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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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2
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Ohta S. Direct Targets and Subsequent Pathways for Molecular Hydrogen to Exert Multiple Functions: Focusing on Interventions in Radical Reactions. Curr Pharm Des 2021; 27:595-609. [PMID: 32767925 DOI: 10.2174/1381612826666200806101137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/27/2020] [Indexed: 01/10/2023]
Abstract
Molecular hydrogen (H2) was long regarded as non-functional in mammalian cells. We overturned the concept by demonstrating that H2 exhibits antioxidant effects and protects cells against oxidative stress. Subsequently, it has been revealed that H2 has multiple functions in addition to antioxidant effects, including antiinflammatory, anti-allergic functions, and as cell death and autophagy regulation. Additionally, H2 stimulates energy metabolism. As H2 does not readily react with most biomolecules without a catalyst, it is essential to identify the primary targets with which H2 reacts or interacts directly. As a first event, H2 may react directly with strong oxidants, such as hydroxyl radicals (•OH) in vivo. This review addresses the key issues related to this in vivo reaction. •OH may have a physiological role because it triggers a free radical chain reaction and may be involved in the regulation of Ca2+- or mitochondrial ATP-dependent K+-channeling. In the subsequent pathway, H2 suppressed a free radical chain reaction, leading to decreases in lipid peroxide and its end products. Derived from the peroxides, 4-hydroxy-2-nonenal functions as a mediator that up-regulates multiple functional PGC-1α. As the other direct target in vitro and in vivo, H2 intervenes in the free radical chain reaction to modify oxidized phospholipids, which may act as an antagonist of Ca2+-channels. The resulting suppression of Ca2+-signaling inactivates multiple functional NFAT and CREB transcription factors, which may explain H2 multi-functionality. This review also addresses the involvement of NFAT in the beneficial role of H2 in COVID-19, Alzheimer's disease and advanced cancer. We discuss some unsolved issues of H2 action on lipopolysaccharide signaling, MAPK and NF-κB pathways and the Nrf2 paradox. Finally, as a novel idea for the direct targeting of H2, this review introduces the possibility that H2 causes structural changes in proteins via hydrate water changes.
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Affiliation(s)
- Shigeo Ohta
- Department of Neurology Medicine, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan
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3
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Fan Q, Neubauer P, Lenz O, Gimpel M. Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview. Int J Mol Sci 2020; 21:E5890. [PMID: 32824336 PMCID: PMC7460606 DOI: 10.3390/ijms21165890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023] Open
Abstract
Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Peter Neubauer
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Oliver Lenz
- Department of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Matthias Gimpel
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
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4
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[FeFe]-hydrogenase active site mimics containing pyridyl-functionalized phosphine ligands: Synthesis, characterization and electrochemical investigation. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Hartmann S, Frielingsdorf S, Ciaccafava A, Lorent C, Fritsch J, Siebert E, Priebe J, Haumann M, Zebger I, Lenz O. O2-Tolerant H2 Activation by an Isolated Large Subunit of a [NiFe] Hydrogenase. Biochemistry 2018; 57:5339-5349. [DOI: 10.1021/acs.biochem.8b00760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sven Hartmann
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alexandre Ciaccafava
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Johannes Fritsch
- Department of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Elisabeth Siebert
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Jacqueline Priebe
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
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6
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Das R, Neese F, van Gastel M. Hydrogen evolution in [NiFe] hydrogenases and related biomimetic systems: similarities and differences. Phys Chem Chem Phys 2016; 18:24681-92. [DOI: 10.1039/c6cp03672d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic overview of the orbitals that play a role in the cycle of reversible hydrogen oxidation in [NiFe] hydrogenases.
