1
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Yadav S, Haas R, Boydas EB, Roemelt M, Happe T, Apfel UP, Stripp ST. Oxygen sensitivity of [FeFe]-hydrogenase: a comparative study of active site mimics inside vs. outside the enzyme. Phys Chem Chem Phys 2024; 26:19105-19116. [PMID: 38957092 DOI: 10.1039/d3cp06048a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
[FeFe]-hydrogenase is nature's most efficient proton reducing and H2-oxidizing enzyme. However, biotechnological applications are hampered by the O2 sensitivity of this metalloenzyme, and the mechanism of aerobic deactivation is not well understood. Here, we explore the oxygen sensitivity of four mimics of the organometallic active site cofactor of [FeFe]-hydrogenase, [Fe2(adt)(CO)6-x(CN)x]x- and [Fe2(pdt)(CO)6-x(CN)x]x- (x = 1, 2) as well as the corresponding cofactor variants of the enzyme by means of infrared, Mössbauer, and NMR spectroscopy. Additionally, we describe a straightforward synthetic recipe for the active site precursor complex Fe2(adt)(CO)6. Our data indicate that the aminodithiolate (adt) complex, which is the synthetic precursor of the natural active site cofactor, is most oxygen sensitive. This observation highlights the significance of proton transfer in aerobic deactivation, and supported by DFT calculations facilitates an identification of the responsible reactive oxygen species (ROS). Moreover, we show that the ligand environment of the iron ions critically influences the reactivity with O2 and ROS like superoxide and H2O2 as the oxygen sensitivity increases with the exchange of ligands from CO to CN-. The trends in aerobic deactivation observed for the model complexes are in line with the respective enzyme variants. Based on experimental and computational data, a model for the initial reaction of [FeFe]-hydrogenase with O2 is developed. Our study underscores the relevance of model systems in understanding biocatalysis and validates their potential as important tools for elucidating the chemistry of oxygen-induced deactivation of [FeFe]-hydrogenase.
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Affiliation(s)
- Shanika Yadav
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Rieke Haas
- Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Esma Birsen Boydas
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str.2, 12489, Berlin, Germany
| | - Michael Roemelt
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str.2, 12489, Berlin, Germany
| | - Thomas Happe
- Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
- Department of Electrosynthesi, Fraunhofer UMSICHT, Osterfelder Str. 3, 46047 Oberhausen, Germany
| | - Sven T Stripp
- Biophysical Chemistry, Technical University Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany.
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2
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Aldinio-Colbachini A, Grossi A, Duarte AG, Daurelle JV, Fourmond V. Combining a Commercial Mixer with a Wall-Tube Electrode Allows the Arbitrary Control of Concentrations in Protein Film Electrochemistry. Anal Chem 2024; 96:4868-4875. [PMID: 38466774 DOI: 10.1021/acs.analchem.3c05293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Protein film electrochemistry is a technique in which an enzyme is immobilized on an electrode in a configuration that allows following the changes in turnover frequency as a response to changes in the experimental conditions. Insights into the reactivity of the enzyme can be obtained by quantitatively modeling such responses. As a consequence, the more the technique allows flexibility in changing conditions, the more useful it becomes. The most commonly used setup, based on the rotating disc electrode, allows easy stepwise increases in the concentration of nongaseous substrates, or exposure to constant concentration of dissolved gas, but does not permit to easily decrease the concentration of nongaseous substrates, or to change the concentration of dissolved gas in a stepwise fashion. To overcome the limitation by mass transport of the substrate toward the electrode when working with fast enzymes, we have designed another kind of electrochemical cell based on the wall-tube electrode (WTE). We demonstrate here that by using a system combining two syringe pumps, a commercial mixer, and the WTE, it is possible to change the concentration of species in a stepwise fashion in all directions, opening new possibilities to study redox enzymes. As a proof of concept, this device was applied to the study of the electrochemical response of the cytochrome c nitrite reductase of Desulfovibrio desulfuricans.
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Affiliation(s)
- Anna Aldinio-Colbachini
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Alain Grossi
- Aix-Marseille Université, CNRS, IMM FR3479, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Jean-Vincent Daurelle
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Vincent Fourmond
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
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3
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Greening C, Kropp A, Vincent K, Grinter R. Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion. Biochem Soc Trans 2023; 51:1921-1933. [PMID: 37743798 PMCID: PMC10657181 DOI: 10.1042/bst20230120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023]
Abstract
The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, VIC 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kylie Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, U.K
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
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4
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Schmidt A, Kalms J, Lorent C, Katz S, Frielingsdorf S, Evans RM, Fritsch J, Siebert E, Teutloff C, Armstrong FA, Zebger I, Lenz O, Scheerer P. Stepwise conversion of the Cys 6[4Fe-3S] to a Cys 4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase. Chem Sci 2023; 14:11105-11120. [PMID: 37860641 PMCID: PMC10583674 DOI: 10.1039/d3sc03739h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O2-tolerant hydrogenase. It catalyzes the oxidation of H2 into 2e- and 2H+ in the presence of high O2 concentrations. This characteristic trait is intimately linked to the unique Cys6[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys5[4Fe-4S] or Cys4[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O2 tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O2 protection mechanism that detoxifies O2 to H2O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O2 binding under electron-deficient conditions.
