products.
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Affiliation(s)
- Maria E. Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ning Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hanne Nørgaard
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Douglas M. Warui
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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105
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Synthesis, characterization and catalase-like activity of the tetranuclear iron(III) complex involving a (μ-oxo)(μ-hydroxo)bis(μ-alkoxo)tetra(μ-carboxylato)tetrairon core. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.07.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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106
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Schöler A, Zaharieva I, Zimmermann S, Wiechen M, Manke AM, Kurz P, Plieth C, Dau H. Biogenic Manganese-Calcium Oxides on the Cell Walls of the AlgaeChara Corallina: Elemental Composition, Atomic Structure, and Water-Oxidation Catalysis. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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107
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Jana A, Aliaga-Alcalde N, Ruiz E, Mohanta S. Structures, Magnetochemistry, Spectroscopy, Theoretical Study, and Catechol Oxidase Activity of Dinuclear and Dimer-of-Dinuclear Mixed-Valence MnIIIMnII Complexes Derived from a Macrocyclic Ligand. Inorg Chem 2013; 52:7732-46. [DOI: 10.1021/ic400916h] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arpita Jana
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700
009, India
| | - Núria Aliaga-Alcalde
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Institut de Ciència de Materials de Barcelona (ICMAB-CSIC)
Campus de la UAB, 08193 Bellaterra, Spain
| | - Eliseo Ruiz
- Departament de Química Inorgànica and
Institut de Recerca de Química Teòrica i Computacional, Universitat de Barcelona, Diagonal 645, E-08028 Barcelona,
Spain
| | - Sasankasekhar Mohanta
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700
009, India
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108
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Lee WT, Xu S, Dickie DA, Smith JM. A Robust Mn Catalyst for H2O2Disproportionation in Aqueous Solution. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300184] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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109
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Roselli S, Nadalig T, Vuilleumier S, Bringel F. The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study. PLoS One 2013; 8:e56598. [PMID: 23593113 PMCID: PMC3621897 DOI: 10.1371/journal.pone.0056598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/11/2013] [Indexed: 12/24/2022] Open
Abstract
Chloromethane (CH3Cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. The only known pathway for bacterial chloromethane utilization (cmu) was characterized in Methylobacterium extorquens CM4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. Previous work demonstrated that tetrahydrofolate and vitamin B12 are essential cofactors of cmuA- and cmuB-encoded methyltransferases of chloromethane dehalogenase, and that the pathway for chloromethane utilization is distinct from that for methanol. This work reports genomic and proteomic data demonstrating that cognate cmu genes are located on the 380 kb pCMU01 plasmid, which drives the previously defined pathway for tetrahydrofolate-mediated chloromethane dehalogenation. Comparison of complete genome sequences of strain CM4 and that of four other M. extorquens strains unable to grow with chloromethane showed that plasmid pCMU01 harbors unique genes without homologs in the compared genomes (bluB2, btuB, cobA, cbiD), as well as 13 duplicated genes with homologs of chromosome-borne genes involved in vitamin B12-associated biosynthesis and transport, or in tetrahydrofolate-dependent metabolism (folC2). In addition, the presence of both chromosomal and plasmid-borne genes for corrinoid salvaging pathways may ensure corrinoid coenzyme supply in challenging environments. Proteomes of M. extorquens CM4 grown with one-carbon substrates chloromethane and methanol were compared. Of the 49 proteins with differential abundance identified, only five (CmuA, CmuB, PurU, CobH2 and a PaaE-like uncharacterized putative oxidoreductase) are encoded by the pCMU01 plasmid. The mainly chromosome-encoded response to chloromethane involves gene clusters associated with oxidative stress, production of reducing equivalents (PntAA, Nuo complex), conversion of tetrahydrofolate-bound one-carbon units, and central metabolism. The mosaic organization of plasmid pCMU01 and the clustering of genes coding for dehalogenase enzymes and for biosynthesis of associated cofactors suggests a history of gene acquisition related to chloromethane utilization.