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Affiliation(s)
- Ranjita Das
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Maurice van Gastel
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
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7
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Song LC, Sun XJ, Jia GJ, Wang MM, Song HB. Synthesis, structural characterization, and electrochemical properties of (diphosphine)Ni-bridged butterfly Fe2E2 (E = S, Se, Te) cluster complexes related to [NiFe]-hydrogenases. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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9
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Li CG, Zhu Y, Jiao XX, Fu XQ. Synthesis, characterization and electrochemistry of phenyl-functionalized diiron propanedithiolate complexes. Polyhedron 2014. [DOI: 10.1016/j.poly.2013.09.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Song LC, Li JP, Xie ZJ, Song HB. Synthesis, Structural Characterization, and Electrochemical Properties of Dinuclear Ni/Mn Model Complexes for the Active Site of [NiFe]-Hydrogenases. Inorg Chem 2013; 52:11618-26. [DOI: 10.1021/ic401978h] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry,
State Key Laboratory
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Jia-Peng Li
- Department of Chemistry,
State Key Laboratory
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao-Jun Xie
- Department of Chemistry,
State Key Laboratory
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Hai-Bin Song
- Department of Chemistry,
State Key Laboratory
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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11
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Song LC, Gai B, Feng ZH, Du ZQ, Xie ZJ, Sun XJ, Song HB. Synthesis, Structures, and Some Properties of Diiron Oxadiselenolate (ODSe) and Thiodiselenolate (TDSe) Complexes as Models for the Active Site of [FeFe]-Hydrogenases. Organometallics 2013. [DOI: 10.1021/om400309j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Cheng Song
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Bin Gai
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Zhan-Heng Feng
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Zong-Qiang Du
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Zhao-Jun Xie
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Xiao-Jing Sun
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
| | - Hai-Bin Song
- Department
of Chemistry, State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin 300071,
China
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12
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Principles of direct (mediator free) bioelectrocatalysis. Bioelectrochemistry 2012; 88:70-5. [DOI: 10.1016/j.bioelechem.2012.05.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 04/24/2012] [Accepted: 05/03/2012] [Indexed: 11/21/2022]
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13
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Li YL, Xie B, Zou LK, Zhang XL, Lin X. Investigations on synthesis, structural characterization, and new pathway to the butterfly [2Fe2Se] cluster complexes. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.07.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Computational study of the electronic structure and magnetic properties of the Ni–C state in [NiFe] hydrogenases including the second coordination sphere. J Biol Inorg Chem 2012; 17:1269-81. [DOI: 10.1007/s00775-012-0941-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/11/2012] [Indexed: 10/27/2022]
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15
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Song LC, Sun XJ, Zhao PH, Li JP, Song HB. Synthesis, characterization and some properties of mononuclear Ni and trinuclear NiFe2 complexes related to the active site of [NiFe]-hydrogenases. Dalton Trans 2012; 41:8941-50. [DOI: 10.1039/c2dt30609c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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17
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Keller KL, Wall JD. Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. Front Microbiol 2011; 2:135. [PMID: 21747813 PMCID: PMC3129016 DOI: 10.3389/fmicb.2011.00135] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 06/10/2011] [Indexed: 11/25/2022] Open
Abstract
Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H2 with CO2 during sulfate reduction are exhibited by some strains. The ability to produce or consume H2 provides Desulfovibrio strains the capacity to participate as either partner in interspecies H2 transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c3 (Tp1-c3), or the Type 1 cytochrome c3:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration.
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Affiliation(s)
- Kimberly L Keller
- Department of Biochemistry, University of Missouri Columbia, MO, USA
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18
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Song LC, Li YL, Li L, Gu ZC, Hu QM. Synthetic and structural investigations of linear and macrocyclic nickel/iron/sulfur cluster complexes. Inorg Chem 2011; 49:10174-82. [PMID: 20879721 DOI: 10.1021/ic101451y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three series of new Ni/Fe/S cluster complexes have been prepared and structurally characterized. One series of such complexes includes the linear type of (diphosphine)Ni-bridged double-butterfly Fe/S complexes [(μ-RS)(μ-S═CS)Fe(2)(CO)(6)](2)[Ni(diphosphine)] (1-6; R = Et, t-Bu, n-Bu, Ph; diphosphine = dppv, dppe, dppb), which were prepared by reactions of monoanions [(μ-RS)(μ-CO)Fe(2)(CO)(6)](-) (generated in situ from Fe(3)(CO)(12), Et(3)N, and RSH) with excess CS(2), followed by treatment of the resulting monoanions [(μ-RS)(μ-S═CS)Fe(2)(CO)(6)](-)with (diphosphine)NiCl(2). The second series consists of the macrocyclic type of (diphosphine)Ni-bridged double-butterfly Fe/S complexes [μ-S(CH(2))(4)S-μ][(μ-S═CS)Fe(2)(CO)(6)](2)[Ni(diphosphine)] (7-9; diphosphine = dppv, dppe, dppb), which were produced by the reaction of dianion [{μ-S(CH(2))(4)S-μ}{(μ-CO)Fe(2)(CO)(6)}(2)](2-) (formed in situ from Fe(3)(CO)(12), Et(3)N, and dithiol HS(CH(2))(4)SH with excess CS(2), followed by treatment of the resulting dianion [{μ-S(CH(2))(4)S-μ}{(μ-S═CS)Fe(2)(CO)(6)}(2)](2-) with (diphosphine)NiCl(2). However, more interestingly, when dithiol HS(CH(2))(4)SH (used for the production of 7-9) was replaced by HS(CH(2))(3)SH (a dithiol with a shorter carbon chain), the sequential reactions afforded another type of macrocyclic Ni/Fe/S complex, namely, the (diphosphine)Ni-bridged quadruple-butterfly Fe/S complexes [{μ-S(CH(2))(3)S-μ}{(μ-S═CS)Fe(2)(CO)(6)}(2)](2)[Ni(diphosphine)](2) (10-12; diphosphine = dppv, dppe, dppb). While a possible pathway for the production of the two types of novel metallomacrocycles 7-12 is suggested, all of the new complexes 1-12 were characterized by elemental analysis and spectroscopy and some of them by X-ray crystallography.
