1
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Lubner CE, Artz JH, Mulder DW, Oza A, Ward RJ, Williams SG, Jones AK, Peters JW, Smalyukh II, Bharadwaj VS, King PW. A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I. Chem Sci 2022; 13:4581-4588. [PMID: 35656134 PMCID: PMC9019909 DOI: 10.1039/d1sc07120c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
One of the many functions of reduction–oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe–4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe–4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor–acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe–4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron–sulfur cluster relay for coupling to reversible H2 activation at the catalytic site. Histidine coordination of the distal [4Fe–4S] cluster in [FeFe]-hydrogenase was demonstrated to tune the cluster spin-states, spin-pairing and surrounding molecular orbitals to enable more facile electron transfer compared to cysteine coordination.![]()
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Affiliation(s)
| | - Jacob H Artz
- National Renewable Energy Laboratory Golden Colorado USA
| | - David W Mulder
- National Renewable Energy Laboratory Golden Colorado USA
| | - Aisha Oza
- National Renewable Energy Laboratory Golden Colorado USA
| | - Rachel J Ward
- Department of Physics, University of Colorado Boulder Boulder Colorado USA
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University Tempe Arizona USA.,Sandia National Laboratories Albuquerque New Mexico USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University Tempe Arizona USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University Pullman Washington USA
| | - Ivan I Smalyukh
- Department of Physics, University of Colorado Boulder Boulder Colorado USA.,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
| | | | - Paul W King
- National Renewable Energy Laboratory Golden Colorado USA .,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
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2
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Németh B, Land H, Magnuson A, Hofer A, Berggren G. The maturase HydF enables [FeFe] hydrogenase assembly via transient, cofactor-dependent interactions. J Biol Chem 2020; 295:11891-11901. [PMID: 32620553 PMCID: PMC7450098 DOI: 10.1074/jbc.ra119.011419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
[FeFe] hydrogenases have attracted extensive attention in the field of renewable energy research because of their remarkable efficiency for H2 gas production. H2 formation is catalyzed by a biologically unique hexanuclear iron cofactor denoted the H-cluster. The assembly of this cofactor requires a dedicated maturation machinery including HydF, a multidomain [4Fe4S] cluster protein with GTPase activity. HydF is responsible for harboring and delivering a precatalyst to the apo-hydrogenase, but the details of this process are not well understood. Here, we utilize gas-phase electrophoretic macromolecule analysis to show that a HydF dimer forms a transient interaction complex with the hydrogenase and that the formation of this complex depends on the cofactor content on HydF. Moreover, Fourier transform infrared, electron paramagnetic resonance, and UV-visible spectroscopy studies of mutants of HydF show that the isolated iron-sulfur cluster domain retains the capacity for binding the precatalyst in a reversible fashion and is capable of activating apo-hydrogenase in in vitro assays. These results demonstrate the central role of the iron-sulfur cluster domain of HydF in the final stages of H-cluster assembly, i.e. in binding and delivering the precatalyst.
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Affiliation(s)
- Brigitta Németh
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Henrik Land
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann Magnuson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Gustav Berggren
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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3
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Németh B, Esmieu C, Redman HJ, Berggren G. Monitoring H-cluster assembly using a semi-synthetic HydF protein. Dalton Trans 2019; 48:5978-5986. [PMID: 30632592 PMCID: PMC6509880 DOI: 10.1039/c8dt04294b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
Abstract
The [FeFe] hydrogenase enzyme interconverts protons and molecular hydrogen with remarkable efficiency. The reaction is catalysed by a unique metallo-cofactor denoted as the H-cluster containing an organometallic dinuclear Fe component, the [2Fe] subsite. The HydF protein delivers a precursor of the [2Fe] subsite to the apo-[FeFe] hydrogenase, thus completing the H-cluster and activating the enzyme. Herein we generate a semi-synthetic form of HydF by loading it with a synthetic low valent dinuclear Fe complex. We show that this semi-synthetic protein is practically indistinguishable from the native protein, and utilize this form of HydF to explore the mechanism of H-cluster assembly. More specifically, we show that transfer of the precatalyst from HydF to the hydrogenase enzyme results in the release of CO, underscoring that the pre-catalyst is a four CO species when bound to HydF. Moreover, we propose that an electron transfer reaction occurs during H-cluster assembly, resulting in an oxidation of the [2Fe] subsite with concomitant reduction of the [4Fe4S] cluster present on the HydF protein.