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Affiliation(s)
- Andrea Schmidt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Jacqueline Kalms
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
| | - Christian Lorent
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | | | - Johannes Fritsch
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Elisabeth Siebert
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | | | - Ingo Zebger
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Oliver Lenz
- Institut für Chemie, Biophysical Chemistry, Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics (CC2), Group Structural Biology of Cellular Signaling Charitéplatz 1 10117 Berlin Germany
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5
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Cha J, Lee J, Jeon BW, Kim YH, Kwon I. Real flue gas CO 2 hydrogenation to formate by an enzymatic reactor using O 2- and CO-tolerant hydrogenase and formate dehydrogenase. Front Bioeng Biotechnol 2023; 11:1265272. [PMID: 37854886 PMCID: PMC10579561 DOI: 10.3389/fbioe.2023.1265272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
It is challenging to capture carbon dioxide (CO2), a major greenhouse gas in the atmosphere, due to its high chemical stability. One potential practical solution to eliminate CO2 is to convert CO2 into formate using hydrogen (H2) (CO2 hydrogenation), which can be accomplished with inexpensive hydrogen from sustainable sources. While industrial flue gas could provide an adequate source of hydrogen, a suitable catalyst is needed that can tolerate other gas components, such as carbon monoxide (CO) and oxygen (O2), potential inhibitors. Our proposed CO2 hydrogenation system uses the hydrogenase derived from Ralstonia eutropha H16 (ReSH) and formate dehydrogenase derived from Methylobacterium extorquens AM1 (MeFDH1). Both enzymes are tolerant to CO and O2, which are typical inhibitors of metalloenzymes found in flue gas. We have successfully demonstrated that combining ReSH- and MeFDH1-immobilized resins can convert H2 and CO2 in real flue gas to formate via a nicotinamide adenine dinucleotide-dependent cascade reaction. We anticipated that this enzyme system would enable the utilization of diverse H2 and CO2 sources, including waste gases, biomass, and gasified plastics.
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Affiliation(s)
- Jaehyun Cha
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jinhee Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (Inn-ECOSysChem), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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6
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Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C. Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 2023; 615:541-547. [PMID: 36890228 PMCID: PMC10017518 DOI: 10.1038/s41586-023-05781-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Moritz Senger
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Jack Badley
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Princess R Cabotaje
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Ruyu Jia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Zehui Duan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Ping Huang
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Christopher K Barlow
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Matthew Belousoff
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ralf B Schittenhelm
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, Australia.
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7
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Ogo S, Yatabe T, Tome T, Takenaka R, Shiota Y, Kato K. Safe, One-Pot, Homogeneous Direct Synthesis of H 2O 2. J Am Chem Soc 2023; 145:4384-4388. [PMID: 36798970 PMCID: PMC9983002 DOI: 10.1021/jacs.2c13149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Hydrogen peroxide is an environmentally friendly oxidizing agent but current synthetic methods are wasteful. This is a result of the high flammability of H2/O2 mixtures and/or the requirement for cocatalysts. In this paper, we report the synthesis of H2O2 by means of a homogeneous catalyst, which allows a safe, one-pot synthesis in water, using only H2 and O2. This catalyst is capable of removing electrons from H2, storing them for the reduction of O2, and then permitting the protonation of the reduced oxygen to H2O2. The turnover number (TON) is 910 under an H2/O2 (95/5) atmosphere (1.9 MPa) for 12 h at 23 °C, which is the highest of any homogeneous catalyst. Furthermore, we propose a reaction mechanism based on two crystal structures.
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Affiliation(s)
- Seiji Ogo
- Department
of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,International
Institute for Carbon-Neutral Energy Research (WPI Academy I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,Center
for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,
| | - Takeshi Yatabe
- Department
of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,International
Institute for Carbon-Neutral Energy Research (WPI Academy I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,Center
for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tamon Tome
- Department
of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Riko Takenaka
- Department
of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Institute
for Materials Chemistry and Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kenji Kato
- Center
for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan,Mitsubishi
Gas Chemical Company Inc., Tokyo 100-8324, Japan
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8
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Cha J, Bak H, Kwon I. Hydrogen-fueled CO 2 reduction using oxygen-tolerant oxidoreductases. Front Bioeng Biotechnol 2023; 10:1078164. [PMID: 36686231 PMCID: PMC9849572 DOI: 10.3389/fbioe.2022.1078164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Hydrogen gas obtained from cheap or sustainable sources has been investigated as an alternative to fossil fuels. By using hydrogenase (H2ase) and formate dehydrogenase (FDH), H2 and CO2 gases can be converted to formate, which can be conveniently stored and transported. However, developing an enzymatic process that converts H2 and CO2 obtained from cheap sources into formate is challenging because even a very small amount of O2 included in the cheap sources damages most H2ases and FDHs. In order to overcome this limitation, we investigated a pair of oxygen-tolerant H2ase and FDH. We achieved the cascade reaction between H2ase from Ralstonia eutropha H16 (ReSH) and FDH from Rhodobacter capsulatus (RcFDH) to convert H2 and CO2 to formate using in situ regeneration of NAD+/NADH in the presence of O2.
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Affiliation(s)
- Jaehyun Cha
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Hyeonseon Bak
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea,Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (Inn-ECOSysChem), Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea,*Correspondence: Inchan Kwon,
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9
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Ogo S, Yatabe T, Nakai H. Insights from hydrogenase model studies on C–C bond forming reactions. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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11
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Birrell JA, Rodríguez-Maciá P, Reijerse EJ, Martini MA, Lubitz W. The catalytic cycle of [FeFe] hydrogenase: A tale of two sites. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214191] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Joseph Srinivasan S, Cleary SE, Ramirez MA, Reeve HA, Paul CE, Vincent KA. E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme Ene-reductases*. Angew Chem Int Ed Engl 2021; 60:13824-13828. [PMID: 33721401 PMCID: PMC8252551 DOI: 10.1002/anie.202101186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Indexed: 11/10/2022]
Abstract
A new activity for the [NiFe] uptake hydrogenase 1 of Escherichia coli (Hyd1) is presented. Direct reduction of biological flavin cofactors FMN and FAD is achieved using H2 as a simple, completely atom-economical reductant. The robust nature of Hyd1 is exploited for flavin reduction across a broad range of temperatures (25-70 °C) and extended reaction times. The utility of this system as a simple, easy to implement FMNH2 or FADH2 regenerating system is then demonstrated by supplying reduced flavin to Old Yellow Enzyme "ene-reductases" to support asymmetric alkene reductions with up to 100 % conversion. Hyd1 turnover frequencies up to 20.4 min-1 and total turnover numbers up to 20 200 were recorded during flavin recycling.
