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Jiang W, Cai Y, Sun S, Wang W, Tišma M, Baganz F, Hao J. Inactivation of hydrogenase-3 leads to enhancement of 1,3-propanediol and 2,3-butanediol production by Klebsiella pneumoniae. Enzyme Microb Technol 2024; 177:110438. [PMID: 38518554 DOI: 10.1016/j.enzmictec.2024.110438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
Klebsiella pneumoniae can use glucose or glycerol as carbon sources to produce 1,3-propanediol or 2,3-butanediol, respectively. In the metabolism of Klebsiella pneumoniae, hydrogenase-3 is responsible for H2 production from formic acid, but it is not directly related to the synthesis pathways for 1,3-propanediol and 2,3-butanediol. In the first part of this research, hycEFG, which encodes subunits of the enzyme hydrogenase-3, was knocked out, so K. pneumoniae ΔhycEFG lost the ability to produce H2 during cultivation using glycerol as a carbon source. As a consequence, the concentration of 1,3-propanediol increased and the substrate (glycerol) conversion ratio reached 0.587 mol/mol. Then, K. pneumoniae ΔldhAΔhycEFG was constructed to erase lactic acid synthesis which led to the further increase of 1,3-propanediol concentration. A substrate (glycerol) conversion ratio of 0.628 mol/mol in batch conditions was achieved, which was higher compared to the wild type strain (0.545 mol/mol). Furthermore, since adhE encodes an alcohol dehydrogenase that catalyzes ethanol production from acetaldehyde, K. pneumoniae ΔldhAΔadhEΔhycEFG was constructed to prevent ethanol production. Contrary to expectations, this did not lead to a further increase, but to a decrease in 1,3-propanediol production. In the second part of this research, glucose was used as the carbon source to produce 2,3-butanediol. Knocking out hycEFG had distinct positive effect on 2,3-butanediol production. Especially in K. pneumoniae ΔldhAΔadhEΔhycEFG, a substrate (glucose) conversion ratio of 0.730 mol/mol was reached, which is higher compared to wild type strain (0.504 mol/mol). This work suggests that the inactivation of hydrogenase-3 may have a global effect on the metabolic regulation of K. pneumoniae, leading to the improvement of the production of two industrially important bulk chemicals, 1,3-propanediol and 2,3-butanediol.
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Affiliation(s)
- Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaoyu Cai
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shaoqi Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenqi Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Marina Tišma
- Josip Juraj Strossmayer University of Osijek, Faculty of Food Technology Osijek, Franje Kuhača 18, Osijek HR-31000, Croatia
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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2
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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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3
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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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4
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Fu B, Mao X, Park Y, Zhao Z, Yan T, Jung W, Francis DH, Li W, Pian B, Salimijazi F, Suri M, Hanrath T, Barstow B, Chen P. Single-cell multimodal imaging uncovers energy conversion pathways in biohybrids. Nat Chem 2023; 15:1400-1407. [PMID: 37500951 DOI: 10.1038/s41557-023-01285-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Microbe-semiconductor biohybrids, which integrate microbial enzymatic synthesis with the light-harvesting capabilities of inorganic semiconductors, have emerged as promising solar-to-chemical conversion systems. Improving the electron transport at the nano-bio interface and inside cells is important for boosting conversion efficiencies, yet the underlying mechanism is challenging to study by bulk measurements owing to the heterogeneities of both constituents. Here we develop a generalizable, quantitative multimodal microscopy platform that combines multi-channel optical imaging and photocurrent mapping to probe such biohybrids down to single- to sub-cell/particle levels. We uncover and differentiate the critical roles of different hydrogenases in the lithoautotrophic bacterium Ralstonia eutropha for bioplastic formation, discover this bacterium's surprisingly large nanoampere-level electron-uptake capability, and dissect the cross-membrane electron-transport pathways. This imaging platform, and the associated analytical framework, can uncover electron-transport mechanisms in various types of biohybrid, and potentially offers a means to use and engineer R. eutropha for efficient chemical production coupled with photocatalytic materials.
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Affiliation(s)
- Bing Fu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Materials Science and Engineering, Institute of Functional Intelligent Materials, and Centre for Advanced 2D Materials, National University of Singapore, Singapore, Singapore
| | - Youngchan Park
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zhiheng Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Tianlei Yan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Danielle H Francis
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Friends School of Baltimore, Baltimore, MD, USA
| | - Wenjie Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Mokshin Suri
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | - Tobias Hanrath
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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5
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Dragelj J, Karafoulidi-Retsou C, Katz S, Lenz O, Zebger I, Caserta G, Sacquin-Mora S, Mroginski MA. Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Front Microbiol 2023; 13:1073315. [PMID: 36733774 PMCID: PMC9886862 DOI: 10.3389/fmicb.2022.1073315] [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: 10/18/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel-iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.