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Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
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19
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Song LC, Xie ZJ, Liu XF, Ming JB, Ge JH, Zhang XG, Yan TY, Gao P. Synthetic and structural studies on new diiron azadithiolate (ADT)-type model compounds for active site of [FeFe]hydrogenases. Dalton Trans 2011; 40:837-46. [DOI: 10.1039/c0dt00909a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Soboh B, Krüger S, Kuhns M, Pinske C, Lehmann A, Sawers RG. Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 ofEscherichia coli. FEBS Lett 2010; 584:4109-14. [DOI: 10.1016/j.febslet.2010.08.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/16/2010] [Accepted: 08/24/2010] [Indexed: 11/27/2022]
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21
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Song LC, Liu XF, Ming JB, Ge JH, Xie ZJ, Hu QM. Reactions Starting from Diiron Propanedithiolate [(μ-SCH2)2CH(OH)]Fe2(CO)6 Leading to Malonyl-, PPh3-, and [60]Fullerene-Containing Compounds Relevant to the Active Site of FeFe-Hydrogenases. Organometallics 2010. [DOI: 10.1021/om9009526] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Xu-Feng Liu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Jiang-Bo Ming
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Jian-Hua Ge
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Zhao-Jun Xie
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Qing-Mei Hu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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Schwarz C, Poss Z, Hoffmann D, Appel J. Hydrogenases and Hydrogen Metabolism in Photosynthetic Prokaryotes. RECENT ADVANCES IN PHOTOTROPHIC PROKARYOTES 2010; 675:305-48. [DOI: 10.1007/978-1-4419-1528-3_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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23
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Song LC, Yan J, Li YL, Wang DF, Hu QM. Synthetic and Structural Studies on l-Cysteinyl Group-Containing Diiron/Triiron Azadithiolates as Active Site Models of [FeFe]-Hydrogenases. Inorg Chem 2009; 48:11376-81. [DOI: 10.1021/ic9006179] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li-Cheng Song
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Jing Yan
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Long Li
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - De-Fu Wang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Qing-Mei Hu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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24
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Francoleon DR, Boontheung P, Yang Y, Kim U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, Ogorzalek Loo RR. S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei. J Proteome Res 2009; 8:1972-82. [PMID: 19228054 PMCID: PMC2666069 DOI: 10.1021/pr800923e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The outermost cell envelope structure of many archaea and bacteria contains a proteinaceous lattice termed the surface layer or S-layer. It is typically composed of only one or two abundant, often posttranslationally modified proteins that self-assemble to form the highly organized arrays. Surprisingly, over 100 proteins were annotated to be S-layer components in the archaeal species Methanosarcina acetivorans C2A and Methanosarcina mazei Gö1, reflecting limitations of current predictions. An in vivo biotinylation methodology was devised to affinity tag surface-exposed proteins while overcoming unique challenges in working with these fragile organisms. Cells were adapted to growth under N2 fixing conditions, thus, minimizing free amines reactive to the NHS-label, and high pH media compatible with the acylation chemistry was used. A 3-phase separation procedure was employed to isolate intact, labeled cells from lysed-cell derived proteins. Streptavidin affinity enrichment followed by stringent wash conditions removed nonspecifically bound proteins. This methodology revealed S-layer proteins in M. acetivorans C2A and M. mazei Gö1 to be MA0829 and MM1976, respectively. Each was demonstrated to exist as multiple glycosylated forms using SDS-PAGE coupled with glycoprotein-specific staining, and by interaction with the lectin, Concanavalin A. A number of additional surface-exposed proteins and glycoproteins were identified and included all three subunits of the thermosome: the latter suggests that the chaperonin complex is both surface- and cytoplasmically localized. This approach provides an alternative strategy to study surface proteins in the archaea.