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Affiliation(s)
- Shiny Joseph Srinivasan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Sarah E Cleary
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Miguel A Ramirez
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Holly A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
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13
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Joseph Srinivasan S, Cleary SE, Ramirez MA, Reeve HA, Paul CE, Vincent KA. E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme Ene-reductases. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:13943-13947. [PMID: 38529476 PMCID: PMC10962552 DOI: 10.1002/ange.202101186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Indexed: 11/10/2022]
Abstract
A new activity for the [NiFe] uptake hydrogenase 1 of Escherichia coli (Hyd1) is presented. Direct reduction of biological flavin cofactors FMN and FAD is achieved using H2 as a simple, completely atom-economical reductant. The robust nature of Hyd1 is exploited for flavin reduction across a broad range of temperatures (25-70 °C) and extended reaction times. The utility of this system as a simple, easy to implement FMNH2 or FADH2 regenerating system is then demonstrated by supplying reduced flavin to Old Yellow Enzyme "ene-reductases" to support asymmetric alkene reductions with up to 100 % conversion. Hyd1 turnover frequencies up to 20.4 min-1 and total turnover numbers up to 20 200 were recorded during flavin recycling.
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Affiliation(s)
- Shiny Joseph Srinivasan
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Sarah E. Cleary
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Miguel A. Ramirez
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Holly A. Reeve
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Kylie A. Vincent
- Department of ChemistryUniversity of OxfordInorganic Chemistry LaboratorySouth Parks RdOxfordOX1 3QRUnited Kingdom
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14
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Evans RM, Krahn N, Murphy BJ, Lee H, Armstrong FA, Söll D. Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance. Proc Natl Acad Sci U S A 2021; 118:e2100921118. [PMID: 33753519 PMCID: PMC8020662 DOI: 10.1073/pnas.2100921118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In [NiFe]-hydrogenases, the active-site Ni is coordinated by four cysteine-S ligands (Cys; C), two of which are bridging to the Fe(CO)(CN)2 fragment. Substitution of a single Cys residue by selenocysteine (Sec; U) occurs occasionally in nature. Using a recent method for site-specific Sec incorporation into proteins, each of the four Ni-coordinating cysteine residues in the oxygen-tolerant Escherichia coli [NiFe]-hydrogenase-1 (Hyd-1) has been replaced by U to identify its importance for enzyme function. Steady-state solution activity of each Sec-substituted enzyme (on a per-milligram basis) is lowered, although this may reflect the unquantified presence of recalcitrant inactive/immature/misfolded forms. Protein film electrochemistry, however, reveals detailed kinetic data that are independent of absolute activities. Like native Hyd-1, the variants have low apparent KMH2 values, do not produce H2 at pH 6, and display the same onset overpotential for H2 oxidation. Mechanistically important differences were identified for the C576U variant bearing the equivalent replacement found in native [NiFeSe]-hydrogenases, its extreme O2 tolerance (apparent KMH2 and Vmax [solution] values relative to native Hyd-1 of 0.13 and 0.04, respectively) implying the importance of a selenium atom in the position cis to the site where exogenous ligands (H-, H2, O2) bind. Observation of the same unusual electrocatalytic signature seen earlier for the proton transfer-defective E28Q variant highlights the direct role of the chalcogen atom (S/Se) at position 576 close to E28, with the caveat that Se is less effective than S in facilitating proton transfer away from the Ni during H2 oxidation by this enzyme.
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Affiliation(s)
- Rhiannon M Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Bonnie J Murphy
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Harrison Lee
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06520
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15
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Ogo S, Ando T, Minh LTT, Mori Y, Matsumoto T, Yatabe T, Yoon KS, Sato Y, Hibino T, Kaneko K. A NiRhS fuel cell catalyst - lessons from hydrogenase. Chem Commun (Camb) 2020; 56:11787-11790. [PMID: 33021266 DOI: 10.1039/d0cc04789a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a novel fuel cell heterogeneous catalyst based on rhodium, nickel and sulfur with power densities 5-28% that of platinum. The NiRhS heterogeneous catalyst was developed via a homogeneous model complex of the [NiFe]hydrogenases (H2ases) and can act as both the cathode and anode of a fuel cell.
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Affiliation(s)
- Seiji Ogo
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
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16
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Zhang L, Morello G, Carr SB, Armstrong FA. Aerobic Photocatalytic H2 Production by a [NiFe] Hydrogenase Engineered to Place a Silver Nanocluster in the Electron Relay. J Am Chem Soc 2020; 142:12699-12707. [DOI: 10.1021/jacs.0c04302] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Liyun Zhang
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
| | - Giorgio Morello
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot OX11 0QX, United Kingdom
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom
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17
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Swartz J. Opportunities toward hydrogen production biotechnologies. Curr Opin Biotechnol 2020; 62:248-255. [PMID: 32278260 DOI: 10.1016/j.copbio.2020.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023]
Abstract
Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.
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Affiliation(s)
- James Swartz
- Dept. of Chemical Engineering, Dept. of Bioengineering Stanford University, United States.