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Affiliation(s)
- Jovan Dragelj
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Sophie Sacquin-Mora
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany,CNRS, UPR, Laboratoire de Biochimie Théorique, Université de Paris Cité, Paris, France,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany,*Correspondence: Maria Andrea Mroginski, ✉
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6
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Vansuch GE, Wu CH, Haja DK, Blair SA, Chica B, Johnson MK, Adams MWW, Dyer RB. Metal-ligand cooperativity in the soluble hydrogenase-1 from Pyrococcus furiosus. Chem Sci 2020; 11:8572-8581. [PMID: 34123117 PMCID: PMC8163435 DOI: 10.1039/d0sc00628a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Metal–ligand cooperativity is an essential feature of bioinorganic catalysis. The design principles of such cooperativity in metalloenzymes are underexplored, but are critical to understand for developing efficient catalysts designed with earth abundant metals for small molecule activation. The simple substrate requirements of reversible proton reduction by the [NiFe]-hydrogenases make them a model bioinorganic system. A highly conserved arginine residue (R355) directly above the exogenous ligand binding position of the [NiFe]-catalytic core is known to be essential for optimal function because mutation to a lysine results in lower catalytic rates. To expand on our studies of soluble hydrogenase-1 from Pyrococcus furiosus (Pf SH1), we investigated the role of R355 by site-directed-mutagenesis to a lysine (R355K) using infrared and electron paramagnetic resonance spectroscopic probes sensitive to active site redox and protonation events. It was found the mutation resulted in an altered ligand binding environment at the [NiFe] centre. A key observation was destabilization of the Nia3+–C state, which contains a bridging hydride. Instead, the tautomeric Nia+–L states were observed. Overall, the results provided insight into complex metal–ligand cooperativity between the active site and protein scaffold that modulates the bridging hydride stability and the proton inventory, which should prove valuable to design principles for efficient bioinspired catalysts. Metal–ligand cooperativity is an essential feature of bioinorganic catalysis.![]()
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Affiliation(s)
| | - Chang-Hao Wu
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,AskGene Pharma Inc. Camarillo CA 93012 USA
| | - Dominik K Haja
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA
| | - Soshawn A Blair
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Bryant Chica
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA .,Biosciences Center, National Renewable Energy Laboratory Golden Colorado 80401 USA
| | - Michael K Johnson
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - R Brian Dyer
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA
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7
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Hartmann S, Frielingsdorf S, Caserta G, Lenz O. A membrane-bound [NiFe]-hydrogenase large subunit precursor whose C-terminal extension is not essential for cofactor incorporation but guarantees optimal maturation. Microbiologyopen 2020; 9:1197-1206. [PMID: 32180370 PMCID: PMC7294309 DOI: 10.1002/mbo3.1029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/20/2023] Open
Abstract
[NiFe]‐hydrogenases catalyze the reversible conversion of molecular hydrogen into protons end electrons. This reaction takes place at a NiFe(CN)2(CO) cofactor located in the large subunit of the bipartite hydrogenase module. The corresponding apo‐protein carries usually a C‐terminal extension that is cleaved off by a specific endopeptidase as soon as the cofactor insertion has been accomplished by the maturation machinery. This process triggers complex formation with the small, electron‐transferring subunit of the hydrogenase module, revealing catalytically active enzyme. The role of the C‐terminal extension in cofactor insertion, however, remains elusive. We have addressed this problem by using genetic engineering to remove the entire C‐terminal extension from the apo‐form of the large subunit of the membrane‐bound [NiFe]‐hydrogenase (MBH) from Ralstonia eutropha. Unexpectedly, the MBH holoenzyme derived from this precleaved large subunit was targeted to the cytoplasmic membrane, conferred H2‐dependent growth of the host strain, and the purified protein showed exactly the same catalytic activity as native MBH. The only difference was a reduced hydrogenase content in the cytoplasmic membrane. These results suggest that in the case of the R. eutropha MBH, the C‐terminal extension is dispensable for cofactor insertion and seems to function only as a maturation facilitator.