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Affiliation(s)
- Sandro Roselli
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Thierry Nadalig
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Stéphane Vuilleumier
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Françoise Bringel
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
- * E-mail:
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110
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Aerobic metabolism and oxidative stress tolerance in the Lactobacillus plantarum group. World J Microbiol Biotechnol 2013; 29:1713-22. [DOI: 10.1007/s11274-013-1334-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/22/2013] [Indexed: 11/25/2022]
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111
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Roos K, Siegbahn PEM. Activation of Dimanganese Class Ib Ribonucleotide Reductase by Hydrogen Peroxide: Mechanistic Insights from Density Functional Theory. Inorg Chem 2013; 52:4173-84. [DOI: 10.1021/ic3008427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Katarina Roos
- Department of Physics, Stockholm University, SE-106 91 Stockholm,
Sweden
| | - Per E. M. Siegbahn
- Department of Physics, Stockholm University, SE-106 91 Stockholm,
Sweden
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112
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Westphal A, Klinkebiel A, Berends HM, Broda H, Kurz P, Tuczek F. Electronic Structure and Spectroscopic Properties of Mononuclear Manganese(III) Schiff Base Complexes: A Systematic Study on [Mn(acen)X] Complexes by EPR, UV/vis, and MCD Spectroscopy (X = Hal, NCS). Inorg Chem 2013; 52:2372-87. [DOI: 10.1021/ic301889e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anne Westphal
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
| | - Arne Klinkebiel
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
| | - Hans-Martin Berends
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
| | - Henning Broda
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
| | - Philipp Kurz
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
| | - Felix Tuczek
- Institut
für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel, D-24118 Kiel, Germany
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113
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Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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114
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Zámocký M, Gasselhuber B, Furtmüller PG, Obinger C. Molecular evolution of hydrogen peroxide degrading enzymes. Arch Biochem Biophys 2012; 525:131-44. [PMID: 22330759 PMCID: PMC3523812 DOI: 10.1016/j.abb.2012.01.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 01/26/2012] [Accepted: 01/27/2012] [Indexed: 12/27/2022]
Abstract
For efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2H(2)O(2) → O(2) + 2H(2)O), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. Here we report on the updated reconstruction of the molecular phylogeny of these three gene families. Ubiquitous typical (monofunctional) heme catalases are found in all domains of life showing a high structural conservation. Their evolution was directed from large subunit towards small subunit proteins and further to fused proteins where the catalase fold was retained but lost its original functionality. Bifunctional catalase-peroxidases were at the origin of one of the two main heme peroxidase superfamilies (i.e. peroxidase-catalase superfamily) and constitute a protein family predominantly present among eubacteria and archaea, but two evolutionary branches are also found in the eukaryotic world. Non-heme manganese catalases are a relatively small protein family with very old roots only present among bacteria and archaea. Phylogenetic analyses of the three protein families reveal features typical (i) for the evolution of whole genomes as well as (ii) for specific evolutionary events including horizontal gene transfer, paralog formation and gene fusion. As catalases have reached a striking diversity among prokaryotic and eukaryotic pathogens, understanding their phylogenetic and molecular relationship and function will contribute to drug design for prevention of diseases of humans, animals and plants.
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Affiliation(s)
- Marcel Zámocký
- Division of Biochemistry, Department of Chemistry, Vienna Institute of BioTechnology at BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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115
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Gómez V, Corbella M, Mautner FA, Roubeau O, Teat SJ, Font-Bardia M, Calvet T. Manganese compounds with phthalate and terephthalate ligands: Synthesis, crystal structure, magnetic properties and catalase activity. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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116
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117
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Abstract
Bacillus pumilus SAFR-032, isolated at spacecraft assembly facilities of the National Aeronautics and Space Administration Jet Propulsion Laboratory, is difficult to kill by the sterilization method of choice, which uses liquid or vapor hydrogen peroxide. We identified two manganese catalases, YjqC and BPUM_1305, in spore protein extracts of several B. pumilus strains by using PAGE and mass spectrometric analyses. While the BPUM_1305 catalase was present in six of the B. pumilus strains tested, YjqC was not detected in ATCC 7061 and BG-B79. Furthermore, both catalases were localized in the spore coat layer along with laccase and superoxide dismutase. Although the initial catalase activity in ATCC 7061 spores was higher, it was less stable over time than the SAFR-032 enzyme. We propose that synergistic activity of YjqC and BPUM_1305, along with other coat oxidoreductases, contributes to the enhanced resistance of B. pumilus spores to hydrogen peroxide. We observed that the product of the catalase reaction, gaseous oxygen, forms expanding vesicles on the spore surface, affecting the mechanical integrity of the coat layer, resulting in aggregation of the spores. The accumulation of oxygen gas and aggregations may play a crucial role in limiting further exposure of Bacilli spore surfaces to hydrogen peroxide or other toxic chemicals when water is present.