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Affiliation(s)
- Deborah R. Francoleon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Pinmanee Boontheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Yanan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Unmi Kim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - A. Jimmy Ytterberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Patricia A. Denny
- University of Southern California School of Dentistry, Los Angeles, CA 90089
| | - Paul C. Denny
- University of Southern California School of Dentistry, Los Angeles, CA 90089
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
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Peters JW. Carbon Monoxide and Cyanide Ligands in the Active Site of [FeFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The [FeFe]-hydrogenases, although share common features when compared to other metal containing hydrogenases, clearly have independent evolutionary origins. Examples of [FeFe]-hydrogenases have been characterized in detail by biochemical and spectroscopic approaches and the high resolution structures of two examples have been determined. The active site H-cluster is a complex bridged metal assembly in which a [4Fe-4S] cubane is bridged to a 2Fe subcluster with unique non-protein ligands including carbon monoxide, cyanide, and a five carbon dithiolate. Carbon monoxide and cyanide ligands as a component of a native active metal center is a property unique to the metal containing hydrogenases and there has been considerable attention to the characterization of the H-cluster at the level of electronic structure and mechanism as well as to defining the biological means to synthesize such a unique metal cluster. The chapter describes the structural architecture of [FeFe]-hydrogenases and key spectroscopic observations that have afforded the field with a fundamental basis for understanding the relationship between structure and reactivity of the H-cluster. In addition, the results and ideas concerning the topic of H-cluster biosynthesis as an emerging and fascinating area of research, effectively reinforcing the potential linkage between iron-sulfur biochemistry to the role of iron-sulfur minerals in prebiotic chemistry and the origin of life.
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Affiliation(s)
- John W. Peters
- Montana State University, Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center Bozeman, MT 59717 USA
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Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF. J Bacteriol 2007; 190:1447-58. [PMID: 18065529 DOI: 10.1128/jb.01610-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0-A resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd (dissociation constant) of approximately 400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2 heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.
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Löscher S, Schwartz L, Stein M, Ott S, Haumann M. Facilitated Hydride Binding in an Fe−Fe Hydrogenase Active−Site Biomimic Revealed by X-ray Absorption Spectroscopy and DFT Calculations. Inorg Chem 2007; 46:11094-105. [DOI: 10.1021/ic701255p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simone Löscher
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Uppsala University, Department of Photochemistry and Molecular Science, Box 523, 75120 Uppsala, Sweden, EML Research gGmbH, Schloss-Wolfbrunnenweg 33, 69118 Heidelberg, Germany
| | - Lennart Schwartz
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Uppsala University, Department of Photochemistry and Molecular Science, Box 523, 75120 Uppsala, Sweden, EML Research gGmbH, Schloss-Wolfbrunnenweg 33, 69118 Heidelberg, Germany
| | - Matthias Stein
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Uppsala University, Department of Photochemistry and Molecular Science, Box 523, 75120 Uppsala, Sweden, EML Research gGmbH, Schloss-Wolfbrunnenweg 33, 69118 Heidelberg, Germany
| | - Sascha Ott
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Uppsala University, Department of Photochemistry and Molecular Science, Box 523, 75120 Uppsala, Sweden, EML Research gGmbH, Schloss-Wolfbrunnenweg 33, 69118 Heidelberg, Germany
| | - Michael Haumann
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany, Uppsala University, Department of Photochemistry and Molecular Science, Box 523, 75120 Uppsala, Sweden, EML Research gGmbH, Schloss-Wolfbrunnenweg 33, 69118 Heidelberg, Germany
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Vignais PM, Billoud B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem Rev 2007; 107:4206-72. [PMID: 17927159 DOI: 10.1021/cr050196r] [Citation(s) in RCA: 1039] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
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Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y. Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms. J Mol Biol 2007; 372:1045-1054. [PMID: 17706667 DOI: 10.1016/j.jmb.2007.07.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 07/06/2007] [Accepted: 07/11/2007] [Indexed: 12/01/2022]
Abstract
The hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively. Comparison of the apo structure with the ATP-bound structure reveals that binding ATP causes an induced-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions.
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Affiliation(s)
- Yasuhito Shomura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan.
| | - Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
| | - Natsuko Miyabe
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masamitsu Tomiyama
- National Institute of Agrobiological Sciences, 2-1-2 Konnondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan.
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Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res 2007; 6:1917-32. [PMID: 17391016 PMCID: PMC2588348 DOI: 10.1021/pr060394e] [Citation(s) in RCA: 298] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. As many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bionformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200 000 proteins from the Swiss-Prot database, each annotated with at least one of the 875 functional keywords, was described in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V.N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Using this tool, we have found that out of the 710 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (see above). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic, S.; Xie, H.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome Res. 2007, 5, 1899-1916). Protein structure and functionality can be modulated by various post-translational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes approximately 80 Swiss-Prot functional keywords that are related to ligands, post-translational modifications, and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins.