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Affiliation(s)
- Sven Hartmann
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Berlin, Germany
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8
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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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9
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Tombolelli D, Mroginski MA. Proton Transfer Pathways between Active Sites and Proximal Clusters in the Membrane-Bound [NiFe] Hydrogenase. J Phys Chem B 2019; 123:3409-3420. [PMID: 30931567 DOI: 10.1021/acs.jpcb.9b00617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
[NiFe] hydrogenases are enzymes that catalyze the splitting of molecular hydrogen according to the reaction H2 → 2H+ + 2e-. Most of these enzymes are inhibited even by low traces of O2. However, a special group of O2-tolerant hydrogenases exists. A member of this group is the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha ( ReMBH). The ReMBH harbors an unusual iron sulfur cluster with composition 4Fe3S(6Cys) that is able to undergo structural changes triggering the flow of two electrons to the [NiFe] active site. These electrons promote oxygen reduction at the active site, preventing, in this way, aerobic inactivation of the enzyme. In the superoxidized state, the [4Fe3S] cluster binds to a hydroxyl group that originates from either molecular oxygen or water reaching the site. Both reactions, oxygen reduction to water at the [NiFe]- or [4Fe3S]-centers and oxygen evolution from water at the proximal cluster, require the delivery of protons regulated by a subtle communication mechanism between these metal centers. In this work, we sequentially apply multiscale modeling techniques as quantum mechanical/molecular mechanics methods and classical molecular dynamics simulations to investigate the role of two distinct proton transfer pathways connecting the [NiFe] active site and the [4Fe3S] proximal cluster of ReMBH in the protection mechanism against an oxygen attack. Although the "glutamate" pathway is preferred by protons migrating toward the active site to avoid inactivation by O2, the "histidine" pathway plays an essential role in delivering protons for O2 reduction at the proximal cluster. The results obtained in this work not only provide new pieces to the puzzling catalytic mechanisms governing O2-tolerant hydrogenases but also highlight the relevance of dynamics in the proper description of biochemical reactions in general.
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Affiliation(s)
- Daria Tombolelli
- Institut für Chemie , Technische Universität Berlin , Sekretariat PC 14 , D-10623 Berlin , Germany
| | - Maria Andrea Mroginski
- Institut für Chemie , Technische Universität Berlin , Sekretariat PC 14 , D-10623 Berlin , Germany
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10
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Abstract
Hydrogenases catalyze the simple yet important interconversion between H2 and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.
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11
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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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12
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Hartmann S, Frielingsdorf S, Ciaccafava A, Lorent C, Fritsch J, Siebert E, Priebe J, Haumann M, Zebger I, Lenz O. O2-Tolerant H2 Activation by an Isolated Large Subunit of a [NiFe] Hydrogenase. Biochemistry 2018; 57:5339-5349. [DOI: 10.1021/acs.biochem.8b00760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sven Hartmann
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alexandre Ciaccafava
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Johannes Fritsch
- Department of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Elisabeth Siebert
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Jacqueline Priebe
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Sekr. PC14, Technische Universität Berlin, 10623 Berlin, Germany
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13
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Harris TGAA, Heidary N, Kozuch J, Frielingsdorf S, Lenz O, Mroginski MA, Hildebrandt P, Zebger I, Fischer A. In Situ Spectroelectrochemical Studies into the Formation and Stability of Robust Diazonium-Derived Interfaces on Gold Electrodes for the Immobilization of an Oxygen-Tolerant Hydrogenase. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23380-23391. [PMID: 29943966 DOI: 10.1021/acsami.8b02273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface-enhanced infrared absorption spectroscopy is used in situ to determine the electrochemical stability of organic interfaces deposited onto the surface of nanostructured, thin-film gold electrodes via the electrochemical reduction of diazonium salts. These interfaces are shown to exhibit a wide electrochemical stability window in both acetonitrile and phosphate buffer, far surpassing the stability window of thiol-derived self-assembled monolayers. Using the same in situ technique, the application of radical scavengers during the electrochemical reduction of diazonium salts is shown to moderate interface formation. Consequently, the heterogeneous charge-transfer resistance can be reduced sufficiently to enhance the direct electron transfer between an immobilized redox-active enzyme and the electrode. This was demonstrated for the oxygen-tolerant [NiFe] hydrogenase from the "Knallgas" bacterium Ralstonia eutropha by relating its electrochemical activity for hydrogen oxidation to the interface properties.
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Affiliation(s)
- Tomos G A A Harris
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Nina Heidary
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Stefan Frielingsdorf
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
- FMF - Freiburger Materialforschungszentrum , Universität Freiburg , Stefan-Meier-Straße 21 , 79104 Freiburg , Germany
- FIT - Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte Technologien , Georges-Köhler-Allee 105 , 79110 Freiburg , Germany
| | - Maria-Andrea Mroginski
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Ingo Zebger
- Institut für Chemie , Technische Universität Berlin , PC 14, Str. des 17. Juni 135 , 10623 Berlin , Germany
| | - Anna Fischer
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21 , 79104 Freiburg , Germany
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14
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Ash PA, Hidalgo R, Vincent KA. Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy. ACS Catal 2017; 7:2471-2485. [PMID: 28413691 PMCID: PMC5387674 DOI: 10.1021/acscatal.6b03182] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/30/2017] [Indexed: 12/11/2022]
Abstract
![]()
Catalysis
of H2 production and oxidation reactions is
critical in renewable energy systems based around H2 as
a clean fuel, but the present reliance on platinum-based catalysts
is not sustainable. In nature, H2 is oxidized at minimal
overpotential and high turnover frequencies at [NiFe] catalytic sites
in hydrogenase enzymes. Although an outline mechanism has been established
for the [NiFe] hydrogenases involving heterolytic cleavage of H2 followed by a first and then second transfer of a proton
and electron away from the active site, details remain vague concerning
how the proton transfers are facilitated by the protein environment
close to the active site. Furthermore, although [NiFe] hydrogenases
from different organisms or cellular environments share a common active
site, they exhibit a broad range of catalytic characteristics indicating
the importance of subtle changes in the surrounding protein in controlling
their behavior. Here we review recent time-resolved infrared (IR)
spectroscopic studies and IR spectroelectrochemical studies carried
out in situ during electrocatalytic turnover. Additionally, we re-evaluate
the significant body of IR spectroscopic data on hydrogenase active
site states determined through more conventional solution studies,
in order to highlight mechanistic steps that seem to apply generally
across the [NiFe] hydrogenases, as well as steps which so far seem
limited to specific groups of these enzymes. This analysis is intended
to help focus attention on the key open questions where further work
is needed to assess important aspects of proton and electron transfer
in the mechanism of [NiFe] hydrogenases.