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Affiliation(s)
- Brigitta Németh
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Charlène Esmieu
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Holly J. Redman
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
| | - Gustav Berggren
- Molecular Biomimetics
, Department of Chemistry – Ångström Laboratory
, Uppsala University
,
75120 Uppsala
, Sweden
.
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4
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Papini C, Sommer C, Pecqueur L, Pramanik D, Roy S, Reijerse EJ, Wittkamp F, Artero V, Lubitz W, Fontecave M. Bioinspired Artificial [FeFe]-Hydrogenase with a Synthetic H-Cluster. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00540] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Constanze Sommer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Souvik Roy
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Florian Wittkamp
- Inorganic Chemistry I, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, CNRS, CEA Fundamental Research Division, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France−CNRS−Sorbonne Université, CNRS UMR 8229, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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5
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Bortolus M, Costantini P, Doni D, Carbonera D. Overview of the Maturation Machinery of the H-Cluster of [FeFe]-Hydrogenases with a Focus on HydF. Int J Mol Sci 2018; 19:E3118. [PMID: 30314343 PMCID: PMC6212873 DOI: 10.3390/ijms19103118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/04/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023] Open
Abstract
Hydrogen production in nature is performed by hydrogenases. Among them, [FeFe]-hydrogenases have a peculiar active site, named H-cluster, that is made of two parts, synthesized in different pathways. The cubane sub-cluster requires the normal iron-sulfur cluster maturation machinery. The [2Fe] sub-cluster instead requires a dedicated set of maturase proteins, HydE, HydF, and HydG that work to assemble the cluster and deliver it to the apo-hydrogenase. In particular, the delivery is performed by HydF. In this review, we will perform an overview of the latest knowledge on the maturation machinery of the H-cluster, focusing in particular on HydF.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
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6
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Scott AG, Szilagyi RK, Mulder DW, Ratzloff MW, Byer AS, King PW, Broderick WE, Shepard EM, Broderick JB. Compositional and structural insights into the nature of the H-cluster precursor on HydF. Dalton Trans 2018; 47:9521-9535. [PMID: 29964288 DOI: 10.1039/c8dt01654b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Assembly of an active [FeFe]-hydrogenase requires dedicated maturation enzymes that generate the active-site H-cluster: the radical SAM enzymes HydE and HydG synthesize the unusual non-protein ligands - carbon monoxide, cyanide, and dithiomethylamine - while the GTPase HydF serves as a scaffold for assembly of the 2Fe subcluster containing these ligands. In the current study, enzymatically cluster-loaded HydF ([2Fe]F) is produced by co-expression with HydE and HydG in an Escherichia coli host followed by isolation and examination by FTIR and EPR spectroscopy. FTIR reveals the presence of well-defined terminal CO and CN- ligands; however, unlike in the [FeFe]-hydrogenase, no bridging CO is observed. Exposure of this loaded HydF to exogenous CO or H2 produces no significant changes to the FTIR spectrum, indicating that, unlike in the [FeFe]-hydrogenase, the 2Fe cluster in loaded HydF is coordinatively saturated and relatively unreactive. EPR spectroscopy reveals the presence of both [4Fe-4S] and [2Fe-2S] clusters on this loaded HydF, but provides no direct evidence for these being linked to the [2Fe]F. Using the chemical reactivity and FTIR data, a large collection of computational models were evaluated. Their scaled quantum chemical vibrational spectra allowed us to score various [2Fe]F structures in terms of their ability to reproduce the diatomic stretching frequencies observed in the FTIR experimental spectra. Collectively, the results provide new insights that support the presence of a diamagnetic, but spin-polarized FeI-FeI oxidation state for the [2Fe]F precursor cluster that is coordinated by 4 CO and 2 CN- ligands, and bridged to an adjacent iron-sulfur cluster through one of the CN- ligands.
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Affiliation(s)
- Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.
