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Abstract
Nickel-containing carbon monoxide dehydrogenases, acetyl-CoA synthases, nickel-iron hydrogenases, and diron hydrogenases are distinct metalloenzymes yet they share a number of important characteristics. All are O(2)-sensitive, with active-sites composed of iron and/or nickel ions coordinated primarily by sulfur ligands. In each case, two metals are juxtaposed at the "heart" of the active site, within range of forming metal-metal bonds. These active-site clusters exhibit multielectron redox abilities and must be reductively activated for catalysis. Reduction potentials are milder than expected based on formal oxidation state changes. When reductively activated, each cluster attacks an electrophilic substrate via an oxidative addition reaction. This affords a two-electron-reduced substrate bound to one or both metals of an oxidized cluster. M-M bonds have been established in hydrogenases where they serve to initiate the oxidative addition of protons and perhaps stabilize active sites in multiple redox states. The same may be true of the CODH and ACS active sites-Ni-Fe and Ni-Ni bonds in these sites may play critical roles in catalysis, stabilizing low-valence states and initiating oxidative addition of CO(2) and methyl group cations, respectively. In this article, the structural and functional commonalities of these metalloenzyme active sites are described, and the case is made for the formation and use of metal-metal bonds in each enzyme mentioned. As a post-script, the importance of Fe-Fe bonds in the nitrogenase FeMoco active site is discussed.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.
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52
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Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 2011; 19:1038-52. [PMID: 21827941 DOI: 10.1016/j.str.2011.06.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/01/2011] [Accepted: 06/09/2011] [Indexed: 01/06/2023]
Abstract
Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.
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53
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Knörzer P, Silakov A, Foster CE, Armstrong FA, Lubitz W, Happe T. Importance of the protein framework for catalytic activity of [FeFe]-hydrogenases. J Biol Chem 2011; 287:1489-99. [PMID: 22110126 DOI: 10.1074/jbc.m111.305797] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met(415) and CrHydA1Lys(228) resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet(353) (CrHydA1Met(223)) and CpICys(299) (CrHydA1Cys(169)) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the H(trans) state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM(353) (CrHydA1M(223)) to leucine led to a strong decrease in turnover without affecting the K(m) value of the electron donor. We suggest that this methionine constitutes a "fine-tuning" element of hydrogenase activity.
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Affiliation(s)
- Philipp Knörzer
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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54
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Greco C, Bruschi M, Fantucci P, Ryde U, De Gioia L. Mechanistic and Physiological Implications of the Interplay among Iron–Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective. J Am Chem Soc 2011; 133:18742-9. [DOI: 10.1021/ja205542k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Claudio Greco
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Maurizio Bruschi
- Department of Environmental Sciences, University of Milan-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Luca De Gioia
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
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55
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Chang CH. Computational Chemical Analysis of [FeFe] Hydrogenase H-Cluster Analogues To Discern Catalytically Relevant Features of the Natural Diatomic Ligand Configuration. J Phys Chem A 2011; 115:8691-704. [DOI: 10.1021/jp112296d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher H. Chang
- Computational Science Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, MS 1608, Golden, Colorado 80401, United States
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56
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Yu L, Greco C, Bruschi M, Ryde U, De Gioia L, Reiher M. Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures. Inorg Chem 2011; 50:3888-900. [PMID: 21443182 DOI: 10.1021/ic102039z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this work, we employ density functional theory to assign vibrational signatures of [FeFe]-hydrogenase intermediates to molecular structures. For this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of CN and CO containing model clusters of the [FeFe]-hydrogenase enzyme active site considering also different charges, counterions, and solvents. The pure density functional BP86 in combination with a triple-ζ polarized basis set produce reliable molecular structures as well as harmonic vibrations. Calculated CN and CO stretching vibrations are analyzed separately. Scaled vibrational frequencies are then applied to assign intermediates in [FeFe]-hydrogenase's reaction cycle. The results nicely complement the previous studies of Darensbourg and Hall, and Zilberman et al. The infrared spectrum of the H(ox) form is in very good agreement with the calculated spectrum of the Fe(I)Fe(II) model complex featuring a free coordination site at the distal Fe atom, as well as, with the calculated spectra of the complexes in which H(2) or H(2)O are coordinated at this site. The spectrum of H(red) measured from Desulfovibrio desulfuricans is compatible with a mixture of a Fe(I)Fe(I) species with all terminal COs, and a Fe(I)Fe(I) species with protonated dtma ligand, while the spectrum of H(red) recently measured from Chlamydomonas reinhardtii is compatible with a mixture of a Fe(I)Fe(I) species with a bridged CO, and a Fe(II)Fe(II) species with a terminal hydride bound to the Fe atom.
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Affiliation(s)
- Lian Yu
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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57
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Hong G, Cornish AJ, Hegg EL, Pachter R. On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:510-7. [PMID: 21296047 DOI: 10.1016/j.bbabio.2011.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 11/19/2022]
Abstract
Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159→Ser198→Glu156→water460→Cys178→DTMA([Fe-Fe](H)) and (Glu282→Ser319→Glu279→water612→Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe-Fe](H) sub-cluster in DdH was readily observed in our results, specifically when [Fe-Fe](H) was in the reduced state ([Fe(I)-Fe(I)]) or in the mixed valence state for the protonated distal iron Fe(d) ([Fe(I)-Fe(II)-H(-)](H)). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in CpI. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe-Fe] hydrogenases in which the proton binds at Fe(d), providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs.