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Affiliation(s)
- Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
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Abstract
Hydrogenases are metalloenzymes subdivided into two classes that contain iron-sulfur clusters and catalyze the reversible oxidation of hydrogen gas (H(2)[Symbol: see text]left arrow over right arrow[Symbol: see text]2H(+)[Symbol: see text]+[Symbol: see text]2e(-)). Two metal atoms are present at their active center: either a Ni and an Fe atom in the [NiFe]hydrogenases, or two Fe atoms in the [FeFe]hydrogenases. They are phylogenetically distinct classes of proteins. The catalytic core of [NiFe]hydrogenases is a heterodimeric protein associated with additional subunits in many of these enzymes. The catalytic core of [FeFe]hydrogenases is a domain of about 350 residues that accommodates the active site (H cluster). Many [FeFe]hydrogenases are monomeric but possess additional domains that contain redox centers, mostly Fe-S clusters. A third class of hydrogenase, characterized by a specific iron-containing cofactor and by the absence of Fe-S cluster, is found in some methanogenic archaea; this Hmd hydrogenase has catalytic properties different from those of [NiFe]- and [FeFe]hydrogenases. The [NiFe]hydrogenases can be subdivided into four subgroups: (1) the H(2) uptake [NiFe]hydrogenases (group 1); (2) the cyanobacterial uptake hydrogenases and the cytoplasmic H(2) sensors (group 2); (3) the bidirectional cytoplasmic hydrogenases able to bind soluble cofactors (group 3); and (4) the membrane-associated, energy-converting, H(2) evolving hydrogenases (group 4). Unlike the [NiFe]hydrogenases, the [FeFe]hydrogenases form a homogeneous group and are primarily involved in H(2) evolution. This review recapitulates the classification of hydrogenases based on phylogenetic analysis and the correlation with hydrogenase function of the different phylogenetic groupings, discusses the possible role of the [FeFe]hydrogenases in the genesis of the eukaryotic cell, and emphasizes the structural and functional relationships of hydrogenase subunits with those of complex I of the respiratory electron transport chain.
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Affiliation(s)
- Paulette M Vignais
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF no. 5092, Institut de Recherches en Technologies et Sciences pour le Vivant, Grenoble cedex 9, France.
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Ngwenya N, Whiteley CG. Recovery of Rhodium(III) from Solutions and Industrial Wastewaters by a Sulfate-Reducing Bacteria Consortium. Biotechnol Prog 2006. [DOI: 10.1002/bp060167h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Manyani H, Rey L, Palacios JM, Imperial J, Ruiz-Argüeso T. Gene products of the hupGHIJ operon are involved in maturation of the iron-sulfur subunit of the [NiFe] hydrogenase from Rhizobium leguminosarum bv. viciae. J Bacteriol 2005; 187:7018-26. [PMID: 16199572 PMCID: PMC1251625 DOI: 10.1128/jb.187.20.7018-7026.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the present study, we investigate the functions of the hupGHIJ operon in the synthesis of an active [NiFe] hydrogenase in the legume endosymbiont Rhizobium leguminosarum bv. viciae. These genes are clustered with 14 other genes including the hydrogenase structural genes hupSL. A set of isogenic mutants with in-frame deletions (deltahupG, deltahupH, deltahupI, and deltahupJ) was generated and tested for hydrogenase activity in cultures grown at different oxygen concentrations (0.2 to 2.0%) and in symbiosis with peas. In free-living cultures, deletions in these genes severely reduced hydrogenase activity. The deltahupH mutant was totally devoid of hydrogenase activity at any of the O2 concentration tested, whereas the requirement of hupGIJ for hydrogenase activity varied with the O2 concentration, being more crucial at higher pO2. Pea bacteroids from the mutant strains affected in hupH, hupI, and hupJ exhibited reduced (20 to 50%) rates of hydrogenase activity compared to the wild type, whereas rates were not affected in the deltahupG mutant. Immunoblot experiments with HupL- and HupS-specific antisera showed that free-living cultures from deltahupH, deltahupI, and deltahupJ mutants synthesized a fully processed mature HupL protein and accumulated an unprocessed form of HupS (pre-HupS). Both the mature HupL and the pre-HupS forms were located in the cytoplasmic fraction of cultures from the deltahupH mutant. Affinity chromatography experiments revealed that cytoplasmic pre-HupS binds to the HupH protein before the pre-HupS-HupL complex is formed. From these results we propose that hupGHIJ gene products are involved in the maturation of the HupS hydrogenase subunit.
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Affiliation(s)
- Hamid Manyani
- Laboratorio de Microbiología, Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Duché O, Elsen S, Cournac L, Colbeau A. Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O2 sensitive without affecting its transductory activity. FEBS J 2005; 272:3899-908. [PMID: 16045760 DOI: 10.1111/j.1742-4658.2005.04806.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the photosynthetic bacterium Rhodobacter capsulatus, the synthesis of the energy-producing hydrogenase, HupSL, is regulated by the substrate H2, which is detected by a regulatory hydrogenase, HupUV. The HupUV protein exhibits typical features of [NiFe] hydrogenases but, interestingly, is resistant to inactivation by O2. Understanding the O2 resistance of HupUV will help in the design of hydrogenases with high potential for biotechnological applications. To test whether this property results from O2 inaccessibility to the active site, we introduced two mutations in order to enlarge the gas access channel in the HupUV protein. We showed that such mutations (Ile65-->Val and Phe113-->Leu in HupV) rendered HupUV sensitive to O2 inactivation. Also, in contrast with the wild-type protein, the mutated protein exhibited an increase in hydrogenase activity after reductive activation in the presence of reduced methyl viologen (up to 30% of the activity of the wild-type). The H2-sensing HupUV protein is the first component of the H2-transduction cascade, which, together with the two-component system HupT/HupR, regulates HupSL synthesis in response to H2 availability. In vitro, the purified mutant HupUV protein was able to interact with the histidine kinase HupT. In vivo, the mutant protein exhibited the same hydrogenase activity as the wild-type enzyme and was equally able to repress HupSL synthesis in the absence of H2.