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118
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Ebrahimi KH, Hagedoorn PL, van der Weel L, Verhaert PDEM, Hagen WR. A novel mechanism of iron-core formation by Pyrococcus furiosus archaeoferritin, a member of an uncharacterized branch of the ferritin-like superfamily. J Biol Inorg Chem 2012; 17:975-85. [PMID: 22739810 PMCID: PMC3401498 DOI: 10.1007/s00775-012-0913-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
Storage of iron in a nontoxic and bioavailable form is essential for many forms of life. Three subfamilies of the ferritin-like superfamily, namely, ferritin, bacterioferritin, and Dps (DNA-binding proteins from starved cells), are able to store iron. Although the function of these iron-storage proteins is constitutive to many organisms to sustain life, the genome of some organisms appears not to encode any of these proteins. In an attempt to identify new iron-storage systems, we have found and characterized a new member of the ferritin-like superfamily of proteins, which unlike the multimeric storage system of ferritin, bacterioferritin, and Dps is monomeric in the absence of iron. Monomers catalyze oxidation of Fe(II) and they store the Fe(III) product as they assemble to form structures comparable to those of 24-meric ferritin. We propose that this mechanism is an alternative method of iron storage by the ferritin-like superfamily of proteins in organisms that lack the regular preassociated 24-meric/12-meric ferritins.
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120
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Gómez V, Corbella M. Catalase Activity of Dinuclear Mn
III
Compounds with Chlorobenzoato Bridges. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Verónica Gómez
- Department de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain, Fax: +34‐934907725
| | - Montserrat Corbella
- Department de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain, Fax: +34‐934907725
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121
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Mishra S, Imlay J. Why do bacteria use so many enzymes to scavenge hydrogen peroxide? Arch Biochem Biophys 2012; 525:145-60. [PMID: 22609271 DOI: 10.1016/j.abb.2012.04.014] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/13/2012] [Accepted: 04/14/2012] [Indexed: 12/16/2022]
Abstract
Hydrogen peroxide (H(2)O(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. Because H(2)O(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. Mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. In order to understand how bacteria cope with oxidative stress, it is important to identify the key enzymes involved in H(2)O(2) degradation. Catalases and NADH peroxidase (Ahp) are primary scavengers in many bacteria, and their activities and physiological impacts have been unambiguously demonstrated through phenotypic analysis and through direct measurements of H(2)O(2) clearance in vivo. Yet a wide variety of additional enzymes have been proposed to serve similar roles: thiol peroxidase, bacterioferritin comigratory protein, glutathione peroxidase, cytochrome c peroxidase, and rubrerythrins. Each of these enzymes can degrade H(2)O(2) in vitro, but their contributions in vivo remain unclear. In this review we examine the genetic, genomic, regulatory, and biochemical evidence that each of these is a bonafide scavenger of H(2)O(2) in the cell. We also consider possible reasons that bacteria might require multiple enzymes to catalyze this process, including differences in substrate specificity, compartmentalization, cofactor requirements, kinetic optima, and enzyme stability. It is hoped that the resolution of these issues will lead to an understanding of stress resistance that is more accurate and perceptive.