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Affiliation(s)
- G Hong
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, OH 45433, USA
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58
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Greco C, Silakov A, Bruschi M, Ryde U, De Gioia L, Lubitz W. Magnetic Properties of [FeFe]-Hydrogenases: A Theoretical Investigation Based on Extended QM and QM/MM Models of the H-Cluster and Its Surroundings. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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59
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Greco C, Bruschi M, Fantucci P, Ryde U, De Gioia L. Isocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]-Hydrogenases. Chemistry 2011; 17:1954-65. [DOI: 10.1002/chem.201001493] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 10/24/2010] [Indexed: 11/07/2022]
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60
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Silakov A, Reijerse EJ, Lubitz W. Unraveling the Electronic Properties of the Photoinduced States of the H-Cluster in the [FeFe] Hydrogenase from D. desulfuricans. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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61
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Silakov A, Shaw JL, Reijerse EJ, Lubitz W. Advanced Electron Paramagnetic Resonance and Density Functional Theory Study of a {2Fe3S} Cluster Mimicking the Active Site of [FeFe] Hydrogenase. J Am Chem Soc 2010; 132:17578-87. [DOI: 10.1021/ja107793e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexey Silakov
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Jennifer L. Shaw
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Eduard J. Reijerse
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, Mülheim an der Ruhr, 45470, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, Mülheim an der Ruhr, 45470, Germany
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62
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Chen S, Raugei S, Rousseau R, Dupuis M, Bullock RM. Homogeneous Ni Catalysts for H2 Oxidation and Production: An Assessment of Theoretical Methods, from Density Functional Theory to Post Hartree−Fock Correlated Wave-Function Theory. J Phys Chem A 2010; 114:12716-24. [DOI: 10.1021/jp106800n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shentan Chen
- Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division Pacific Northwest National Laboratory, Richland WA
| | - Simone Raugei
- Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division Pacific Northwest National Laboratory, Richland WA
| | - Roger Rousseau
- Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division Pacific Northwest National Laboratory, Richland WA
| | - Michel Dupuis
- Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division Pacific Northwest National Laboratory, Richland WA
| | - R. Morris Bullock
- Center for Molecular Electrocatalysis, Chemical and Materials Sciences Division Pacific Northwest National Laboratory, Richland WA
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63
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Lenz O, Ludwig M, Schubert T, Bürstel I, Ganskow S, Goris T, Schwarze A, Friedrich B. H2 conversion in the presence of O2 as performed by the membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. Chemphyschem 2010; 11:1107-19. [PMID: 20186906 DOI: 10.1002/cphc.200901002] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[NiFe]-hydrogenases catalyze the oxidation of H(2) to protons and electrons. This reversible reaction is based on a complex interplay of metal cofactors including the Ni-Fe active site and several [Fe-S] clusters. H(2) catalysis of most [NiFe]-hydrogenases is sensitive to dioxygen. However, some bacteria contain hydrogenases that activate H(2) even in the presence of O(2). There is now compelling evidence that O(2) affects hydrogenase on three levels: 1) H(2) catalysis, 2) hydrogenase maturation, and 3) H(2)-mediated signal transduction. Herein, we summarize the genetic, biochemical, electrochemical, and spectroscopic properties related to the O(2) tolerance of hydrogenases resident in the facultative chemolithoautotroph Ralstonia eutropha H16. A focus is given to the membrane-bound [NiFe]-hydogenase, which currently represents the best-characterized member of O(2)-tolerant hydrogenases.