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Affiliation(s)
- Ophélie Duché
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (UMR 5092 CNRS-CEA-UJF), Département Réponse et Dynamique Cellulaires, Grenoble, France
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Detkova EN, Soboleva GS, Pikuta EV, Pusheva MA. The Effect of Sodium Salts and pH on the Hydrogenase Activity of Haloalkaliphilic Sulfate-Reducing Bacteria. Microbiology (Reading) 2005. [DOI: 10.1007/s11021-005-0079-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Burgdorf T, Löscher S, Liebisch P, Van der Linden E, Galander M, Lendzian F, Meyer-Klaucke W, Albracht SPJ, Friedrich B, Dau H, Haumann M. Structural and oxidation-state changes at its nonstandard Ni-Fe site during activation of the NAD-reducing hydrogenase from Ralstonia eutropha detected by X-ray absorption, EPR, and FTIR spectroscopy. J Am Chem Soc 2005; 127:576-92. [PMID: 15643882 DOI: 10.1021/ja0461926] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure and oxidation state of the Ni-Fe cofactor of the NAD-reducing soluble hydrogenase (SH) from Ralstonia eutropha were studied employing X-ray absorption spectroscopy (XAS) at the Ni K-edge, EPR, and FTIR spectroscopy. The SH comprises a nonstandard (CN)Ni-Fe(CN)(3)(CO) site; its hydrogen-cleavage reaction is resistant against inhibition by dioxygen and carbon monoxide. Simulations of the XANES and EXAFS regions of XAS spectra revealed that, in the oxidized SH, the Ni(II) is six-coordinated ((CN)O(3)S(2)); only two of the four conserved cysteines, which bind the Ni in standard Ni-Fe hydrogenases, provide thiol ligands to the Ni. Upon the exceptionally rapid reductive activation of the SH by NADH, an oxygen species is detached from the Ni; hydrogen may subsequently bind to the vacant coordination site. Prolonged reducing conditions cause the two thiols that are remote from the Ni in the native SH to become direct Ni ligands, creating a standardlike Ni(II)(CysS)(4) site, which could be further reduced to form the Ni-C (Ni(III)-H(-)) state. The Ni-C state does not seem to be involved in hydrogen cleavage. Two site-directed mutants (HoxH-I64A, HoxH-L118F) revealed structural changes at their Ni sites and were employed to further dissect the role of the extra CN ligand at the Ni. It is proposed that the predominant coordination by (CN),O ligands stabilizes the Ni(II) oxidation state throughout the catalytic cycle and is a prerequisite for the rapid activation of the SH in the presence of oxygen.
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Affiliation(s)
- Tanja Burgdorf
- Humboldt-Universität zu Berlin, Mikrobiologie, Chausseestr. 117, D-10115 Berlin, Germany
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Glatzel P, Bergmann U. High resolution 1s core hole X-ray spectroscopy in 3d transition metal complexes—electronic and structural information. Coord Chem Rev 2005. [DOI: 10.1016/j.ccr.2004.04.011] [Citation(s) in RCA: 519] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sawers RG, Blokesch M, Böck A. Anaerobic Formate and Hydrogen Metabolism. EcoSal Plus 2004; 1. [PMID: 26443350 DOI: 10.1128/ecosalplus.3.5.4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Indexed: 06/05/2023]
Abstract
During fermentative growth, Escherichia coli degrades carbohydrates via the glycolytic route into two pyruvate molecules. Pyruvate can be reduced to lactate or nonoxidatively cleaved by pyruvate formate lyase into acetyl-coenzyme A (acetyl-CoA) and formate. Acetyl-CoA can be utilized for energy conservation in the phosphotransacetylase (PTA) and acetate kinase (ACK) reaction sequence or can serve as an acceptor for reducing equivalents gathered during pyruvate formation, through the action of alcohol dehydrogenase (AdhE). Formic acid is strongly acidic and has a redox potential of -420 mV under standard conditions and therefore can be classified as a high-energy compound. Its disproportionation into CO2 and molecular hydrogen (Em,7 -420 mV) via the formate hydrogenlyase (FHL) system is therefore of high selective value. The FHL reaction involves the participation of at least seven proteins, most of which are metalloenzymes, with requirements for iron, molybdenum, nickel, or selenium. Complex auxiliary systems incorporate these metals. Reutilization of the hydrogen evolved required the evolution of H2 oxidation systems, which couple the oxidation process to an appropriate energy-conserving terminal reductase. E. coli has two hydrogen-oxidizing enzyme systems. Finally, fermentation is the "last resort" of energy metabolism, since it gives the minimal energy yield when compared with respiratory processes. Consequently, fermentation is used only when external electron acceptors are absent. This has necessitated the establishment of regulatory cascades, which ensure that the metabolic capability is appropriately adjusted to the physiological condition. Here we review the genetics, biochemistry, and regulation of hydrogen metabolism and its hydrogenase maturation system.