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18
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Wang VCC, Esmieu C, Redman HJ, Berggren G, Hammarström L. The reactivity of molecular oxygen and reactive oxygen species with [FeFe] hydrogenase biomimetics: reversibility and the role of the second coordination sphere. Dalton Trans 2020; 49:858-865. [DOI: 10.1039/c9dt04618f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new one-electron reduced and oxygenated species from H2-evolving complexes, inspired by [FeFe] hydrogenase, was prepared by directly reacting with O2 and chemical reductants. Its structure and reactivity were investigated by spectroscopic tools.
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Affiliation(s)
- Vincent C.-C. Wang
- Program of Physical Chemistry
- Department of Chemistry – Ångström Laboratory
- Uppsala University
- Uppsala 75120
- Sweden
| | - Charlène Esmieu
- Program of Molecular Biomimetics
- Department of Chemistry – Ångström Laboratory
- Uppsala University
- Uppsala 75120
- Sweden
| | - Holly J. Redman
- Program of Molecular Biomimetics
- Department of Chemistry – Ångström Laboratory
- Uppsala University
- Uppsala 75120
- Sweden
| | - Gustav Berggren
- Program of Molecular Biomimetics
- Department of Chemistry – Ångström Laboratory
- Uppsala University
- Uppsala 75120
- Sweden
| | - Leif Hammarström
- Program of Physical Chemistry
- Department of Chemistry – Ångström Laboratory
- Uppsala University
- Uppsala 75120
- Sweden
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19
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Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
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20
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Evans RM, Siritanaratkul B, Megarity CF, Pandey K, Esterle TF, Badiani S, Armstrong FA. The value of enzymes in solar fuels research – efficient electrocatalysts through evolution. Chem Soc Rev 2019; 48:2039-2052. [DOI: 10.1039/c8cs00546j] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes which evolved more than 2 billion years ago set exceptional standards for electrocatalysts being sought today.
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Affiliation(s)
- Rhiannon M. Evans
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
| | | | - Clare F. Megarity
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
| | - Kavita Pandey
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
| | - Thomas F. Esterle
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
| | - Selina Badiani
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
| | - Fraser A. Armstrong
- Department of Chemistry
- Inorganic Chemistry Laboratory
- University of Oxford
- Oxford
- UK
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21
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Mori Y, Ando T, Matsumoto T, Yatabe T, Kikkawa M, Yoon K, Ogo S. Multifunctional Catalysts for H
2
O
2
‐Resistant Hydrogen Fuel Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuki Mori
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Tatsuya Ando
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takahiro Matsumoto
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takeshi Yatabe
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Mitsuhiro Kikkawa
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Ki‐Seok Yoon
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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22
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Mori Y, Ando T, Matsumoto T, Yatabe T, Kikkawa M, Yoon K, Ogo S. Multifunctional Catalysts for H
2
O
2
‐Resistant Hydrogen Fuel Cells. Angew Chem Int Ed Engl 2018; 57:15792-15796. [PMID: 30303292 DOI: 10.1002/anie.201810270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Yuki Mori
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Tatsuya Ando
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takahiro Matsumoto
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Takeshi Yatabe
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Mitsuhiro Kikkawa
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Ki‐Seok Yoon
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Seiji Ogo
- Department of Chemistry and Biochemistry Graduate School of Engineering, Center for Small Molecule Energy International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University, 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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23
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Tai H, Higuchi Y, Hirota S. Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases. Dalton Trans 2018. [PMID: 29532823 DOI: 10.1039/c7dt04910b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.
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Affiliation(s)
- Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan.
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24
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Ahmed ME, Dey S, Darensbourg MY, Dey A. Oxygen-Tolerant H 2 Production by [FeFe]-H 2ase Active Site Mimics Aided by Second Sphere Proton Shuttle. J Am Chem Soc 2018; 140:12457-12468. [PMID: 30180564 DOI: 10.1021/jacs.8b05983] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The instability of [FeFe]-H2ases and their biomimetics toward O2 renders them inefficient to implement in practical H2 generation (HER). Previous investigations on synthetic models as well as natural enzymes proved that reactive oxygen species (ROS) generated on O2 exposure oxidatively degrades the 2Fe subcluster within the H-cluster active site. Recent electrochemical studies, coupled with theoretical investigations on [FeFe]-H2ase suggested that selective O2 reduction to H2O could eliminate the ROS, and hence, tolerance against oxidative degradation could be achieved ( Nat. Chem. 2017, 9, 88-95). We have prepared a series of 2Fe subsite mimics with substituted arenes attached to bridgehead N atoms in the S to S linker, (μ-S2(CH2)2NAr)[Fe(CO)3]2. Structural analyses find the nature of the substituent on the arene offers steric control of the orientation of bridgehead N atoms, affecting their proton uptake and translocation ability. The heterogeneous electrochemical studies of these complexes physiadsorbed on edge plane graphite (EPG) electrode show the onset of HER activity at ∼180 mV overpotential in pH 5.5 water. In addition, bridgehead N-protonation and subsequent H-bonding capability are established to facilitate the O-O bond cleavage resulting in selective O2 reduction to H2O. This allows a synthetic [FeFe]-H2ase model to reduce protons to H2 unabated in the presence of dissolved O2 in water at nearly neutral pH (pH 5.5); i.e., O2-tolerant, stable HER activity is achieved.