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Affiliation(s)
- Oliver Lenz
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
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64
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Surawatanawong P, Hall MB. Density Functional Study of the Thermodynamics of Hydrogen Production by Tetrairon Hexathiolate, Fe4[MeC(CH2S)3]2(CO)8, a Hydrogenase Model. Inorg Chem 2010; 49:5737-47. [DOI: 10.1021/ic100687v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
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65
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Fourmond V, Infossi P, Giudici-Orticoni MT, Bertrand P, Léger C. “Two-Step” Chronoamperometric Method for Studying the Anaerobic Inactivation of an Oxygen Tolerant NiFe Hydrogenase. J Am Chem Soc 2010; 132:4848-57. [DOI: 10.1021/ja910685j] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, UPR 9036, Institut de Biologie de la Méditerranée and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Pascale Infossi
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, UPR 9036, Institut de Biologie de la Méditerranée and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, UPR 9036, Institut de Biologie de la Méditerranée and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Patrick Bertrand
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, UPR 9036, Institut de Biologie de la Méditerranée and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, UPR 9036, Institut de Biologie de la Méditerranée and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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66
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Silakov A, Kamp C, Reijerse E, Happe T, Lubitz W. Spectroelectrochemical characterization of the active site of the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii. Biochemistry 2009; 48:7780-6. [PMID: 19634879 DOI: 10.1021/bi9009105] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogenases catalyze the reversible oxidation of molecular hydrogen. The active site of the [FeFe] hydrogenases (H-cluster) contains a catalytically active binuclear subcluster ([2Fe](H)) connected to a "cubane" [4Fe4S](H) subcluster. Here we present an IR spectroelectrochemical study of the [FeFe] hydrogenase HydA1 isolated from the green alga Chlamydomonas reinhardtii. The enzyme shows IR bands similar to those observed for bacterial [FeFe] hydrogenases. They are assigned to the stretching vibrations of the CN(-) and CO ligands on both irons of the [2Fe](H) subcluster. By following changes in frequencies of the IR bands during electrochemical titrations, two one-electron redox processes of the active enzyme could be distinguished. The reduction of the oxidized state (H(ox)) occurred at a midpoint potential of -400 mV vs NHE (H(ox)/H(red) transition) and relates to a change of the formal oxidation state of the binuclear subcluster. A subsequent reduction (H(red)/H(sred) transition) was determined to have a midpoint potential of -460 mV vs NHE. On the basis of the IR spectra, it is suggested that the oxidation state of the binuclear subcluster does not change in this transition. Tentatively, a reduction of the [4Fe4S](H) cluster has been proposed. In contrast to the bacterial [FeFe] hydrogenases, where the bridging CO ligand becomes terminal when going from H(ox) to H(red), in HydA1 the bridging CO is present in both the H(ox) and H(red) state. The removal of the bridging CO moiety has been observed in the H(red) to H(sred) transition. The significance of this result for the hydrogen conversion mechanism of this class of enzymes is discussed.
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Affiliation(s)
- Alexey Silakov
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
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67
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Mulder DW, Ortillo DO, Gardenghi DJ, Naumov AV, Ruebush SS, Szilagyi RK, Huynh B, Broderick JB, Peters JW. Activation of HydA(DeltaEFG) requires a preformed [4Fe-4S] cluster. Biochemistry 2009; 48:6240-8. [PMID: 19435321 DOI: 10.1021/bi9000563] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The H-cluster is a complex bridged metal assembly at the active site of [FeFe]-hydrogenases that consists of a [4Fe-4S] subcluster bridged to a 2Fe-containing subcluster with unique nonprotein ligands, including carbon monoxide, cyanide, and a dithiolate ligand of unknown composition. Specific biosynthetic gene products (HydE, HydF, and HydG) responsible for the biosynthesis of the H-cluster and the maturation of active [FeFe]-hydrogenase have previously been identified and shown to be required for the heterologous expression of active [FeFe]-hydrogenase [Posewitz, M. C., et al. (2004) J. Biol. Chem. 279, 25711-25720]. The precise roles of the maturation proteins are unknown; the most likely possibility is that they are directed at the synthesis of the entire 6Fe-containing H-cluster, the 2Fe subcluster, or only the unique ligands of the 2Fe subcluster. The spectroscopic and biochemical characterization of HydA(DeltaEFG) (the [FeFe]-hydrogenase structural protein expressed in the absence of the maturation machinery) reported here indicates that a [4Fe-4S] cluster is incorporated into the H-cluster site. The purified protein in a representative preparation contains Fe (3.1 +/- 0.5 Fe atoms per HydA(DeltaEFG)) and S(2-) (1.8 +/- 0.5 S(2-) atoms per HydA(DeltaEFG)) and exhibits UV-visible spectroscopic features characteristic of iron-sulfur clusters, including a bleaching of the visible chromophore upon addition of dithionite. The reduced protein gave rise to an axial S = (1)/(2) EPR signal (g = 2.04 and 1.91) characteristic of a reduced [4Fe-4S](+) cluster. Mossbauer spectroscopic characterization of (57)Fe-enriched HydA(DeltaEFG) provided further evidence of the presence of a redox active [4Fe-4S](2+/+) cluster. Iron K-edge EXAFS data provided yet further support for the presence of a [4Fe-4S] cluster in HydA(DeltaEFG). These spectroscopic studies were combined with in vitro activation studies that demonstrate that HydA(DeltaEFG) can be activated by the specific maturases only when a [4Fe-4S] cluster is present in the protein. In sum, this work supports a model in which the role of the maturation machinery is to synthesize and insert the 2Fe subcluster and/or its ligands and not the entire 6Fe-containing H-cluster bridged assembly.