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Gu W, Jacquamet L, Patil DS, Wang HX, Evans DJ, Smith MC, Millar M, Koch S, Eichhorn DM, Latimer M, Cramer SP. Refinement of the nickel site structure in Desulfovibrio gigas hydrogenase using range-extended EXAFS spectroscopy. J Inorg Biochem 2003; 93:41-51. [PMID: 12538051 DOI: 10.1016/s0162-0134(02)00494-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have reexamined the Ni EXAFS of oxidized, inactive (as-isolated) and H(2) reduced Desulfovibrio gigas hydrogenase. Better spatial resolution was achieved by analyzing the data over a 50% wider k-range than was previously available. A lower k(min) was obtained using the FEFF code for phase shifts and amplitudes. A higher k(max) was obtained by removing an interfering Cu signal from the raw spectra using multiple energy fluorescence detection. The larger k-range allowed us to better resolve the Ni-S bond lengths and to define more accurately the Ni-O and Ni-Fe bond lengths. We find that as-isolated, hydrogenase has two Ni-S bonds at approximately 2.2 A, but also 1-2 Ni-S bonds in the 2.35+/-0.05 A range. A Ni-O interaction is evident at 1.91 A. The as-isolated Ni-Fe distance cannot be unambiguously determined. Upon H(2) reduction, two short Ni-S bonds persist at approximately 2.2 A, but the remaining Ni-S bonds lengthen to 2.47+/-0.05 A. Good simulations are obtained with a Ni-Fe distance at 2.52 A, in agreement with crystal structures of the reduced enzyme. Although not evident in the crystal structures, an improvement in the fit is obtained by inclusion of one Ni-O interaction at 2.03 A. Implications of these distances for the spin-state of H(2) reduced H(2)ase are discussed.
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Affiliation(s)
- Weiwei Gu
- Department of Applied Science, University of California, 1 Shields Ave, Davis, CA 95616, USA
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40
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Wilmot CM, Sjögren T, Carlsson GH, Berglund GI, Hajdu J. Defining redox state of X-ray crystal structures by single-crystal ultraviolet-visible microspectrophotometry. Methods Enzymol 2002; 353:301-18. [PMID: 12078505 DOI: 10.1016/s0076-6879(02)53057-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carrie M Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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41
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Wang H, Ralston CY, Patil DS, Jones RM, Gu W, Verhagen M, Adams M, Ge P, Riordan C, Marganian CA, Mascharak P, Kovacs J, Miller CG, Collins TJ, Brooker S, Croucher PD, Wang K, Stiefel EI, Cramer SP. Nickel L-Edge Soft X-ray Spectroscopy of Nickel−Iron Hydrogenases and Model CompoundsEvidence for High-Spin Nickel(II) in the Active Enzyme. J Am Chem Soc 2000. [DOI: 10.1021/ja000945g] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hongxin Wang
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - C. Y. Ralston
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - D. S. Patil
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - R. M. Jones
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - W. Gu
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - M. Verhagen
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - M. Adams
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - P. Ge
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - C. Riordan
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - C. A. Marganian
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - P. Mascharak
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - J. Kovacs
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - C. G. Miller
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - T. J. Collins
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - S. Brooker
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - P. D. Croucher
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - Kun Wang
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - E. I. Stiefel
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
| | - S. P. Cramer
- Contribution from the Department of Applied Science, University of California, Davis, California 95616, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Biochemistry, University of Georgia, Athens, Georgia 55455, Department of Chemistry, University of Delaware, Newark, Delaware 19716, Department of Chemistry, University of California, Santa Cruz, California 95064, Department of Chemistry, University of Washington, Seattle, Washington 98195, Department of Chemistry,
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De Lacey AL, Santamaria E, Hatchikian EC, Fernandez VM. Kinetic characterization of Desulfovibrio gigas hydrogenase upon selective chemical modification of amino acid groups as a tool for structure-function relationships. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:371-80. [PMID: 11018729 DOI: 10.1016/s0167-4838(00)00180-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of amino acid residues modification of Desulfovibrio gigas hydrogenase on different activity assays is reported. The first method consisted in the modification of glutamic and aspartic acid residues of the enzyme with ethylenediamine in order to change the polarity of certain regions of the protein surface. The second method consisted in the modification of histidine residues with a Ru complex in order to change the acid-base properties of the histidine residues. The implication of these modifications in the enzyme kinetics has been studied by measuring in parallel the activities of para/ortho hydrogen conversion, deuterium/hydrogen exchange and dyes reduction with hydrogen. Our experimental data support some hypothesis based on the three-dimensional structure of this enzyme: (a) electrostactic interactions between the hydrogenase and the redox partner play an essential role in the kinetics; (b) the histidine ligand and the surrounding acidic residues of the distal [4Fe4S] cluster form the recognition site of the redox partner of the hydrogenase; and (c) histidine residues are involved in the hydron transfer pathway of the hydrogenase.