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7
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Kubas A, Maszota P. Theoretical Insights into the Unique Ligation of [Fe
4
S
4
] Iron–Sulfur Clusters. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adam Kubas
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01‐224 Warsaw Poland
| | - Paweł Maszota
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01‐224 Warsaw Poland
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8
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Todorovic S, Teixeira M. Resonance Raman spectroscopy of Fe-S proteins and their redox properties. J Biol Inorg Chem 2018; 23:647-661. [PMID: 29368020 PMCID: PMC6006211 DOI: 10.1007/s00775-018-1533-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/14/2017] [Indexed: 12/02/2022]
Abstract
Resonance Raman spectra of Fe-S proteins are sensitive to the cluster type, structure and symmetry. Furthermore, bands that originate from bridging and terminal Fe-S vibrations in the 2Fe-2S, 3Fe-4S and 4Fe-4S clusters can be sensitively distinguished in the spectra, as well as the type of non-cysteinyl coordinating ligands, if present. For these reasons, resonance Raman spectroscopy has been playing an exceptionally active role in the studies of Fe-S proteins of diverse structures and functions. We provide here a concise overview of the structural information that can be obtained from resonance Raman spectroscopy on Fe-S clusters, and in parallel, refer to their thermodynamic properties (e.g., reduction potential), which together define the physiological roles of Fe-S proteins. We demonstrate how the knowledge gained over the past several decades on simple clusters nowadays enables studies of complex structures that include Fe-S clusters coupled to other centers and transient processes that involve cluster inter-conversion, biogenesis, disassembly and catalysis.
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Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
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9
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Esmieu C, Raleiras P, Berggren G. From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production. SUSTAINABLE ENERGY & FUELS 2018; 2:724-750. [PMID: 31497651 PMCID: PMC6695573 DOI: 10.1039/c7se00582b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.
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Affiliation(s)
- C Esmieu
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - P Raleiras
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - G Berggren
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
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10
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Shepard EM, Byer AS, Aggarwal P, Betz JN, Scott AG, Shisler KA, Usselman RJ, Eaton GR, Eaton SS, Broderick JB. Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation. Biochemistry 2017; 56:3234-3247. [PMID: 28525271 PMCID: PMC5490485 DOI: 10.1021/acs.biochem.7b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 and protons and electrons. Catalysis occurs at the H-cluster, a carbon monoxide-, cyanide-, and dithiomethylamine-coordinated 2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis of this unique metallocofactor is accomplished by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG belong to the radical S-adenosylmethionine superfamily of enzymes and synthesize the nonprotein ligands of the H-cluster. These enzymes interact with HydF, a GTPase that acts as a scaffold or carrier protein during 2Fe subcluster assembly. Prior characterization of HydF demonstrated the protein exists in both dimeric and tetrameric states and coordinates both [4Fe-4S]2+/+ and [2Fe-2S]2+/+ clusters [Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick, J. B. (2016) Biochemistry 55, 3514-3527]. Herein, electron paramagnetic resonance (EPR) is utilized to characterize the [2Fe-2S]+ and [4Fe-4S]+ clusters bound to HydF. Examination of spin relaxation times using pulsed EPR in HydF samples exhibiting both [4Fe-4S]+ and [2Fe-2S]+ cluster EPR signals supports a model in which the two cluster types either are bound to widely separated sites on HydF or are not simultaneously bound to a single HydF species. Gel filtration chromatographic analyses of HydF spectroscopic samples strongly suggest the [2Fe-2S]+ and [4Fe-4S]+ clusters are coordinated to the dimeric form of the protein. Lastly, we examined the 2Fe subcluster-loaded form of HydF and showed the dimeric state is responsible for [FeFe]-hydrogenase activation. Together, the results indicate a specific role for the HydF dimer in the H-cluster biosynthesis pathway.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Priyanka Aggarwal
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Krista A Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Robert J Usselman
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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11
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Caserta G, Pecqueur L, Adamska-Venkatesh A, Papini C, Roy S, Artero V, Atta M, Reijerse E, Lubitz W, Fontecave M. Structural and functional characterization of the hydrogenase-maturation HydF protein. Nat Chem Biol 2017; 13:779-784. [DOI: 10.1038/nchembio.2385] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 03/06/2017] [Indexed: 11/09/2022]
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12
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Galazzo L, Maso L, De Rosa E, Bortolus M, Doni D, Acquasaliente L, De Filippis V, Costantini P, Carbonera D. Identifying conformational changes with site-directed spin labeling reveals that the GTPase domain of HydF is a molecular switch. Sci Rep 2017; 7:1714. [PMID: 28490758 PMCID: PMC5431965 DOI: 10.1038/s41598-017-01886-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/05/2017] [Indexed: 11/17/2022] Open
Abstract
[FeFe]-hydrogenases catalyse the reduction of protons to hydrogen at a complex 2Fe[4Fe4S] center called H-cluster. The assembly of this active site is a multistep process involving three proteins, HydE, HydF and HydG. According to the current models, HydF has the key double role of scaffold, upon which the final H-cluster precursor is assembled, and carrier to transfer it to the target hydrogenase. The X-ray structure of HydF indicates that the protein is a homodimer with both monomers carrying two functional domains: a C-terminal FeS cluster-binding domain, where the precursor is assembled, and a N-terminal GTPase domain, whose exact contribution to cluster biogenesis and hydrogenase activation is still elusive. We previously obtained several hints suggesting that the binding of GTP to HydF could be involved in the interactions of this scaffold protein with the other maturases and with the hydrogenase itself. In this work, by means of site directed spin labeling coupled to EPR/PELDOR spectroscopy, we explored the conformational changes induced in a recombinant HydF protein by GTP binding, and provide the first clue that the HydF GTPase domain could be involved in the H-cluster assembly working as a molecular switch similarly to other known small GTPases.