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Affiliation(s)
- David W Mulder
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA
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68
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Greco C, Bruschi M, Fantucci P, De Gioia L. Relation between coordination geometry and stereoelectronic properties in DFT models of the CO-inhibited [FeFe]-hydrogenase cofactor. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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69
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Stiebritz MT, Reiher M. Theoretical Study of Dioxygen Induced Inhibition of [FeFe]-Hydrogenase. Inorg Chem 2009; 48:7127-40. [DOI: 10.1021/ic9002127] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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70
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Silakov A, Wenk B, Reijerse E, Lubitz W. (14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge. Phys Chem Chem Phys 2009; 11:6592-9. [PMID: 19639134 DOI: 10.1039/b905841a] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogenases are enzymes catalyzing the reversible heterolytic splitting of molecular hydrogen. Despite extensive investigations of this class of enzymes its catalytic mechanism is not yet well understood. In this paper spectroscopic investigations of the active site of [FeFe] hydrogenase are presented. The so-called H-cluster consists of a bi-nuclear catalytically active subcluster connected to a [4Fe4S] ferredoxin-like unit via a Cys-thiol bridge. An important feature of the H-cluster is that both irons in the bi-nuclear subcluster are coordinated by CN and CO ligands. The bi-nuclear site also carries a dithiol bridge, whose central atom has not yet been identified. Nitrogen and oxygen are the most probable candidates from a mechanistic point of view. Here we present a study of the (14)N nuclear quadrupole and hyperfine interactions of the active oxidized state of the H-cluster using advanced EPR methods. In total three (14)N nuclei with quadrupole couplings of 0.95 MHz, 0.35 MHz and 1.23 MHz were detected using hyperfine sublevel correlation spectroscopy (HYSCORE). The assignment of the signals is based on their (14)N quadrupole couplings in combination with DFT calculations. One signal is assigned to the CN ligand of the distal iron, one to a Lys side chain nitrogen and one to the putative nitrogen of the dithiol bridge. Hence, these results provide the first experimental evidence for a di-(thiomethyl)amine ligand (-S-CH(2)-NH-CH(2)-S-) in the bi-nuclear subcluster. This finding is important for understanding the mechanism of [FeFe] hydrogenases, since the nitrogen is likely to act as an internal base facilitating the heterolytic splitting/formation of H(2).
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Affiliation(s)
- Alexey Silakov
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470, Mülheim a. d. Ruhr, Germany.
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71
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Stripp S, Sanganas O, Happe T, Haumann M. The Structure of the Active Site H-Cluster of [FeFe] Hydrogenase from the Green Alga Chlamydomonas reinhardtii Studied by X-ray Absorption Spectroscopy. Biochemistry 2009; 48:5042-9. [DOI: 10.1021/bi900010b] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sven Stripp
- Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Oliver Sanganas
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Thomas Happe
- Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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72
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Bruschi M, Greco C, Kaukonen M, Fantucci P, Ryde U, De Gioia L. Influence of the [2Fe]HSubcluster Environment on the Properties of Key Intermediates in the Catalytic Cycle of [FeFe] Hydrogenases: Hints for the Rational Design of Synthetic Catalysts. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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73
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Bruschi M, Greco C, Kaukonen M, Fantucci P, Ryde U, De Gioia L. Influence of the [2Fe]HSubcluster Environment on the Properties of Key Intermediates in the Catalytic Cycle of [FeFe] Hydrogenases: Hints for the Rational Design of Synthetic Catalysts. Angew Chem Int Ed Engl 2009; 48:3503-6. [DOI: 10.1002/anie.200900494] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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74
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Liptak MD, Van Heuvelen KM, Brunold* TC. Computational Studies of Bioorganometallic Enzymes and Cofactors. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Because of their complex geometric and electronic structures, the active sites and cofactors of bioorganometallic enzymes, which are characterized by their metal–carbon bonds, pose a major challenge for computational chemists. However, recent progress in computer technology and theoretical chemistry, along with insights gained from mechanistic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of computational studies aimed at elucidating the electronic structures and catalytic cycles of these species. This chapter briefly reviews the most popular computational approaches employed in theoretical studies of bioorganometallic species and summarizes important information obtained from computational studies of (i) the enzymatic formation and cleavage of the Co–C bond of coenzyme B12; (ii) the catalytic cycle of methyl-coenzyme M reductase and its nickel-containing cofactor F430; (iii) the polynuclear active-site clusters of the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-coenzyme A synthase; and (iv) the magnetic properties of the active-site cluster of Fe-only hydrogenases.
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Affiliation(s)
- Matthew D. Liptak
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | | | - Thomas C. Brunold*
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
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75
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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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76
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Rakowski DuBois M, DuBois DL. The roles of the first and second coordination spheres in the design of molecular catalysts for H2production and oxidation. Chem Soc Rev 2009; 38:62-72. [DOI: 10.1039/b801197b] [Citation(s) in RCA: 548] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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Silakov A, Wenk B, Reijerse E, Albracht SPJ, Lubitz W. Spin distribution of the H-cluster in the Hox–CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of 14N and 13C nuclear interactions. J Biol Inorg Chem 2008; 14:301-13. [DOI: 10.1007/s00775-008-0449-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 11/02/2008] [Indexed: 10/21/2022]
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78
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DuBois MR, DuBois DL. The role of pendant bases in molecular catalysts for H2 oxidation and production. CR CHIM 2008. [DOI: 10.1016/j.crci.2008.01.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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79
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Bruschi M, Greco C, Zampella G, Ryde U, Pickett CJ, De Gioia L. A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site. CR CHIM 2008. [DOI: 10.1016/j.crci.2008.04.010] [Citation(s) in RCA: 13] [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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80
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Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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81
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Desulfovibrio vulgaris Hildenborough HydE and HydG interact with the HydA subunit of the [FeFe] hydrogenase. Biotechnol Lett 2008; 30:1765-9. [PMID: 18563582 DOI: 10.1007/s10529-008-9755-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/07/2008] [Accepted: 05/21/2008] [Indexed: 10/21/2022]
Abstract
HydE, HydF, and HydG participate in the synthesis of the complex di-iron center of [FeFe] hydrogenases. The hydE, hydF, hydG, hydA, and hydB genes of Desulfovibrio vulgaris Hildenborough were cloned and His-tag pull-down assays were used to study the potential interaction between HydE, HydF, and HydG with the HydA and HydB protein subunits of the D. vulgaris [FeFe] hydrogenase. Interaction of HydE and HydG with HydA was demonstrated. HydF did not interact with HydA, and none of the accessory proteins appeared to interact with HydB. This suggests that specific protein-protein interactions may be required during [FeFe] cluster synthesis and/or insertion.