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Affiliation(s)
- Surabhi Mishra
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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122
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Corbella M, Fernández G, González P, Maestro M, Font‐Bardia M, Stoeckli‐Evans H. Dinuclear Mn
III
Compounds [{Mn(bpy)(H
2
O)}
2
(μ‐4‐RC
6
H
4
COO)
2
(μ‐O)](NO
3
)
2
(R = Me, F, CF
3
, MeO,
t
Bu): Effect of the R Group on the Magnetic Properties and the Catalase Activity. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201101433] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Montserrat Corbella
- Departament de Química Inorgànica and Institut de Nanociènciai Nanotecnologia (INIUB), Universitat de Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain, Fax: +34‐934907725
| | - Gema Fernández
- Departament de Química Inorgànica and Institut de Nanociènciai Nanotecnologia (INIUB), Universitat de Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain, Fax: +34‐934907725
| | - Patricia González
- Departament de Química Inorgànica and Institut de Nanociènciai Nanotecnologia (INIUB), Universitat de Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain, Fax: +34‐934907725
| | - Miguel Maestro
- Departamento de Química Fundamental and Servicios Xerais de Apoio a Investigación, Universidade da Coruña, 15071 A Coruña, Spain
| | - Mercè Font‐Bardia
- Departamento de Cristallografia, Mineralogia i DipòsitsMinerals, Universitat de Barcelona, Martí i Franquès s/n, and Unitat de Difracció de RX, Serveis Científico‐Tècnics, Universitat de Barcelona, Solé i Sabarís 1–3, 08028 Barcelona, Spain
| | - Helen Stoeckli‐Evans
- Institut de Chimie, Université de Neuchâtel, Av. Bellevaux 51, 2007 Neuchâtel, Switzerland
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123
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McConnell IL, Grigoryants VM, Scholes CP, Myers WK, Chen PY, Whittaker JW, Brudvig GW. EPR-ENDOR characterization of (17O, 1H, 2H) water in manganese catalase and its relevance to the oxygen-evolving complex of photosystem II. J Am Chem Soc 2012; 134:1504-12. [PMID: 22142421 DOI: 10.1021/ja203465y] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of efficient water-oxidation catalysts demands insight into the only known, naturally occurring water-oxidation catalyst, the oxygen-evolving complex (OEC) of photosystem II (PSII). Understanding the water oxidation mechanism requires knowledge of where and when substrate water binds to the OEC. Mn catalase in its Mn(III)-Mn(IV) state is a protein model of the OEC's S(2) state. From (17)O-labeled water exchanged into the di-μ-oxo di-Mn(III,IV) coordination sphere of Mn catalase, CW Q-band ENDOR spectroscopy revealed two distinctly different (17)O signals incorporated in distinctly different time regimes. First, a signal appearing after 2 h of (17)O exchange was detected with a 13.0 MHz hyperfine coupling. From similarity in the time scale of isotope incorporation and in the (17)O μ-oxo hyperfine coupling of the di-μ-oxo di-Mn(III,IV) bipyridine model (Usov, O. M.; Grigoryants, V. M.; Tagore, R.; Brudvig, G. W.; Scholes, C. P. J. Am. Chem. Soc. 2007, 129, 11886-11887), this signal was assigned to μ-oxo oxygen. EPR line broadening was obvious from this (17)O μ-oxo species. Earlier exchange proceeded on the minute or faster time scale into a non-μ-oxo position, from which (17)O ENDOR showed a smaller 3.8 MHz hyperfine coupling and possible quadrupole splittings, indicating a terminal water of Mn(III). Exchangeable proton/deuteron hyperfine couplings, consistent with terminal water ligation to Mn(III), also appeared. Q-band CW ENDOR from the S(2) state of the OEC was obtained following multihour (17)O exchange, which showed a (17)O hyperfine signal with a 11 MHz hyperfine coupling, tentatively assigned as μ-oxo-(17)O by resemblance to the μ-oxo signals from Mn catalase and the di-μ-oxo di-Mn(III,IV) bipyridine model.