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Affiliation(s)
- Philip A. Ash
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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15
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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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16
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Radu V, Frielingsdorf S, Lenz O, Jeuken LJC. Reactivation from the Ni–B state in [NiFe] hydrogenase of Ralstonia eutropha is controlled by reduction of the superoxidised proximal cluster. Chem Commun (Camb) 2016; 52:2632-5. [DOI: 10.1039/c5cc10382g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tolerance towards oxic conditions of O2-tolerant [NiFe] hydrogenases has been attributed to an unusual [4Fe–3S] cluster that lies proximal to the [NiFe] active site.
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Affiliation(s)
- Valentin Radu
- School of Biomedical Sciences
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
| | - Stefan Frielingsdorf
- Institut für Chemie
- Sekretariat PC14
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Oliver Lenz
- Institut für Chemie
- Sekretariat PC14
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Lars J. C. Jeuken
- School of Biomedical Sciences
- The Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
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17
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Orientation-Controlled Electrocatalytic Efficiency of an Adsorbed Oxygen-Tolerant Hydrogenase. PLoS One 2015; 10:e0143101. [PMID: 26580976 PMCID: PMC4651547 DOI: 10.1371/journal.pone.0143101] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/30/2015] [Indexed: 11/21/2022] Open
Abstract
Protein immobilization on electrodes is a key concept in exploiting enzymatic processes for bioelectronic devices. For optimum performance, an in-depth understanding of the enzyme-surface interactions is required. Here, we introduce an integral approach of experimental and theoretical methods that provides detailed insights into the adsorption of an oxygen-tolerant [NiFe] hydrogenase on a biocompatible gold electrode. Using atomic force microscopy, ellipsometry, surface-enhanced IR spectroscopy, and protein film voltammetry, we explore enzyme coverage, integrity, and activity, thereby probing both structure and catalytic H2 conversion of the enzyme. Electrocatalytic efficiencies can be correlated with the mode of protein adsorption on the electrode as estimated theoretically by molecular dynamics simulations. Our results reveal that pre-activation at low potentials results in increased current densities, which can be rationalized in terms of a potential-induced re-orientation of the immobilized enzyme.
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18
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Siebert E, Rippers Y, Frielingsdorf S, Fritsch J, Schmidt A, Kalms J, Katz S, Lenz O, Scheerer P, Paasche L, Pelmenschikov V, Kuhlmann U, Mroginski MA, Zebger I, Hildebrandt P. Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elisabeth Siebert
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Fritsch
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Andrea Schmidt
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Jacqueline Kalms
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Sagie Katz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Oliver Lenz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Lars Paasche
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Vladimir Pelmenschikov
- Technische
Universität Berlin, Institut für Chemie, Sekr. C7, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Uwe Kuhlmann
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
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19
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Ash PA, Liu J, Coutard N, Heidary N, Horch M, Gudim I, Simler T, Zebger I, Lenz O, Vincent KA. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO. J Phys Chem B 2015; 119:13807-15. [PMID: 26115011 DOI: 10.1021/acs.jpcb.5b04164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases.
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Affiliation(s)
- Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Juan Liu
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nathan Coutard
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nina Heidary
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Ingvild Gudim
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Thomas Simler
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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20
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Murphy BJ, Hidalgo R, Roessler MM, Evans RM, Ash PA, Myers WK, Vincent KA, Armstrong FA. Discovery of Dark pH-Dependent H(+) Migration in a [NiFe]-Hydrogenase and Its Mechanistic Relevance: Mobilizing the Hydrido Ligand of the Ni-C Intermediate. J Am Chem Soc 2015; 137:8484-9. [PMID: 26103582 PMCID: PMC4500644 DOI: 10.1021/jacs.5b03182] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite extensive studies on [NiFe]-hydrogenases,
the mechanism
by which these enzymes produce and activate H2 so efficiently
remains unclear. A well-known EPR-active state produced under H2 and known as Ni-C is assigned as a NiIII–FeII species with a hydrido ligand in the bridging position between
the two metals. It has long been known that low-temperature photolysis
of Ni-C yields distinctive EPR-active states, collectively termed
Ni-L, that are attributed to migration of the bridging-H species as
a proton; however, Ni-L has mainly been regarded as an artifact with
no mechanistic relevance. It is now demonstrated, based on EPR and
infrared spectroscopic studies, that the Ni-C to Ni-L interconversion
in Hydrogenase-1 (Hyd-1) from Escherichia coli is a pH-dependent process that proceeds readily in the dark—proton
migration from Ni-C being favored as the pH is increased. The persistence
of Ni-L in Hyd-1 must relate to unassigned differences in proton affinities
of metal and adjacent amino acid sites, although the unusually high
reduction potentials of the adjacent Fe–S centers in this O2-tolerant hydrogenase might also be a contributory factor,
impeding elementary electron transfer off the [NiFe] site after proton
departure. The results provide compelling evidence that Ni-L is a
true, albeit elusive, catalytic intermediate of [NiFe]-hydrogenases.