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82
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Bruschi M, Greco C, Fantucci P, De Gioia L. Structural and electronic properties of the [FeFe] hydrogenase H-cluster in different redox and protonation states. A DFT investigation. Inorg Chem 2008; 47:6056-71. [PMID: 18540595 DOI: 10.1021/ic8006298] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular and electronic structure of the Fe 6S 6 H-cluster of [FeFe] hydrogenase in relevant redox and protonation states have been investigated by DFT. The calculations have been carried out according to the broken symmetry approach and considering different environmental conditions. The large negative charge of the H-cluster leads, in a vacuum, to structures different from those observed experimentally in the protein. A better agreement with experimental data is observed for solvated complexes, suggesting that the protein environment could buffer the large negative charge of the H-cluster. The comparison of Fe 6S 6 and Fe 2S 2 DFT models shows that the presence of the Fe 4S 4 moiety does not affect appreciably the geometry of the [2Fe] H cluster. In particular, the Fe 4S 4 cluster alone cannot be invoked to explain the stabilization of the mu-CO forms observed in the enzyme (relative to all-terminal CO species). As for protonation of the hydrogen cluster, it turned out that mu-H species are always more stable than terminal hydride isomers, leading to the conclusion that specific interactions of the H-cluster with the environment, not considered in our calculations, would be necessary to reverse the stability order of mu-H and terminal hydrides. Otherwise, protonation of the metal center and H 2 evolution in the enzyme are predicted to be kinetically controlled processes. Finally, subtle modifications in the H-cluster environment can change the relative stability of key frontier orbitals, triggering electron transfer between the Fe 4S 4 and the Fe 2S 2 moieties forming the H-cluster.
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Affiliation(s)
- Maurizio Bruschi
- Department of Environmental Science, University of Milano-Bicocca, Piazza della Scienza 1 20126-Milan, Italy.
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83
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Nimlos MR, Chang CH, Curtis CJ, Miedaner A, Pilath HM, DuBois DL. Calculated Hydride Donor Abilities of Five-Coordinate Transition Metal Hydrides [HM(diphosphine)2]+ (M = Ni, Pd, Pt) as a Function of the Bite Angle and Twist Angle of Diphosphine Ligands. Organometallics 2008. [DOI: 10.1021/om701218x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark R. Nimlos
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
| | - Christopher H. Chang
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
| | - Calvin J. Curtis
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
| | - Alex Miedaner
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
| | - Heidi M. Pilath
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
| | - Daniel L. DuBois
- National Renewable Energy Laboratory, Golden, Colorado 80401, and Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352
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84
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Tye JW, Darensbourg MY, Hall MB. Refining the active site structure of iron-iron hydrogenase using computational infrared spectroscopy. Inorg Chem 2008; 47:2380-8. [PMID: 18307282 DOI: 10.1021/ic7013732] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-iron hydrogenases ([FeFe]H2ases) are exceptional natural catalysts for the reduction of protons to dihydrogen. Future biotechnological applications based on these enzymes require a precise understanding of their structures and properties. Although the [FeFe]H2ases have been characterized by single-crystal X-ray crystallography and a range of spectroscopic techniques, ambiguities remain regarding the details of the molecular structures of the spectroscopically observed forms. We use density functional theory (DFT) computations on small-molecule computational models of the [FeFe]H2ase active site to address this problem. Specifically, a series of structural candidates are geometry optimized and their infrared (IR) spectra are simulated using the computed C-O and C-N stretching frequencies and infrared intensities. Structural assignments are made by comparing these spectra to the experimentally determined IR spectra for each form. The H red form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide has been protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox(air)(ox) form is assigned as an Fe(II)Fe(II) redox level with OH(-) or OOH(-) bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker. Comparisons of the computed IR spectra of the (12)CO and (13)CO inhibited form with the experimental IR spectra show that exogenous CO binds terminally to the distal iron center.