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Affiliation(s)
- Md Estak Ahmed
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata 700032 , India
| | - Subal Dey
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata 700032 , India
| | - Marcetta Y Darensbourg
- Department of Chemistry , Texas A&M University , College Station , Texas 77843-3255 , United States
| | - Abhishek Dey
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , Kolkata 700032 , India
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25
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Koo J, Swartz JR. System analysis and improved [FeFe] hydrogenase O2 tolerance suggest feasibility for photosynthetic H2 production. Metab Eng 2018; 49:21-27. [DOI: 10.1016/j.ymben.2018.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 11/16/2022]
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26
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Evans RM, Ash PA, Beaton SE, Brooke EJ, Vincent KA, Carr SB, Armstrong FA. Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase. J Am Chem Soc 2018; 140:10208-10220. [DOI: 10.1021/jacs.8b04798] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rhiannon M. Evans
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Stephen E. Beaton
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Emily J. Brooke
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot OX11 0QX, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Fraser A. Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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27
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Esmieu C, Raleiras P, Berggren G. From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production. SUSTAINABLE ENERGY & FUELS 2018; 2:724-750. [PMID: 31497651 PMCID: PMC6695573 DOI: 10.1039/c7se00582b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.
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Affiliation(s)
- C Esmieu
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - P Raleiras
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - G Berggren
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
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28
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Huang G, Wagner T, Ermler U, Bill E, Ataka K, Shima S. Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates. Angew Chem Int Ed Engl 2018; 57:4917-4920. [PMID: 29462510 DOI: 10.1002/anie.201712293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 01/27/2023]
Abstract
Mono-iron hydrogenase ([Fe]-hydrogenase) reversibly catalyzes the transfer of a hydride ion from H2 to methenyltetrahydromethanopterin (methenyl-H4 MPT+ ) to form methylene-H4 MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H2 activation. Evidence is presented for O2 sensitivity of [Fe]-hydrogenase under turnover conditions in the presence of reducing substrates, methylene-H4 MPT or methenyl-H4 MPT+ /H2 . Only then, H2 O2 is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O2 reduction to H2 O2 requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]-hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.
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Affiliation(s)
- Gangfeng Huang
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Tristan Wagner
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438, Frankfurt/Main, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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29
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Huang G, Wagner T, Ermler U, Bill E, Ataka K, Shima S. Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Gangfeng Huang
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Tristan Wagner
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt/Main Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion; 45470 Mülheim Germany
| | - Kenichi Ataka
- Department of Physics; Freie Universität Berlin; Berlin 14195 Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
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30
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Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P. Tracking the route of molecular oxygen in O 2-tolerant membrane-bound [NiFe] hydrogenase. Proc Natl Acad Sci U S A 2018; 115:E2229-E2237. [PMID: 29463722 PMCID: PMC5877991 DOI: 10.1073/pnas.1712267115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2 tolerance of the enzyme.
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Affiliation(s)
- Jacqueline Kalms
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany
| | - Andrea Schmidt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany
| | | | - Tillmann Utesch
- Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | | | | | - Peter van der Linden
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), F-38043 Grenoble, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France
| | | | - Philippe Carpentier
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biosciences et Biotechnologies de Grenoble (BIG)-Laboratoire Chimie et Biologie des Métaux (LCBM), F-38000 Grenoble, France
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany;
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31
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Abstract
Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.
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32
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Matsumoto T, Kishima T, Yatabe T, Yoon KS, Ogo S. Mechanistic Insight into Switching between H2- or O2-Activation by Simple Ligand Effects of [NiFe]hydrogenase Models. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Takahiro Matsumoto
- Center for Small Molecule Energy, ‡Department of Chemistry and Biochemistry,
Graduate School of Engineering, and §International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Kishima
- Center for Small Molecule Energy, ‡Department of Chemistry and Biochemistry,
Graduate School of Engineering, and §International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeshi Yatabe
- Center for Small Molecule Energy, ‡Department of Chemistry and Biochemistry,
Graduate School of Engineering, and §International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ki-Seok Yoon
- Center for Small Molecule Energy, ‡Department of Chemistry and Biochemistry,
Graduate School of Engineering, and §International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- Center for Small Molecule Energy, ‡Department of Chemistry and Biochemistry,
Graduate School of Engineering, and §International Institute for Carbon-Neutral Energy
Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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33
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Rodríguez-Maciá P, Pawlak K, Rüdiger O, Reijerse EJ, Lubitz W, Birrell JA. Intercluster Redox Coupling Influences Protonation at the H-cluster in [FeFe] Hydrogenases. J Am Chem Soc 2017; 139:15122-15134. [DOI: 10.1021/jacs.7b08193] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Krzysztof Pawlak
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
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34
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35
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Brooke EJ, Evans RM, Islam STA, Roberts GM, Wehlin SAM, Carr SB, Phillips SEV, Armstrong FA. Importance of the Active Site “Canopy” Residues in an O2-Tolerant [NiFe]-Hydrogenase. Biochemistry 2016; 56:132-142. [DOI: 10.1021/acs.biochem.6b00868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Gerri M. Roberts
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Stephen B. Carr
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, U.K
- Department
of Biochemistry, University of Oxford, Oxford, U.K
| | - Simon E. V. Phillips
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, U.K
- Department
of Biochemistry, University of Oxford, Oxford, U.K
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36
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Abstract
Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.
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37
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Kubas A, Orain C, De Sancho D, Saujet L, Sensi M, Gauquelin C, Meynial-Salles I, Soucaille P, Bottin H, Baffert C, Fourmond V, Best RB, Blumberger J, Léger C. Mechanism of O 2 diffusion and reduction in FeFe hydrogenases. Nat Chem 2016; 9:88-95. [PMID: 27995927 DOI: 10.1038/nchem.2592] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/08/2016] [Indexed: 11/09/2022]
Abstract
FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage.