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Affiliation(s)
- Bonnie J Murphy
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Maxie M Roessler
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Rhiannon M Evans
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Philip A Ash
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - William K Myers
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Kylie A Vincent
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
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21
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Hidalgo R, Ash PA, Healy AJ, Vincent KA. Infrared Spectroscopy During Electrocatalytic Turnover Reveals the Ni-L Active Site State During H2 Oxidation by a NiFe Hydrogenase. Angew Chem Int Ed Engl 2015; 54:7110-3. [PMID: 25925315 PMCID: PMC4531817 DOI: 10.1002/anie.201502338] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/01/2015] [Indexed: 01/25/2023]
Abstract
A novel in situ IR spectroscopic approach is demonstrated for the characterization of hydrogenase during catalytic turnover. E. coli hydrogenase 1 (Hyd-1) is adsorbed on a high surface-area carbon electrode and subjected to the same electrochemical control and efficient supply of substrate as in protein film electrochemistry during spectral acquisition. The spectra reveal that the active site state known as Ni-L, observed in other NiFe hydrogenases only under illumination or at cryogenic temperatures, can be generated reversibly in the dark at ambient temperature under both turnover and non-turnover conditions. The observation that Ni-L is present at all potentials during turnover under H2 suggests that the final steps in the catalytic cycle of H2 oxidation by Hyd-1 involve sequential proton and electron transfer via Ni-L. A broadly applicable IR spectroscopic technique is presented for addressing electrode-adsorbed redox enzymes under fast catalytic turnover.
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Affiliation(s)
- Ricardo Hidalgo
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Philip A Ash
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Adam J Healy
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK)
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR (UK).
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22
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Hidalgo R, Ash PA, Healy AJ, Vincent KA. Infrared Spectroscopy During Electrocatalytic Turnover Reveals the Ni-L Active Site State During H2Oxidation by a NiFe Hydrogenase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502338] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Greene BL, Wu CH, McTernan PM, Adams MWW, Dyer RB. Proton-coupled electron transfer dynamics in the catalytic mechanism of a [NiFe]-hydrogenase. J Am Chem Soc 2015; 137:4558-66. [PMID: 25790178 DOI: 10.1021/jacs.5b01791] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The movement of protons and electrons is common to the synthesis of all chemical fuels such as H2. Hydrogenases, which catalyze the reversible reduction of protons, necessitate transport and reactivity between protons and electrons, but a detailed mechanism has thus far been elusive. Here, we use a phototriggered chemical potential jump method to rapidly initiate the proton reduction activity of a [NiFe] hydrogenase. Coupling the photochemical initiation approach to nanosecond transient infrared and visible absorbance spectroscopy afforded direct observation of interfacial electron transfer and active site chemistry. Tuning of intramolecular proton transport by pH and isotopic substitution revealed distinct concerted and stepwise proton-coupled electron transfer mechanisms in catalysis. The observed heterogeneity in the two sequential proton-associated reduction processes suggests a highly engineered protein environment modulating catalysis and implicates three new reaction intermediates; Nia-I, Nia-D, and Nia-SR(-). The results establish an elementary mechanistic understanding of catalysis in a [NiFe] hydrogenase with implications in enzymatic proton-coupled electron transfer and biomimetic catalyst design.