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Affiliation(s)
- Iain L McConnell
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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124
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Xie YE, Tian CB, Zhang HB, Peng Y, Li XQ, Li ZH, Lin P, Du SW. A new 2D honeycomb-like cluster polymer built by a {Mn6Na3} cluster: Synthesis and magnetic property. INORG CHEM COMMUN 2012. [DOI: 10.1016/j.inoche.2011.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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125
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Berends HM, Manke AM, Näther C, Tuczek F, Kurz P. A manganese oxido complex bearing facially coordinating trispyridyl ligands – is coordination geometry crucial for water oxidation catalysis? Dalton Trans 2012; 41:6215-24. [DOI: 10.1039/c2dt30129f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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126
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Pace RJ, Stranger R, Petrie S. Why nature chose Mn for the water oxidase in Photosystem II. Dalton Trans 2012; 41:7179-89. [DOI: 10.1039/c2dt30185g] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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127
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Wiechen M, Berends HM, Kurz P. Wateroxidation catalysed by manganese compounds: from complexes to ‘biomimetic rocks’. Dalton Trans 2012; 41:21-31. [PMID: 22068958 DOI: 10.1039/c1dt11537e] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Mathias Wiechen
- Institute for Inorganic Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Straße 2, 24118, Kiel, Germany
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128
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Whittaker JW. Non-heme manganese catalase--the 'other' catalase. Arch Biochem Biophys 2011; 525:111-20. [PMID: 22198285 DOI: 10.1016/j.abb.2011.12.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 12/09/2011] [Accepted: 12/10/2011] [Indexed: 12/24/2022]
Abstract
Non-heme manganese catalases are widely distributed over microbial life and represent an environmentally important alternative to heme-containing catalases in antioxidant defense. Manganese catalases contain a binuclear manganese complex as their catalytic active site rather than a heme, and cycle between Mn(2)(II,II) and Mn(2)(III,III) states during turnover. X-ray crystallography has revealed the key structural elements of the binuclear manganese active site complex that can serve as the starting point for computational studies on the protein. Four manganese catalase enzymes have been isolated and characterized, and the enzyme appears to have a broad phylogenetic distribution including both bacteria and archae. More than 100 manganese catalase genes have been annotated in genomic databases, although the assignment of many of these putative manganese catalases needs to be experimentally verified. Iron limitation, exposure to low levels of peroxide stress, thermostability and cyanide resistance may provide the biological and environmental context for the occurrence of manganese catalases.
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Affiliation(s)
- James W Whittaker
- Institute for Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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129
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Liers C, Ullrich R, Hofrichter M, Minibayeva FV, Beckett RP. A heme peroxidase of the ascomyceteous lichen Leptogium saturninum oxidizes high-redox potential substrates. Fungal Genet Biol 2011; 48:1139-45. [DOI: 10.1016/j.fgb.2011.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/18/2011] [Accepted: 10/21/2011] [Indexed: 11/16/2022]
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130
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Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM. The catalase activity of diiron adenine deaminase. Protein Sci 2011; 20:2080-94. [PMID: 21998098 DOI: 10.1002/pro.748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 09/28/2011] [Accepted: 09/29/2011] [Indexed: 11/05/2022]
Abstract
Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mössbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 × 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.
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Affiliation(s)
- Siddhesh S Kamat
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3012, USA
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131
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Cotruvo JA, Stubbe J. Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo. Annu Rev Biochem 2011; 80:733-67. [PMID: 21456967 DOI: 10.1146/annurev-biochem-061408-095817] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Incorporation of metallocofactors essential for the activity of many enyzmes is a major mechanism of posttranslational modification. The cellular machinery required for these processes in the case of mono- and dinuclear nonheme iron and manganese cofactors has remained largely elusive. In addition, many metallocofactors can be converted to inactive forms, and pathways for their repair have recently come to light. The class I ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and require dinuclear metal clusters for activity: an Fe(III)Fe(III)-tyrosyl radical (Y•) cofactor (class Ia), a Mn(III)Mn(III)-Y• cofactor (class Ib), and a Mn(IV)Fe(III) cofactor (class Ic). The class Ia, Ib, and Ic RNRs are structurally homologous and contain almost identical metal coordination sites. Recent progress in our understanding of the mechanisms by which the cofactor of each of these RNRs is generated in vitro and in vivo and by which the damaged cofactors are repaired is providing insight into how nature prevents mismetallation and orchestrates active cluster formation in high yields.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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132