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Affiliation(s)
- Jesse W Tye
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA
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85
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Siegbahn PEM, Tye JW, Hall MB. Computational studies of [NiFe] and [FeFe] hydrogenases. Chem Rev 2008; 107:4414-35. [PMID: 17927160 DOI: 10.1021/cr050185y] [Citation(s) in RCA: 361] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Per E M Siegbahn
- Department of Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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86
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Blackburn JL, Svedruzic D, McDonald TJ, Kim YH, King PW, Heben MJ. Raman spectroscopy of charge transfer interactions between single wall carbon nanotubes and [FeFe] hydrogenase. Dalton Trans 2008:5454-61. [DOI: 10.1039/b806379f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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87
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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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88
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Kubas GJ. Fundamentals of H2 Binding and Reactivity on Transition Metals Underlying Hydrogenase Function and H2 Production and Storage. Chem Rev 2007; 107:4152-205. [DOI: 10.1021/cr050197j] [Citation(s) in RCA: 796] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Gregory J. Kubas
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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89
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Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 2007; 107:4273-303. [PMID: 17850165 DOI: 10.1021/cr050195z] [Citation(s) in RCA: 1004] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juan C Fontecilla-Camps
- Laboratoire de Cristallographie et Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel, CEA, CNRS, Universitè Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.
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90
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Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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91
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Ma Y, Balbuena PB. Density functional theory approach for improving the catalytic activity of a biomimetic model based on the Fe-only hydrogenase active site. J Electroanal Chem (Lausanne) 2007. [DOI: 10.1016/j.jelechem.2006.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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92
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Jacobsen GM, Shoemaker RK, Rakowski DuBois M, DuBois DL. Syntheses and Reactions of Iron(II) Complexes Containing Diphosphine Ligands with Pendant Nitrogen Bases. Organometallics 2007. [DOI: 10.1021/om700510b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George M. Jacobsen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352
| | - R. K. Shoemaker
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352
| | - M. Rakowski DuBois
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352
| | - Daniel L. DuBois
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352
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93
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Silakov A, Reijerse EJ, Albracht SPJ, Hatchikian EC, Lubitz W. The Electronic Structure of the H-Cluster in the [FeFe]-Hydrogenase from Desulfovibrio desulfuricans: A Q-band 57Fe-ENDOR and HYSCORE Study. J Am Chem Soc 2007; 129:11447-58. [PMID: 17722921 DOI: 10.1021/ja072592s] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active site of the (57)Fe-enriched [FeFe]-hydrogenase (i.e., the "H-cluster") from Desulfovibrio desulfuricans has been examined using advanced pulse EPR methods at X- and Q-band frequencies. For both the active oxidized state (H(ox)) and the CO inhibited form (H(ox)-CO) all six (57)Fe hyperfine couplings were detected. The analysis shows that the apparent spin density extends over the whole H-cluster. The investigations revealed different hyperfine couplings of all six (57)Fe nuclei in the H-cluster of the H(ox)-CO state. Four large 57Fe hyperfine couplings in the range 20-40 MHz were found (using pulse ENDOR and TRIPLE methods) and were assigned to the [4Fe-4S](H) (cubane) subcluster. Two weak (57)Fe hyperfine couplings below 5 MHz were identified using Q-band HYSCORE spectroscopy and were assigned to the [2Fe](H) subcluster. For the H(ox) state only two different 57Fe hyperfine couplings in the range 10-13 MHz were detected using pulse ENDOR. An (57)Fe line broadening analysis of the X-band CW EPR spectrum indicated, however, that all six (57)Fe nuclei in the H-cluster are contributing to the hyperfine pattern. It is concluded that in both states the binuclear subcluster [2Fe](H) assumes a [Fe(I)Fe(II)] redox configuration where the paramagnetic Fe(I) atom is attached to the [4Fe-4S](H) subcluster. The (57)Fe hyperfine interactions of the formally diamagnetic [4Fe-4S](H) are due to an exchange interaction between the two subclusters as has been discussed earlier by Popescu and Münck [Popescu, C.V.; Münck, E., J. Am. Chem. Soc. 1999, 121, 7877-7884]. This exchange coupling is strongly enhanced by binding of the extrinsic CO ligand. Binding of the dihydrogen substrate may induce a similar effect, and it is therefore proposed that the observed modulation of the electronic structure by the changing ligand surrounding plays an important role in the catalytic mechanism of [FeFe]-hydrogenase.