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Affiliation(s)
- Brandon L Greene
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
| | - Chang-Hao Wu
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Patrick M McTernan
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael W W Adams
- ‡Department of Biochemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R Brian Dyer
- †Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
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24
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Horch M, Lauterbach L, Mroginski MA, Hildebrandt P, Lenz O, Zebger I. Reversible active site sulfoxygenation can explain the oxygen tolerance of a NAD+-reducing [NiFe] hydrogenase and its unusual infrared spectroscopic properties. J Am Chem Soc 2015; 137:2555-64. [PMID: 25647259 DOI: 10.1021/ja511154y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oxygen-tolerant [NiFe] hydrogenases are metalloenzymes that represent valuable model systems for sustainable H2 oxidation and production. The soluble NAD(+)-reducing [NiFe] hydrogenase (SH) from Ralstonia eutropha couples the reversible cleavage of H2 with the reduction of NAD(+) and displays a unique O2 tolerance. Here we performed IR spectroscopic investigations on purified SH in various redox states in combination with density functional theory to provide structural insights into the catalytic [NiFe] center. These studies revealed a standard-like coordination of the active site with diatomic CO and cyanide ligands. The long-lasting discrepancy between spectroscopic data obtained in vitro and in vivo could be solved on the basis of reversible cysteine oxygenation in the fully oxidized state of the [NiFe] site. The data are consistent with a model in which the SH detoxifies O2 catalytically by means of an NADH-dependent (per)oxidase reaction involving the intermediary formation of stable cysteine sulfenates. The occurrence of two catalytic activities, hydrogen conversion and oxygen reduction, at the same cofactor may inspire the design of novel biomimetic catalysts performing H2-conversion even in the presence of O2.
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Affiliation(s)
- Marius Horch
- Institut für Chemie, Technische Universität Berlin , Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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25
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Structural differences of oxidized iron–sulfur and nickel–iron cofactors in O 2 -tolerant and O 2 -sensitive hydrogenases studied by X-ray absorption spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:162-170. [DOI: 10.1016/j.bbabio.2014.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022]
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26
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Karstens K, Wahlefeld S, Horch M, Grunzel M, Lauterbach L, Lendzian F, Zebger I, Lenz O. Impact of the iron-sulfur cluster proximal to the active site on the catalytic function of an O2-tolerant NAD(+)-reducing [NiFe]-hydrogenase. Biochemistry 2015; 54:389-403. [PMID: 25517969 DOI: 10.1021/bi501347u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The soluble NAD(+)-reducing hydrogenase (SH) from Ralstonia eutropha H16 belongs to the O2-tolerant subtype of pyridine nucleotide-dependent [NiFe]-hydrogenases. To identify molecular determinants for the O2 tolerance of this enzyme, we introduced single amino acids exchanges in the SH small hydrogenase subunit. The resulting mutant strains and proteins were investigated with respect to their physiological, biochemical, and spectroscopic properties. Replacement of the four invariant conserved cysteine residues, Cys41, Cys44, Cys113, and Cys179, led to unstable protein, strongly supporting their involvement in the coordination of the iron-sulfur cluster proximal to the catalytic [NiFe] center. The Cys41Ser exchange, however, resulted in an SH variant that displayed up to 10% of wild-type activity, suggesting that the coordinating role of Cys41 might be partly substituted by the nearby Cys39 residue, which is present only in O2-tolerant pyridine nucleotide-dependent [NiFe]-hydrogenases. Indeed, SH variants carrying glycine, alanine, or serine in place of Cys39 showed increased O2 sensitivity compared to that of the wild-type enzyme. Substitution of further amino acids typical for O2-tolerant SH representatives did not greatly affect the H2-oxidizing activity in the presence of O2. Remarkably, all mutant enzymes investigated by electron paramagnetic resonance spectroscopy did not reveal significant spectral changes in relation to wild-type SH, showing that the proximal iron-sulfur cluster does not contribute to the wild-type spectrum. Interestingly, exchange of Trp42 by serine resulted in a completely redox-inactive [NiFe] site, as revealed by infrared spectroscopy and H2/D(+) exchange experiments. The possible role of this residue in electron and/or proton transfer is discussed.
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Affiliation(s)
- Katja Karstens
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin , Chausseestr. 117, 10115 Berlin, Germany
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27
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Horch M, Hildebrandt P, Zebger I. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes. Phys Chem Chem Phys 2015; 17:18222-37. [DOI: 10.1039/c5cp02447a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
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28
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Radu V, Frielingsdorf S, Evans SD, Lenz O, Jeuken LJC. Enhanced oxygen-tolerance of the full heterotrimeric membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. J Am Chem Soc 2014; 136:8512-5. [PMID: 24866391 PMCID: PMC4073834 DOI: 10.1021/ja503138p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrogenases are oxygen-sensitive enzymes that catalyze the conversion between protons and hydrogen. Water-soluble subcomplexes of membrane-bound [NiFe]-hydrogenases (MBH) have been extensively studied for applications in hydrogen-oxygen fuel cells as they are relatively tolerant to oxygen, although even these catalysts are still inactivated in oxidative conditions. Here, the full heterotrimeric MBH of Ralstonia eutropha, including the membrane-integral cytochrome b subunit, was investigated electrochemically using electrodes modified with planar tethered bilayer lipid membranes (tBLM). Cyclic voltammetry and chronoamperometry experiments show that MBH, in equilibrium with the quinone pool in the tBLM, does not anaerobically inactivate under oxidative redox conditions. In aerobic environments, the MBH is reversibly inactivated by O2, but reactivation was found to be fast even under oxidative redox conditions. This enhanced resistance to inactivation is ascribed to the oligomeric state of MBH in the lipid membrane.