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Corbella M, Gómez V, Garcia B, Rodriguez E, Albela B, Maestro MA. Synthesis, crystal structure and magnetic properties of new dinuclear Mn(III) compounds with 4-ClC6H4COO and 4-BrC6H4COO bridges. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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133
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Palopoli C, Bruzzo N, Hureau C, Ladeira S, Murgida D, Signorella S. Synthesis, Characterization, and Catalase Activity of a Water-Soluble diMnIII Complex of a Sulphonato-Substituted Schiff Base Ligand: An Efficient Catalyst for H2O2 Disproportionation. Inorg Chem 2011; 50:8973-83. [DOI: 10.1021/ic2011452] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Claudia Palopoli
- Departamento de Química Física/IQUIR-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Natalia Bruzzo
- Departamento de Química Física/IQUIR-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205, route de Narbonne, F-31077 Toulouse, France and Université de Toulouse, UPS, INPT, LCC, F-31077 Toulouse, France
| | - Sonia Ladeira
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205, route de Narbonne, F-31077 Toulouse, France and Université de Toulouse, UPS, INPT, LCC, F-31077 Toulouse, France
- Institut de Chimie de Toulouse, FR2599, 118 route de Narbonne, F-31062 Toulouse, France
| | - Daniel Murgida
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA, Argentina
| | - Sandra Signorella
- Departamento de Química Física/IQUIR-CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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134
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Cox N, Ames W, Epel B, Kulik LV, Rapatskiy L, Neese F, Messinger J, Wieghardt K, Lubitz W. Electronic structure of a weakly antiferromagnetically coupled Mn(II)Mn(III) model relevant to manganese proteins: a combined EPR, 55Mn-ENDOR, and DFT study. Inorg Chem 2011; 50:8238-51. [PMID: 21834536 DOI: 10.1021/ic200767e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An analysis of the electronic structure of the [Mn(II)Mn(III)(μ-OH)-(μ-piv)(2)(Me(3)tacn)(2)](ClO(4))(2) (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the Mn(III). All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the (55)Mn-ENDOR constrains the (55)Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the Mn(II) and Mn(III) ions. The large effective hyperfine tensor anisotropy of the Mn(II), a d(5) ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the Mn(III) ion strongly perturbs the zero-field energy levels of the Mn(II)Mn(III) complex. An estimate of the fine structure parameter (d) for the Mn(III) of -4 cm(-1) was made, by assuming the intrinsic anisotropy of the Mn(II) ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the Mn(III) is consistent with the known coordination environment of the Mn(III) ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.
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Affiliation(s)
- Nicholas Cox
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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135
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Synthesis and catalase-like activity of dimanganese complexes with phthalazine-based ligands. TRANSIT METAL CHEM 2011. [DOI: 10.1007/s11243-011-9508-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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136
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Structure, magnetic properties, catalase activity and DFT studies of [Mn2(μ-RCOO)2(μ-OR)2]2+ type dinuclear manganese(III,III) complexes. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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137
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Oguchi R, Terashima I, Kou J, Chow WS. Operation of dual mechanisms that both lead to photoinactivation of Photosystem II in leaves by visible light. PHYSIOLOGIA PLANTARUM 2011; 142:47-55. [PMID: 21288248 DOI: 10.1111/j.1399-3054.2011.01452.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Photosystem II (PS II) is photoinactivated during photosynthesis, requiring repair to maintain full function during the day. What is the mechanism(s) of the initial events that lead to photoinactivation of PS II? Two hypotheses have been put forward. The 'excess-energy hypothesis' states that excess energy absorbed by chlorophyll (Chl), neither utilized in photosynthesis nor dissipated harmlessly in non-photochemical quenching, leads to PS II photoinactivation; the 'Mn hypothesis' (also termed the two-step hypothesis) states that light absorption by the Mn cluster in PS II is the primary effect that leads to dissociation of Mn, followed by damage to the reaction centre by light absorption by Chl. Observations from various studies support one or the other hypothesis, but each hypothesis alone cannot explain all the observations. We propose that both mechanisms operate in the leaf, with the relative contribution from each mechanism depending on growth conditions or plant species. Indeed, in a single system, namely, the interior of a leaf, we could observe one or the other mechanism at work, depending on the location within the tissue. There is no reason to expect the two mechanisms to be mutually exclusive.