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Affiliation(s)
- Laura Galazzo
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Edith De Rosa
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Davide Doni
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy.
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13
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Shepard EM, Byer AS, Betz JN, Peters JW, Broderick JB. A Redox Active [2Fe-2S] Cluster on the Hydrogenase Maturase HydF. Biochemistry 2016; 55:3514-27. [PMID: 27232385 DOI: 10.1021/acs.biochem.6b00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
[FeFe]-hydrogenases are nature's most prolific hydrogen catalysts, excelling at facilely interconverting H2 and protons. The catalytic core common to all [FeFe]-hydrogenases is a complex metallocofactor, referred to as the H-cluster, which is composed of a standard [4Fe-4S] cluster linked through a bridging thiolate to a 2Fe subcluster harboring dithiomethylamine, carbon monoxide, and cyanide ligands. This 2Fe subcluster is synthesized and inserted into [FeFe]-hydrogenase by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG are radical S-adenosylmethionine enzymes and synthesize the nonprotein ligands of the H-cluster. HydF is a GTPase that functions as a scaffold or carrier for 2Fe subcluster production. Herein, we utilize UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopic studies to establish the existence of redox active [4Fe-4S] and [2Fe-2S] clusters bound to HydF. We have used spectroelectrochemical titrations to assign iron-sulfur cluster midpoint potentials, have shown that HydF purifies with a reduced [2Fe-2S] cluster in the absence of exogenous reducing agents, and have tracked iron-sulfur cluster spectroscopic changes with quaternary structural perturbations. Our results provide an important foundation for understanding the maturation process by defining the iron-sulfur cluster content of HydF prior to its interaction with HydE and HydG. We speculate that the [2Fe-2S] cluster of HydF either acts as a placeholder for HydG-derived Fe(CO)2CN species or serves as a scaffold for 2Fe subcluster assembly.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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Suess DLM, Kuchenreuther JM, De La Paz L, Swartz JR, Britt RD. Biosynthesis of the [FeFe] Hydrogenase H Cluster: A Central Role for the Radical SAM Enzyme HydG. Inorg Chem 2016; 55:478-87. [PMID: 26703931 PMCID: PMC4780679 DOI: 10.1021/acs.inorgchem.5b02274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hydrogenase enzymes catalyze the rapid and reversible interconversion of H2 with protons and electrons. The active site of the [FeFe] hydrogenase is the H cluster, which consists of a [4Fe-4S]H subcluster linked to an organometallic [2Fe]H subcluster. Understanding the biosynthesis and catalytic mechanism of this structurally unusual active site will aid in the development of synthetic and biological hydrogenase catalysts for applications in solar fuel generation. The [2Fe]H subcluster is synthesized and inserted by three maturase enzymes-HydE, HydF, and HydG-in a complex process that involves inorganic, organometallic, and organic radical chemistry. HydG is a member of the radical S-adenosyl-l-methionine (SAM) family of enzymes and is thought to play a prominent role in [2Fe]H subcluster biosynthesis by converting inorganic Fe(2+), l-cysteine (Cys), and l-tyrosine (Tyr) into an organometallic [(Cys)Fe(CO)2(CN)](-) intermediate that is eventually incorporated into the [2Fe]H subcluster. In this Forum Article, the mechanism of [2Fe]H subcluster biosynthesis is discussed with a focus on how this key [(Cys)Fe(CO)2(CN)](-) species is formed. Particular attention is given to the initial metallocluster composition of HydG, the modes of substrate binding (Fe(2+), Cys, Tyr, and SAM), the mechanism of SAM-mediated Tyr cleavage to CO and CN(-), and the identification of the final organometallic products of the reaction.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jon M. Kuchenreuther
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Liliana De La Paz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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Goux M, Fateh A, Defontaine A, Cinier M, Tellier C. In vivo phosphorylation of a peptide tag for protein purification. Biotechnol Lett 2016; 38:767-72. [DOI: 10.1007/s10529-016-2040-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/06/2016] [Indexed: 01/31/2023]
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Abstract