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Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK.,Institute of Physical Chemistry, Polish Academy of Science, ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Christophe Orain
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,CIC nanoGUNE, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain.,IKERBASQUE; Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain
| | - Laure Saujet
- Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France.,Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA, CNRS, Université Paris Sud, F-91191 Gif sur Yvette, France
| | - Matteo Sensi
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Charles Gauquelin
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Isabelle Meynial-Salles
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Philippe Soucaille
- Université de Toulouse, INSA, UPS, INP, LISBP, INRA:UMR792, CNRS:UMR 5504, 135 avenue de Rangueil, Toulouse 31077 Cedex 04, France
| | - Hervé Bottin
- Institut de Biologie et de Technologies de Saclay IBITECS, SB2SM, F-91191 Gif sur Yvette, France.,Institut de Biologie Intégrative de la Cellule I2BC, UMR 9198, CEA, CNRS, Université Paris Sud, F-91191 Gif sur Yvette, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Christophe Léger
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France
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38
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Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
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Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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39
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Ogata H, Lubitz W, Higuchi Y. Structure and function of [NiFe] hydrogenases. J Biochem 2016; 160:251-258. [PMID: 27493211 DOI: 10.1093/jb/mvw048] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/06/2016] [Indexed: 12/22/2022] Open
Abstract
Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN- ligands. The catalytic activity of the standard (O2-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O2-tolerant [NiFe] hydrogenases can sustain H2 oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process. An important structural difference between these hydrogenases has been found for the proximal iron-sulphur cluster located in the vicinity of the active site. This unprecedented [4Fe-3S]-6Cys cluster can supply two electrons, which lead to rapid recovery of the O2 inactivation, to the [NiFe] active site.
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Affiliation(s)
- Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - 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-cho, Sayo-gun, Hyogo 679-5148, Japan.,CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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40
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Birrell JA, Laurich C, Reijerse EJ, Ogata H, Lubitz W. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima. Biochemistry 2016; 55:4344-55. [PMID: 27396836 DOI: 10.1021/acs.biochem.6b00341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions. Here, we generate mutations in a [2Fe-2S] cluster protein, the TmHydC subunit of the trimeric [FeFe]-hydrogenase from Thermotoga maritima, to study the factors that affect its redox potential. Saturation mutagenesis of Val131 was used to tune the redox potential over a 135 mV range and revealed that cluster redox potential and electronic properties correlate with amino acid hydrophobicity and the ability to form hydrogen bonds to the cluster. Proline scanning mutagenesis between pairs of ligating cysteines was used to remove backbone amide hydrogen bonds to the cluster and decrease the redox potential by up to 132 mV, without large structural changes in most cases. However, substitution of Gly83 with proline caused a change of HydC to a [4Fe-4S] cluster protein with a redox potential of -526 mV. Together, these results confirm the importance of hydrogen bonding in tuning cluster redox potentials and demonstrate the versatility of iron-sulfur cluster protein folds at binding different types of clusters.
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Affiliation(s)
- James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Laurich
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
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41
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Koo J, Shiigi S, Rohovie M, Mehta K, Swartz JR. Characterization of [FeFe] Hydrogenase O2 Sensitivity Using a New, Physiological Approach. J Biol Chem 2016; 291:21563-21570. [PMID: 27435671 DOI: 10.1074/jbc.m116.737122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/15/2016] [Indexed: 11/06/2022] Open
Abstract
[FeFe] hydrogenases catalyze rapid H2 production but are highly O2-sensitive. Developing O2-tolerant enzymes is needed for sustainable H2 production technologies, but the lack of a quantitative and predictive assay for O2 tolerance has impeded progress. We describe a new approach to provide quantitative assessment of O2 sensitivity by using an assay employing ferredoxin NADP+ reductase (FNR) to transfer electrons from NADPH to hydrogenase via ferredoxins (Fd). Hydrogenase inactivation is measured during H2 production in an O2-containing environment. An alternative assay uses dithionite (DTH) to provide reduced Fd. This second assay measures the remaining hydrogenase activity in periodic samples taken from the NADPH-driven reaction solutions. The second assay validates the more convenient NADPH-driven assay, which better mimics physiological conditions. During development of the NADPH-driven assay and while characterizing the Clostridium pasteurianum (Cp) [FeFe] hydrogenase, CpI, we detected significant rates of direct electron loss from reduced Fd to O2 However, this loss does not interfere with measurement of first order hydrogenase inactivation, providing rate constants insensitive to initial hydrogenase concentration. We show increased activity and O2 tolerance for a protein fusion between Cp ferredoxin (CpFd) and CpI mediated by a 15-amino acid linker but not for a longer linker. We suggest that this precise, solution phase assay for [FeFe] hydrogenase O2 sensitivity and the insights we provide constitute an important advance toward the discovery of the O2-tolerant [FeFe] hydrogenases required for photosynthetic, biological H2 production.