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Affiliation(s)
- Riichi Oguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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138
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Shevela D, Koroidov S, Najafpour MM, Messinger J, Kurz P. Calcium Manganese Oxides as Oxygen Evolution Catalysts: O
2
Formation Pathways Indicated by
18
O‐Labelling Studies. Chemistry 2011; 17:5415-23. [DOI: 10.1002/chem.201002548] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Dmitriy Shevela
- Department of Chemistry, Umeå University, Linnaeus Väg 6 (KBC huset), 90187 Umeå (Sweden), Fax: (+46) 90‐786‐5293
- Current address: Center for Organelle Research (CORE), University of Stavanger, Kristine Bonnevis vei 22, 4036 Stavanger (Norway)
| | - Sergey Koroidov
- Department of Chemistry, Umeå University, Linnaeus Väg 6 (KBC huset), 90187 Umeå (Sweden), Fax: (+46) 90‐786‐5293
| | - M. Mahdi Najafpour
- Institute for Advanced Studies in Basic Sciences (IASBS), P. O. Box 45195‐1159, 45195 Zanjan (Iran)
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus Väg 6 (KBC huset), 90187 Umeå (Sweden), Fax: (+46) 90‐786‐5293
| | - Philipp Kurz
- Institute for Inorganic Chemistry, Christian‐Albrechts‐University Kiel, Max‐Eyth‐Strasse 2, 24118 Kiel (Germany), Fax: (+49)431‐880‐1520
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139
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Wałęsa-Chorab M, Stefankiewicz AR, Ciesielski D, Hnatejko Z, Kubicki M, Kłak J, Korabik MJ, Patroniak V. New mononuclear manganese(II) and zinc(II) complexes with a terpyridine ligand: Structural, magnetic and spectroscopic properties. Polyhedron 2011. [DOI: 10.1016/j.poly.2010.12.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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140
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Lal R, Basumatary D, Chanu O, Lemtur A, Asthana M, Kumar A, De A. Synthesis, characterization, reactivity, and electrochemical studies of manganese(IV) complexes of bis(2-hydroxy-1-naphthaldehyde)adipoyldihydrazone. J COORD CHEM 2011. [DOI: 10.1080/00958972.2010.542238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R.A. Lal
- a Department of Chemistry , North-Eastern Hill University , Shillong 793022, Meghalaya, India
| | - D. Basumatary
- a Department of Chemistry , North-Eastern Hill University , Shillong 793022, Meghalaya, India
| | - O.B. Chanu
- a Department of Chemistry , North-Eastern Hill University , Shillong 793022, Meghalaya, India
| | - A. Lemtur
- a Department of Chemistry , North-Eastern Hill University , Shillong 793022, Meghalaya, India
| | - M. Asthana
- a Department of Chemistry , North-Eastern Hill University , Shillong 793022, Meghalaya, India
| | - A. Kumar
- b Department of Chemistry, Faculty of Science and Agriculture , The University of the West Indies , St. Augustine, Trinidad and Tobago, West Indies
| | - A.K. De
- c Department of Science and Humanities , Tripura Institute of Technology , Natsingarh 799009, Tripura, India
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141
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Högbom M. Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear—an intricate bioinorganic workaround to use different metals for the same reaction. Metallomics 2011; 3:110-20. [DOI: 10.1039/c0mt00095g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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142
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Allen JP, Williams JC. The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers. PHOTOSYNTHESIS RESEARCH 2011; 107:59-69. [PMID: 20449659 DOI: 10.1007/s11120-010-9552-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 04/05/2010] [Indexed: 05/29/2023]
Abstract
In photosynthetic organisms, such as purple bacteria, cyanobacteria, and plants, light is captured and converted into energy to create energy-rich compounds. The primary process of energy conversion involves the transfer of electrons from an excited donor molecule to a series of electron acceptors in pigment-protein complexes. Two of these complexes, the bacterial reaction center and photosystem II, are evolutionarily related and structurally similar. However, only photosystem II is capable of performing the unique reaction of water oxidation. An understanding of the evolutionary process that lead to the development of oxygenic photosynthesis can be found by comparison of these two complexes. In this review, we summarize how insight is being gained by examination of the differences in critical functional properties of these complexes and by experimental efforts to alter pigment-protein interactions of the bacterial reaction center in order to enable it to perform reactions, such as amino acid and metal oxidation, observable in photosystem II.
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Affiliation(s)
- J P Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.