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Affiliation(s)
- Valentin Radu
- School of Biomedical Sciences, the Astbury Centre for Structural Molecular Biology, and School of Physics & Astronomy, University of Leeds , Leeds LS2 9JT, United Kingdom
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29
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Frielingsdorf S, Fritsch J, Schmidt A, Hammer M, Löwenstein J, Siebert E, Pelmenschikov V, Jaenicke T, Kalms J, Rippers Y, Lendzian F, Zebger I, Teutloff C, Kaupp M, Bittl R, Hildebrandt P, Friedrich B, Lenz O, Scheerer P. Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Nat Chem Biol 2014; 10:378-85. [DOI: 10.1038/nchembio.1500] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/13/2014] [Indexed: 12/27/2022]
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30
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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31
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Fritsch J, Siebert E, Priebe J, Zebger I, Lendzian F, Teutloff C, Friedrich B, Lenz O. Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase. J Biol Chem 2014; 289:7982-93. [PMID: 24448806 DOI: 10.1074/jbc.m113.544668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster.
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Affiliation(s)
- Johannes Fritsch
- From the Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin
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32
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Abstract
The origin of the tolerance of a subclass of [NiFe]-hydrogenases to the presence of oxygen was unclear for a long time. Recent spectroscopic studies showed a conserved active site between oxygen-sensitive and oxygen-tolerant hydrogenases, and modifications in the vicinity of the active site in the large subunit could be excluded as the origin of catalytic activity even in the presence of molecular oxygen. A combination of bioinformatics and protein structural modelling revealed an unusual co-ordination motif in the vicinity of the proximal Fe-S cluster in the small subunit. Mutational experiments confirmed the relevance of two additional cysteine residues for the oxygen-tolerance. This new binding motif can be used to classify sequences from [NiFe]-hydrogenases according to their potential oxygen-tolerance. The X-ray structural analysis of the reduced form of the enzyme displayed a new type of [4Fe-3S] cluster co-ordinated by six surrounding cysteine residues in a distorted cubanoid geometry. The unusual electronic structure of the proximal Fe-S cluster can be analysed using the broken-symmetry approach and gave results in agreement with experimental Mößbauer studies. An electronic effect of the proximal Fe-S cluster on the remote active site can be detected and quantified. In the oxygen-tolerant hydrogenases, the hydride occupies an asymmetric binding position in the Ni-C state. This may rationalize the more facile activation and catalytic turnover in this subclass of enzymes.
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33
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Pelmenschikov V, Kaupp M. Redox-Dependent Structural Transformations of the [4Fe-3S] Proximal Cluster in O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase: A DFT Study. J Am Chem Soc 2013; 135:11809-23. [DOI: 10.1021/ja402159u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Vladimir Pelmenschikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie, Sekr. C7, Strasse
des 17. Juni 135, 10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie, Sekr. C7, Strasse
des 17. Juni 135, 10623 Berlin, Germany
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34
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Siebert E, Horch M, Rippers Y, Fritsch J, Frielingsdorf S, Lenz O, Velazquez Escobar F, Siebert F, Paasche L, Kuhlmann U, Lendzian F, Mroginski M, Zebger I, Hildebrandt P. Resonance Raman Spectroscopy as a Tool to Monitor the Active Site of Hydrogenases. Angew Chem Int Ed Engl 2013; 52:5162-5. [DOI: 10.1002/anie.201209732] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Elisabeth Siebert
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Marius Horch
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Yvonne Rippers
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Johannes Fritsch
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Stefan Frielingsdorf
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Oliver Lenz
- Institut für Biologie/Mikrobiologie, Humboldt Universität zu Berlin, Chausseestrasse 117, 10115 Berlin (Germany)
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Friedrich Siebert
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Lars Paasche
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Uwe Kuhlmann
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Friedhelm Lendzian
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Maria‐Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Ingo Zebger
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Strasse des 17. Juni 135, 10623 Berlin (Germany)
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35
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Siebert E, Horch M, Rippers Y, Fritsch J, Frielingsdorf S, Lenz O, Velazquez Escobar F, Siebert F, Paasche L, Kuhlmann U, Lendzian F, Mroginski MA, Zebger I, Hildebrandt P. Resonanz-Raman-Spektroskopie als Methode zur Untersuchung des aktiven Zentrums von Hydrogenasen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Hawkins AS, McTernan PM, Lian H, Kelly RM, Adams MWW. Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals. Curr Opin Biotechnol 2013; 24:376-84. [PMID: 23510698 DOI: 10.1016/j.copbio.2013.02.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
Abstract
Non-photosynthetic routes for biological fixation of carbon dioxide into valuable industrial chemical precursors and fuels are moving from concept to reality. The development of 'electrofuel'-producing microorganisms leverages techniques in synthetic biology, genetic and metabolic engineering, as well as systems-level multi-omic analysis, directed evolution, and in silico modeling. Electrofuel processes are being developed for a range of microorganisms and energy sources (e.g. hydrogen, formate, electricity) to produce a variety of target molecules (e.g. alcohols, terpenes, alkenes). This review examines the current landscape of electrofuel projects with a focus on hydrogen-utilizing organisms covering the biochemistry of hydrogenases and carbonic anhydrases, kinetic and energetic analyses of the known carbon fixation pathways, and the state of genetic systems for current and prospective electrofuel-producing microorganisms.