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Affiliation(s)
- Alexey Silakov
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, Mülheim a. d. Ruhr, 45470, Germany
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94
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De Lacey AL, Fernandez VM, Rousset M, Cammack R. Activation and Inactivation of Hydrogenase Function and the Catalytic Cycle: Spectroelectrochemical Studies. Chem Rev 2007; 107:4304-30. [PMID: 17715982 DOI: 10.1021/cr0501947] [Citation(s) in RCA: 364] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio L De Lacey
- Instituto de CatAlisis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
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95
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Fraze K, Wilson AD, Appel AM, Rakowski DuBois M, DuBois DL. Thermodynamic Properties of the Ni−H Bond in Complexes of the Type [HNi(P2RN2R‘)2](BF4) and Evaluation of Factors That Control Catalytic Activity for Hydrogen Oxidation/Production. Organometallics 2007. [DOI: 10.1021/om070143v] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kendra Fraze
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Pacific Northwest National Laboratory, Batelle Boulevard, Richland, Washington 99352
| | - Aaron D. Wilson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Pacific Northwest National Laboratory, Batelle Boulevard, Richland, Washington 99352
| | - Aaron M. Appel
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Pacific Northwest National Laboratory, Batelle Boulevard, Richland, Washington 99352
| | - M. Rakowski DuBois
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Pacific Northwest National Laboratory, Batelle Boulevard, Richland, Washington 99352
| | - Daniel L. DuBois
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, and Pacific Northwest National Laboratory, Batelle Boulevard, Richland, Washington 99352
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96
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Greco C, Bruschi M, De Gioia L, Ryde U. A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases. Inorg Chem 2007; 46:5911-21. [PMID: 17602468 DOI: 10.1021/ic062320a] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fe-only hydrogenases are enzymes that catalyze dihydrogen production or oxidation, due to the presence of an unusual Fe(6)S(6) cluster (the so-called H-cluster) in their active site, which is composed of a Fe(2)S(2) subsite, directly involved in catalysis, and a classical Fe(4)S(4) cubane cluster. Here, we present a hybrid quantum mechanical and molecular mechanical (QM/MM) investigation of the Fe-only hydrogenase from Desulfovibrio desulfuricans, in order to unravel key issues regarding the activation of the enzyme from its completely oxidized inactive state (Hoxinact) and the influence of the protein environment on the structural and catalytic properties of the H-cluster. Our results show that the Fe(2)S(2) subcluster in the Fe(II)Fe(II) redox state - which is experimentally observed for the completely oxidized form of the enzyme - binds a water molecule to one of its metal centers. The computed QM/MM energy values for water binding to the diferrous subsite are in fact over 70 kJ mol(-1); however, the affinity toward water decreases by 1 order of magnitude after a one-electron reduction of H(ox)(inact), thus leading to the release of coordinated water from the H-cluster. The investigation of a catalytic cycle of the Fe-only hydrogenase that implies formation of a terminal hydride ion and a di(thiomethyl)amine (DTMA) molecule acting as an acid/base catalyst indicates that all steps have reasonable reaction energies and that the influence of the protein on the thermodynamic profile of H(2) production catalysis is not negligible. QM/MM results show that the interactions between the Fe(2)S(2) subsite and the protein environment could give place to structural rearrangements of the H-cluster functional for catalysis, provided that the bidentate ligand that bridges the iron atoms in the binuclear subsite is actually a DTMA residue.
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Affiliation(s)
- Claudio Greco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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97
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Wilson AD, Shoemaker RK, Miedaner A, Muckerman JT, DuBois DL, DuBois MR. Nature of hydrogen interactions with Ni(II) complexes containing cyclic phosphine ligands with pendant nitrogen bases. Proc Natl Acad Sci U S A 2007; 104:6951-6. [PMID: 17360385 PMCID: PMC1855379 DOI: 10.1073/pnas.0608928104] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Studies of the role of proton relays in molecular catalysts for the electrocatalytic production and oxidation of H(2) have been carried out. The electrochemical production of hydrogen from protonated DMF solutions catalyzed by [Ni(P(2)(Ph)N(2)(Ph))(2)(CH(3)CN)](BF(4))(2), 3a (where P(2)(Ph)N(2)(Ph) is 1,3,5,7-tetraphenyl-1,5-diaza-3,7-diphosphacyclooctane), permits a limiting value of the H(2) production rate to be determined. The turnover frequency of 350 s(-1) establishes that the rate of H(2) production for the mononuclear nickel catalyst 3a is comparable to those observed for Ni-Fe hydrogenase enzymes. In the electrochemical oxidation of hydrogen catalyzed by [Ni(P(2)(Cy)N(2)(Bz))(2)](BF(4))(2), 3b (where Cy is cyclohexyl and Bz is benzyl), the initial step is the reversible addition of hydrogen to 3b (K(eq) = 190 atm(-1) at 25 degrees C). The hydrogen addition product exists as three nearly isoenergetic isomers 4A-4C, which have been identified by a combination of one- and two-dimensional (1)H, (31)P, and (15)N NMR spectroscopies as Ni(0) complexes with a protonated amine in each cyclic ligand. The nature of the isomers, together with calculations, suggests a mode of hydrogen activation that involves a symmetrical interaction of a nickel dihydrogen ligand with two amine bases in the diphosphine ligands. Single deprotonation of 4 by an external base results in a rearrangement to [HNi(P(2)(Cy)N(2)(Bz))(2)](BF(4)), 5, and this reaction is reversed by the addition of a proton to the nickel hydride complex. The small energy differences associated with significantly different distributions in electron density and protons within these molecules may contribute to their high catalytic activity.