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143
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Synthesis, spectral characterization, and single crystal X-ray structures of a series of manganese-2,2′-bipyridine complexes derived from substituted aromatic carboxylic acids. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2010.09.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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144
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Diversity of stress tolerance in Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum: A multivariate screening study. Int J Food Microbiol 2010; 144:270-9. [DOI: 10.1016/j.ijfoodmicro.2010.10.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 11/19/2022]
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145
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Bolshakov IA, Vygodina TV, Gennis R, Karyakin AA, Konstantinov AA. Catalase Activity of Cytochrome c Oxidase Assayed with Hydrogen Peroxide-Sensitive Electrode Microsensor. BIOCHEMISTRY (MOSCOW) 2010; 75:1352-60. [DOI: 10.1134/s0006297910110064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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146
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Stich TA, Whittaker JW, Britt RD. Multifrequency EPR studies of manganese catalases provide a complete description of proteinaceous nitrogen coordination. J Phys Chem B 2010; 114:14178-88. [PMID: 20055466 PMCID: PMC3418057 DOI: 10.1021/jp908064y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Pulse electron paramagnetic resonance (EPR) spectroscopy is employed at two very different excitation frequencies, 9.77 and 30.67 GHz, in the study of the nitrogen coordination environment of the Mn(III)Mn(IV) state of the dimanganese-containing catalases from Lactobacillus plantarum and Thermus thermophilus. Consistent with previous studies, the lower-frequency results reveal one unique histidine nitrogen-Mn cluster interaction. For the first time, a second, more strongly hyperfine-coupled (14)N atom is unambiguously observed through the use of higher frequency/higher field EPR spectroscopy. The low excitation frequency spectral features are rationalized as arising from the interaction of a histidine nitrogen that is bound to the Mn(IV) ion, and the higher excitation frequency features are attributed to the histidine nitrogen bound to the Mn(III) ion. These results allow for the computation of intrinsic hyperfine coupling constants, which range from 2.2 to 2.9 MHz, for sp(2)-hybridized nitrogens coordinating equatorially to high-valence Mn ions. The relevance of these findings is discussed in the context of recent results from analogous higher frequency EPR studies of the Mn cluster in photosystem II and other exchange-coupled, transition metal-containing systems.
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Affiliation(s)
- Troy A. Stich
- Department of Chemistry, University of California–Davis, One Shields Avenue, Davis, CA 95616
| | - James W. Whittaker
- Department of Science and Engineering, School of Medicine, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006
| | - R. David Britt
- Department of Chemistry, University of California–Davis, One Shields Avenue, Davis, CA 95616
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147
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Chi Z, Liu R, Zhang H. Potential enzyme toxicity of oxytetracycline to catalase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:5399-5404. [PMID: 20800878 DOI: 10.1016/j.scitotenv.2010.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 05/29/2023]
Abstract
Oxytetracycline (OTC) is a kind of widely used veterinary drugs. The residue of OTC in the environment is potentially harmful. In the present work, the non-covalent toxic interaction of OTC with catalase was investigated by the fluorescence spectroscopy, UV-vis absorption and circular dichroism (CD) spectroscopy at physiological pH 7.4. OTC can interact with catalase to form a complex mainly by van der Waals' interactions and hydrogen bonds with one binding site. The association constants K were determined to be K(293K)=7.09×10(4)Lmol(-1) and K(311K)=3.31×10(4)Lmol(-1). The thermodynamic parameters (ΔH°, ΔG° and ΔS°) of the interaction were calculated. Based on the Förster theory of non-radiative energy transfer, the distance between bound OTC and the tryptophan residues of catalase was determined to be 6.48nm. The binding of OTC can result in change of the micro-environment of the tryptophan residues and the secondary structure of catalase. The activity of catalase was also inhibited for the bound OTC. This work establishes a new strategy to probe the enzyme toxicity of veterinary drug residues and is helpful for clarifying the molecular toxic mechanism of OTC in vivo. The established strategy can be used to investigate the potential enzyme toxicity of other small organic pollutants and drugs.
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Affiliation(s)
- Zhenxing Chi
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road,Jinan 250100, PR China
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148
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Harding MM, Nowicki MW, Walkinshaw MD. Metals in protein structures: a review of their principal features. CRYSTALLOGR REV 2010. [DOI: 10.1080/0889311x.2010.485616] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Marjorie M. Harding
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Matthew W. Nowicki
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Malcolm D. Walkinshaw
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
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149
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150
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Boal AK, Cotruvo JA, Stubbe J, Rosenzweig AC. Structural basis for activation of class Ib ribonucleotide reductase. Science 2010; 329:1526-30. [PMID: 20688982 DOI: 10.1126/science.1190187] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y•) or a Fe(III)2-Y• cofactor in the NrdF subunit. Whereas Fe(III)2-Y• can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y• cofactor assembly.
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Affiliation(s)
- Amie K Boal
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA
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