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Affiliation(s)
- Aaron S Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
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37
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[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:986-1002. [PMID: 23399489 DOI: 10.1016/j.bbabio.2013.01.015] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/06/2012] [Accepted: 01/26/2013] [Indexed: 01/05/2023]
Abstract
Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.
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38
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39
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013; 52:2002-6. [DOI: 10.1002/anie.201209063] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Indexed: 11/08/2022]
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40
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2
Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Horch M, Rippers Y, Mroginski MA, Hildebrandt P, Zebger I. Combining Spectroscopy and Theory to Evaluate Structural Models of Metalloenzymes: A Case Study on the Soluble [NiFe] Hydrogenase fromRalstonia eutropha. Chemphyschem 2012; 14:185-91. [DOI: 10.1002/cphc.201200853] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Indexed: 11/09/2022]
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42
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Wang B, Wang J, Zhang W, Meldrum DR. Application of synthetic biology in cyanobacteria and algae. Front Microbiol 2012; 3:344. [PMID: 23049529 PMCID: PMC3446811 DOI: 10.3389/fmicb.2012.00344] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO2 and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed.
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Affiliation(s)
- Bo Wang
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University Tempe, AZ, USA ; Biological Design Graduate Program, Arizona State University Tempe, AZ, USA
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43
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Roessler MM, Evans RM, Davies RA, Harmer J, Armstrong FA. EPR Spectroscopic Studies of the Fe–S Clusters in the O2-Tolerant [NiFe]-Hydrogenase Hyd-1 from Escherichia coli and Characterization of the Unique [4Fe–3S] Cluster by HYSCORE. J Am Chem Soc 2012; 134:15581-94. [DOI: 10.1021/ja307117y] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Maxie M. Roessler
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Rhiannon M. Evans
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Rosalind A. Davies
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Jeffrey Harmer
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Fraser A. Armstrong
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
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44
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Rippers Y, Horch M, Hildebrandt P, Zebger I, Mroginski MA. Revealing the Absolute Configuration of the CO and CN−Ligands at the Active Site of a [NiFe] Hydrogenase. Chemphyschem 2012; 13:3852-6. [DOI: 10.1002/cphc.201200562] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Indexed: 11/12/2022]
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45
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Pandelia ME, Lubitz W, Nitschke W. Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O2-tolerance? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1565-75. [DOI: 10.1016/j.bbabio.2012.04.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
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46
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Lojou E. Hydrogenases as catalysts for fuel cells: Strategies for efficient immobilization at electrode interfaces. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.03.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase. Nature 2011; 479:253-6. [PMID: 22002607 DOI: 10.1038/nature10504] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/23/2011] [Indexed: 01/26/2023]
Abstract
Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2) → 2H(+) + 2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32 Å. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.
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48
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Fritsch J, Scheerer P, Frielingsdorf S, Kroschinsky S, Friedrich B, Lenz O, Spahn CMT. The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre. Nature 2011; 479:249-52. [PMID: 22002606 DOI: 10.1038/nature10505] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 08/23/2011] [Indexed: 11/10/2022]
Abstract
Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5 Å resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air.
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Affiliation(s)
- Johannes Fritsch
- Mikrobiologie, Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
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49
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Lukey MJ, Roessler MM, Parkin A, Evans RM, Davies RA, Lenz O, Friedrich B, Sargent F, Armstrong FA. Oxygen-Tolerant [NiFe]-Hydrogenases: The Individual and Collective Importance of Supernumerary Cysteines at the Proximal Fe-S Cluster. J Am Chem Soc 2011; 133:16881-92. [DOI: 10.1021/ja205393w] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Oliver Lenz
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Baerbel Friedrich
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Frank Sargent
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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50
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Sezer M, Frielingsdorf S, Millo D, Heidary N, Utesch T, Mroginski MA, Friedrich B, Hildebrandt P, Zebger I, Weidinger IM. Role of the HoxZ Subunit in the Electron Transfer Pathway of the Membrane-Bound [NiFe]-Hydrogenase from Ralstonia eutropha Immobilized on Electrodes. J Phys Chem B 2011; 115:10368-74. [DOI: 10.1021/jp204665r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Murat Sezer
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | | | - Diego Millo
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Nina Heidary
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Tillman Utesch
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Maria-Andrea Mroginski
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Bärbel Friedrich
- Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Peter Hildebrandt
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Inez M. Weidinger
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
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