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Affiliation(s)
- Aaron D. Wilson
- *Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
| | - R. K. Shoemaker
- *Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
| | - A. Miedaner
- National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401; and
| | - J. T. Muckerman
- Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973
| | - Daniel L. DuBois
- Division of Chemical Sciences, Pacific Northwest National Laboratory, Richland, WA 99352
| | - M. Rakowski DuBois
- *Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
- To whom correspondence should be addressed at:
Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309. E-mail:
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98
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Parkin A, Cavazza C, Fontecilla-Camps JC, Armstrong FA. Electrochemical Investigations of the Interconversions between Catalytic and Inhibited States of the [FeFe]-Hydrogenase from Desulfovibrio desulfuricans. J Am Chem Soc 2006; 128:16808-15. [PMID: 17177431 DOI: 10.1021/ja064425i] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies of the catalytic properties of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans by protein film voltammetry, under a H2 atmosphere, reveal and establish a variety of interesting properties not observed or measured quantitatively with other techniques. The catalytic bias (inherent ability to oxidize hydrogen vs reduce protons) is quantified over a wide pH range: the enzyme is proficient at both H2 oxidation (from pH > 6) and H2 production (pH < 6). Hydrogen production is inhibited by H2, but the effect is much smaller than observed for [NiFe]-hydrogenases from Allochromatium vinosum or Desulfovibrio fructosovorans. Under anaerobic conditions and positive potentials, the [FeFe]-hydrogenase is oxidized to an inactive form, inert toward reaction with CO and O2, that rapidly reactivates upon one-electron reduction under 1 bar of H2. The potential dependence of this interconversion shows that the oxidized inactive form exists in two pH-interconvertible states with pK(ox) = 5.9. Studies of the CO-inhibited enzyme under H2 reveals a strong enhancement of the rate of activation by white light at -109 mV (monitoring H2 oxidation) that is absent at low potential (-540 mV, monitoring H+ reduction), thus demonstrating photolability that is dependent upon the oxidation state.
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Affiliation(s)
- Alison Parkin
- Inorganic Chemistry Laboratory, Department of Chemistry, Oxford University, South Parks Road, Oxford OX1 3QR, England
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99
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Valente FMA, Almeida CC, Pacheco I, Carita J, Saraiva LM, Pereira IAC. Selenium is involved in regulation of periplasmic hydrogenase gene expression in Desulfovibrio vulgaris Hildenborough. J Bacteriol 2006; 188:3228-35. [PMID: 16621815 PMCID: PMC1447438 DOI: 10.1128/jb.188.9.3228-3235.2006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Desulfovibrio vulgaris Hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. Hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. The D. vulgaris Hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [FeFe], [FeNi]1, and [FeNiSe] hydrogenases, are usually detected. In this work, we studied the synthesis of each of these enzymes in response to different electron donors and acceptors for growth as well as in response to the availability of Ni and Se. The formation of the three hydrogenases was not very strongly affected by the electron donors or acceptors used, but the highest levels were observed after growth with hydrogen as electron donor and lowest with thiosulfate as electron acceptor. The major effect observed was with inclusion of Se in the growth medium, which led to a strong repression of the [FeFe] and [NiFe]1 hydrogenases and a strong increase in the [NiFeSe] hydrogenase that is not detected in the absence of Se. Ni also led to increased formation of the [NiFe]1 hydrogenase, except for growth with H2, where its synthesis is very high even without Ni added to the medium. Growth with H2 results in a strong increase in the soluble forms of the [NiFe]1 and [NiFeSe] hydrogenases. This study is an important contribution to understanding why D. vulgaris Hildenborough has three periplasmic hydrogenases. It supports their similar physiological role in H2 oxidation and reveals that element availability has a strong influence in their relative expression.
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Affiliation(s)
- Filipa M A Valente
- Instituto de Tecnologia Química e Biológica, Apt. 127, 2781-901 Oeiras, Portugal
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100
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Henry RM, Shoemaker RK, DuBois DL, DuBois MR. Pendant Bases as Proton Relays in Iron Hydride and Dihydrogen Complexes. J Am Chem Soc 2006; 128:3002-10. [PMID: 16506781 DOI: 10.1021/ja057242p] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex trans-[HFe(PNP)(dmpm)(CH(3)CN)]BPh(4), 3, (where PNP is Et(2)PCH(2)N(CH(3))CH(2)PEt(2) and dmpm is Me(2)PCH(2)PMe(2)) can be successively protonated in two steps using increasingly strong acids. Protonation with 1 equiv of p-cyanoanilinium tetrafluoroborate in acetone-d(6) at -80 degrees C results in ligand protonation and the formation of endo (4a) and exo (4b) isomers of trans-[HFe(PNHP)(dmpm)(CH(3)CN)](BPh(4))(2). The endo isomer undergoes rapid intramolecular proton/hydride exchange with an activation barrier of 12 kcal/mol. The exo isomer does not exchange. Studies of the reaction of 3 with a weaker acid (anisidinium tetrafluoroborate) in acetonitrile indicate that a rapid intermolecular proton exchange interconverts isomers 4a and 4b, and a pK(a) value of 12 was determined for these two isomers. Protonation of 3 with 2 equiv of triflic acid results in the protonation of both the PNP ligand and the metal hydride to form the dihydrogen complex [(H(2))Fe(PNHP)(dmpm)(CH(3)CN)](3+), 11. Studies of related complexes [HFe(PNP)(dmpm)(CO)](+) (12) and [HFe(depp)(dmpm)(CH(3)CN)](+) (10) (where depp is bis(diethylphosphino)propane) confirm the important roles of the pendant base and the ligand trans to the hydride ligand in the rapid intra- and intermolecular hydride/proton exchange reactions observed for 4. Features required for an effective proton relay and their potential relevance to the iron-only hydrogenase enzymes are discussed.
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Affiliation(s)
- Renee M Henry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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