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Affiliation(s)
- Jamin Koo
- From the Departments of Chemical Engineering and
| | - Stacey Shiigi
- Bioengineering, Stanford University, Stanford, California 94305
| | | | - Kunal Mehta
- Bioengineering, Stanford University, Stanford, California 94305
| | - James R Swartz
- From the Departments of Chemical Engineering and .,Bioengineering, Stanford University, Stanford, California 94305
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42
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Armstrong FA, Evans RM, Hexter SV, Murphy BJ, Roessler MM, Wulff P. Guiding Principles of Hydrogenase Catalysis Instigated and Clarified by Protein Film Electrochemistry. Acc Chem Res 2016; 49:884-92. [PMID: 27104487 DOI: 10.1021/acs.accounts.6b00027] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein film electrochemistry (PFE) is providing cutting-edge insight into the chemical principles underpinning biological hydrogen. Attached to an electrode, many enzymes exhibit "reversible" electrocatalytic behavior, meaning that a catalyzed redox reaction appears reversible or quasi-reversible when viewed by cyclic voltammetry. This efficiency is most relevant for enzymes that are inspiring advances in renewable energy, such as hydrogen-activating and CO2-reducing enzymes. Exploiting the rich repertoire of available instrumental methods, PFE experiments yield both a general snapshot and fine detail, all from tiny samples of enzyme. The dynamic electrochemical investigations blaze new trails and add exquisite detail to the information gained from structural and spectroscopic studies. This Account describes recent investigations of hydrogenases carried out in Oxford, including ideas initiated with PFE and followed through with complementary techniques, all contributing to an eventual complete picture of fast and efficient H2 activation without Pt. By immobilization of an enzyme on an electrode, catalytic electron flow and the chemistry controlling it can be addressed at the touch of a button. The buried nature of the active site means that structures that have been determined by crystallography or spectroscopy are likely to be protected, retained, and fully relevant in a PFE experiment. An electrocatalysis model formulated for the PFE of immobilized enzymes predicts interesting behavior and gives insight into why some hydrogenases are H2 producers and others are H2 oxidizers. Immobilization also allows for easy addition and removal of inhibitors along with precise potential control, one interesting outcome being that formaldehyde forms a reversible complex with reduced [FeFe]-hydrogenases, thereby providing insight into the order of electron and proton transfers. Experiments on O2-tolerant [NiFe]-hydrogenases show that O2 behaves like a reversible inhibitor: it is also a substrate, and implicit in the description of some hydrogenases as "H2/O2 oxidoreductases" is the hypothesis that fast and efficient multielectron transfer is a key to O2 tolerance because it promotes complete reduction of O2 to harmless water. Not only is a novel [4Fe-3S] cluster (able to transfer two electrons consecutively) an important component, but connections to additional electron sources (other Fe-S clusters, an electrode, another quaternary structure unit, or the physiological membrane itself) ensure that H2 oxidation can be sustained in the presence of O2, as demonstrated with enzyme fuel cells able to operate on a H2/air mixture. Manipulating the H-H bond in the active site is the simplest proton-coupled electron-transfer reaction to be catalyzed by an enzyme. Unlike small molecular catalysts or the surfaces of materials, metalloenzymes are far better suited to engineering the all-important outer-coordination shell. Hence, recent successful site-directed mutagenesis of the conserved outer-shell "canopy" residues in a [NiFe]-hydrogenase opens up new opportunities for understanding the mechanism of H2 activation beyond the role of the inner coordination shell.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Rhiannon M. Evans
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Suzannah V. Hexter
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Bonnie J. Murphy
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Maxie M. Roessler
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Philip Wulff
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
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Krypton Derivatization of an O
2
‐Tolerant Membrane‐Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport. Angew Chem Int Ed Engl 2016; 55:5586-90. [DOI: 10.1002/anie.201508976] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/17/2015] [Indexed: 01/29/2023]
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Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P. Ein Netzwerk aus hydrophoben Tunneln zum Transport gasförmiger Reaktanten in einer O
2
‐toleranten, membrangebundenen [NiFe]‐ Hydrogenase, aufgedeckt durch Derivatisierung mit Krypton. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jacqueline Kalms
- Institut für Medizinische Physik und Biophysik (CC2) Group Protein X-ray Crystallography and Signal Transduction Charité – Universitätsmedizin Berlin Charitéplatz 1 10117 Berlin Deutschland
| | - Andrea Schmidt
- Institut für Medizinische Physik und Biophysik (CC2) Group Protein X-ray Crystallography and Signal Transduction Charité – Universitätsmedizin Berlin Charitéplatz 1 10117 Berlin Deutschland
| | - Stefan Frielingsdorf
- Institut für Chemie, Sekr. PC14 Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Peter van der Linden
- ESRF – European Synchrotron Radiation Facility 71 Avenue des Martyrs Grenoble Cedex 9 38043 Frankreich
| | - David von Stetten
- ESRF – European Synchrotron Radiation Facility 71 Avenue des Martyrs Grenoble Cedex 9 38043 Frankreich
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14 Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Philippe Carpentier
- ESRF – European Synchrotron Radiation Facility 71 Avenue des Martyrs Grenoble Cedex 9 38043 Frankreich
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik (CC2) Group Protein X-ray Crystallography and Signal Transduction Charité – Universitätsmedizin Berlin Charitéplatz 1 10117 Berlin Deutschland
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Wulff P, Thomas C, Sargent F, Armstrong FA. How the oxygen tolerance of a [NiFe]-hydrogenase depends on quaternary structure. J Biol Inorg Chem 2016; 21:121-34. [PMID: 26861789 PMCID: PMC4771823 DOI: 10.1007/s00775-015-1327-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 12/23/2015] [Indexed: 11/28/2022]
Abstract
‘Oxygen-tolerant’ [NiFe]-hydrogenases can catalyze H2 oxidation under aerobic conditions, avoiding oxygenation and destruction of the active site. In one mechanism accounting for this special property, membrane-bound [NiFe]-hydrogenases accommodate a pool of electrons that allows an O2 molecule attacking the active site to be converted rapidly to harmless water. An important advantage may stem from having a dimeric or higher-order quaternary structure in which the electron-transfer relay chain of one partner is electronically coupled to that in the other. Hydrogenase-1 from E. coli has a dimeric structure in which the distal [4Fe-4S] clusters in each monomer are located approximately 12 Å apart, a distance conducive to fast electron tunneling. Such an arrangement can ensure that electrons from H2 oxidation released at the active site of one partner are immediately transferred to its counterpart when an O2 molecule attacks. This paper addresses the role of long-range, inter-domain electron transfer in the mechanism of O2-tolerance by comparing the properties of monomeric and dimeric forms of Hydrogenase-1. The results reveal a further interesting advantage that quaternary structure affords to proteins.