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Affiliation(s)
- A L De Lacey
- Instituto de Catálisis, C.S.I.C., Campus Universidad Autónoma-Cantoblanco, Madrid, Spain.
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43
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Erkizia E, Conry RR. Synthesis and characterization of square planar nickel(II)-arylthiolate complexes with the biphenyl-2,2'-dithiolate ligand. Inorg Chem 2000; 39:1674-9. [PMID: 12526553 DOI: 10.1021/ic990931f] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two new NiIIS4 complexes with the biphenyl-2,2'-dithiolate ligand (L) are reported. The dinuclear complex 1, [Ni2L3]2-, was formed in the reaction of 2-3 equiv of Na2L and [NiCl4]2- and the mononuclear complex [NiL2]2- (2) by using 4-10 equiv of Na2L. Complexes 1 and 2 have been crystallographically characterized. (Et4N)2[1].0.5S2Ph2, CH3CN: C60H71N3Ni2S7, triclinic, P1, a = 13.806(2) A, b = 14.267(2) A, c = 16.873(2) A, alpha = 69.263(10) degrees, beta = 69.267(8) degrees, gamma = 83.117(10) degrees, Z = 2, R1 = 0.0752 (wR2 = 0.2011). (Et4N)(Na.CH3CN)[2]: C34H39N2NaNiS4, triclinic, P1, a = 9.9570(10) A, b = 13.2670(10) A, c = 13.9560(10) A, alpha = 108.489(7) degrees, beta = 90.396(6) degrees, gamma = 103.570(4) degrees, Z = 2, R1 = 0.0390 (wR2 = 0.0995). Both complexes are square planar about the nickel ion in the solid state as well as in solution. Most Ni(II)-thiolate complexes are square planar except the tetrahedral mononuclear complexes with monodentate arylthiolate ligands that cannot force a square planar geometry. The ligand (L) has some flexibility to change its bite angle via the phenyl-phenyl bond and should not force a planar geometry on its complexes either. Therefore, it is interesting that 2 has adopted a square planar structure. Complex 2 readily converts to 1 in solution when not in the presence of excess L in a process that is presumably similar to that known for other mononuclear, bidentate ligated Ni(II) complexes. Both complexes, at least in the solid state, appear to have an inclination to bind another metal ion on one face of the complex (Ni2+ in 1, Na+ in 2). We hope to take advantage of this in future work to synthesize relevant model complexes for the active sites of the nickel-iron hydrogenases after suitable modifications are made to L.
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Affiliation(s)
- E Erkizia
- Department of Chemistry/216, University of Nevada, Reno, Nevada 89557, USA
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Ishii M, Takishita S, Iwasaki T, Peerapornpisal Y, Yoshino J, Kodama T, Igarashi Y. Purification and characterization of membrane-bound hydrogenase from Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium. Biosci Biotechnol Biochem 2000; 64:492-502. [PMID: 10803945 DOI: 10.1271/bbb.64.492] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A membrane-bound hydrogenase was purified to electrophoretic homogeneity from the cells of Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium. Solubilization and purification were done aerobically in the presence of Triton X-100. Three chromatography steps were done for purification; Butyl-Sepharose, Mono-Q, and Superose 6, in this order. Purification was completed with 6.73% yield of total activity and with 21.4-fold increase of specific activity when compared with the values for the membrane fraction. The purified hydrogenase was shown to be a tetramer with alpha2beta2 structure, with a molecular mass of 60,000 Da for the large subunit and 38,000 Da for the small subunit. The purified hydrogenase directly reduced methionaquinone with an apparent Km of around 300 microM and with a turnover number around 2900 (min(-1)). Metal analysis and EPR properties of the hydrogenase have shown that the enzyme is one of the [NiFe]-hydrogenases. Also, optimum pH and temperature for reaction, thermal stability, and electron acceptor specificity were reported. Finally, a model is presented for energy and central metabolism of H. thermophilus strain TK-6.
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Affiliation(s)
- M Ishii
- Department of Biotechnology, the University of Tokyo, Japan
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