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Affiliation(s)
- Philip Wulff
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Claudia Thomas
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Frank Sargent
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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46
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Structure of an Actinobacterial-Type [NiFe]-Hydrogenase Reveals Insight into O 2 -Tolerant H 2 Oxidation. Structure 2016; 24:285-92. [DOI: 10.1016/j.str.2015.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022]
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47
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Chambers GM, Huynh MT, Li Y, Hammes-Schiffer S, Rauchfuss TB, Reijerse E, Lubitz W. Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site. Inorg Chem 2016; 55:419-31. [PMID: 26421729 PMCID: PMC4807737 DOI: 10.1021/acs.inorgchem.5b01662] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new class of synthetic models for the active site of [NiFe]-hydrogenases are described. The Ni(I/II)(SCys)2 and Fe(II)(CN)2CO sites are represented with (RC5H4)Ni(I/II) and Fe(II)(diphos)(CO) modules, where diphos = 1,2-C2H4(PPh2)2(dppe) or cis-1,2-C2H2(PPh2)2(dppv). The two bridging thiolate ligands are represented by CH2(CH2S)2(2-) (pdt(2-)), Me2C(CH2S)2(2-) (Me2pdt(2-)), and (C6H5S)2(2-). The reaction of Fe(pdt)(CO)2(dppe) and [(C5H5)3Ni2]BF4 affords [(C5H5)Ni(pdt)Fe(dppe)(CO)]BF4 ([1a]BF4). Monocarbonyl [1a]BF4 features an S = 0 Ni(II)Fe(II) center with five-coordinated iron, as proposed for the Ni-SIa state of the enzyme. One-electron reduction of [1a](+) affords the S = 1/2 derivative [1a](0), which, according to density functional theory (DFT) calculations and electron paramagnetic resonance and Mössbauer spectroscopies, is best described as a Ni(I)Fe(II) compound. The Ni(I)Fe(II) assignment matches that for the Ni-L state in [NiFe]-hydrogenase, unlike recently reported Ni(II)Fe(I)-based models. Compound [1a](0) reacts with strong acids to liberate 0.5 equiv of H2 and regenerate [1a](+), indicating that H2 evolution is catalyzed by [1a](0). DFT calculations were used to investigate the pathway for H2 evolution and revealed that the mechanism can proceed through two isomers of [1a](0) that differ in the stereochemistry of the Fe(dppe)CO center. Calculations suggest that protonation of [1a](0) (both isomers) affords Ni(III)-H-Fe(II) intermediates, which represent mimics of the Ni-C state of the enzyme.
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Abstract
In Escherichia coli, hydrogen metabolism plays a prominent role in anaerobic physiology. The genome contains the capability to produce and assemble up to four [NiFe]-hydrogenases, each of which are known, or predicted, to contribute to different aspects of cellular metabolism. In recent years, there have been major advances in the understanding of the structure, function, and roles of the E. coli [NiFe]-hydrogenases. The membrane-bound, periplasmically oriented, respiratory Hyd-1 isoenzyme has become one of the most important paradigm systems for understanding an important class of oxygen-tolerant enzymes, as well as providing key information on the mechanism of hydrogen activation per se. The membrane-bound, periplasmically oriented, Hyd-2 isoenzyme has emerged as an unusual, bidirectional redox valve able to link hydrogen oxidation to quinone reduction during anaerobic respiration, or to allow disposal of excess reducing equivalents as hydrogen gas. The membrane-bound, cytoplasmically oriented, Hyd-3 isoenzyme is part of the formate hydrogenlyase complex, which acts to detoxify excess formic acid under anaerobic fermentative conditions and is geared towards hydrogen production under those conditions. Sequence identity between some Hyd-3 subunits and those of the respiratory NADH dehydrogenases has led to hypotheses that the activity of this isoenzyme may be tightly coupled to the formation of transmembrane ion gradients. Finally, the E. coli genome encodes a homologue of Hyd-3, termed Hyd-4, however strong evidence for a physiological role for E. coli Hyd-4 remains elusive. In this review, the versatile hydrogen metabolism of E. coli will be discussed and the roles and potential applications of the spectrum of different types of [NiFe]-hydrogenases available will be explored.
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Hugenbruch S, Shafaat HS, Krämer T, Delgado-Jaime MU, Weber K, Neese F, Lubitz W, DeBeer S. In search of metal hydrides: an X-ray absorption and emission study of [NiFe] hydrogenase model complexes. Phys Chem Chem Phys 2016; 18:10688-99. [DOI: 10.1039/c5cp07293j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Insight into the factors that favor metal–hydride interactions in NiFe-hydrogenase models is obtained through X-ray spectroscopic and quantum chemical studies.
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Affiliation(s)
| | - Hannah S. Shafaat
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
- The Ohio State University
- Department of Chemistry and Biochemistry
| | - Tobias Krämer
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
- Heriot-Watt University
- Institute of Chemical Sciences
| | - Mario Ulises Delgado-Jaime
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
- Inorganic Chemistry and Catalysis Group
- Debye Institute for Nanomaterials Science
| | - Katharina Weber
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion
- D-45470
- Germany
- Cornell University
- Department of Chemistry and Chemical Biology
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50
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The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. EcoSal Plus 2015; 6. [PMID: 26442941 DOI: 10.1128/ecosalplus.esp-0005-2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. Salmonella is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δp) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H+/2e- ratios for most respiratory chains are in the range from 2 to 6 H+/2e-. The energetics of the individual redox reactions and the respiratory chains is described and related to the H+/2e- ratios.
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