Proton reduction and H2 oxidation are key elementary reactions for solar fuel production. Hydrogenases interconvert H+ and H2 with remarkable efficiency and have therefore received much attention in this context. For [FeFe]-hydrogenases, catalysis occurs at a unique cofactor called the H-cluster. In this article, we discuss ways in which EPR spectroscopy has elucidated aspects of the bioassembly of the H-cluster, with a focus on four case studies: EPR spectroscopic identification of a radical en route to the CO and CN- ligands of the H-cluster, tracing 57Fe from the maturase HydG into the H-cluster, characterization of the auxiliary Fe-S cluster in HydG, and isotopic labeling of the CN- ligands of HydA for electronic structure studies of its Hox state. Advances in cell-free maturation protocols have enabled several of these mechanistic studies, and understanding H-cluster maturation may in turn provide insights leading to improvements in hydrogenase production for biotechnological applications.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - R. David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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Artero V, Berggren G, Atta M, Caserta G, Roy S, Pecqueur L, Fontecave M. From enzyme maturation to synthetic chemistry: the case of hydrogenases. Acc Chem Res 2015; 48:2380-7. [PMID: 26165393 DOI: 10.1021/acs.accounts.5b00157] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Water splitting into oxygen and hydrogen is one of the most attractive strategies for storing solar energy and electricity. Because the processes at work are multielectronic, there is a crucial need for efficient and stable catalysts, which in addition have to be cheap for future industrial developments (electrolyzers, photoelectrochemicals, and fuel cells). Specifically for the water/hydrogen interconversion, Nature is an exquisite source of inspiration since this chemistry contributes to the bioenergetic metabolism of a number of living organisms via the activity of fascinating metalloenzymes, the hydrogenases. In this Account, we first briefly describe the structure of the unique dinuclear organometallic active sites of the two classes of hydrogenases as well as the complex protein machineries involved in their biosynthesis, their so-called maturation processes. This knowledge allows for the development of a fruitful bioinspired chemistry approach, which has already led to a number of interesting and original catalysts mimicking the natural active sites. More specifically, we describe our own attempts to prepare artificial hydrogenases. This can be achieved via the standard bioinspired approach using the combination of a synthetic bioinspired catalyst and a polypeptide scaffold. Such hybrid complexes provide the opportunity to optimize the system by manipulating both the catalyst through chemical synthesis and the protein component through mutagenesis. We also raise the possibility to reach such artificial systems via an original strategy based on mimicking the enzyme maturation pathways. This is illustrated in this Account by two examples developed in our laboratory. First, we show how the preparation of a lysozyme-{Mn(I)(CO)3} hybrid and its clean reaction with a nickel complex led us to generate a new class of binuclear Ni-Mn H2-evolving catalysts mimicking the active site of [NiFe]-hydrogenases. Then we describe how we were able to rationally design and prepare a hybrid system, displaying remarkable structural similarities to an [FeFe]-hydrogenase, and we show here for the first time that it is catalytically active for proton reduction. This system is based on the combination of HydF, a protein involved in the maturation of [FeFe]-hydrogenase (HydA), and a close mimic of the active site of this class of enzymes. Moreover, the synthetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-)= aza-propanedithiol) mimic, alone or within a HydF hybrid system, was shown to be able to maturate and activate a form of HydA itself lacking its diiron active site. We discuss the exciting perspectives this "synthetic maturation" opens regarding the "invention" of novel hydrogenases by the chemists.
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Affiliation(s)
- Vincent Artero
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Gustav Berggren
- Department of Chemistry−the
Ångström Laboratory, Uppsala University, Lägerhyddsvägen
1, 751 20 Uppsala, Sweden
| | - Mohamed Atta
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Souvik Roy
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38000 Grenoble, France
- Laboratoire de Chimie des Processus Biologiques,
Collège de France, CNRS, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, 75005 Paris, France
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18
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Albertini M, Galazzo L, Maso L, Vallese F, Berto P, De Rosa E, Di Valentin M, Costantini P, Carbonera D. Characterization of the [FeFe]-Hydrogenase Maturation Protein HydF by EPR Techniques: Insights into the Catalytic Mechanism. Top Catal 2015. [DOI: 10.1007/s11244-015-0413-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Albertini M, Berto P, Vallese F, Di Valentin M, Costantini P, Carbonera D. Probing the Solvent Accessibility of the [4Fe-4S] Cluster of the Hydrogenase Maturation Protein HydF from Thermotoga neapolitana by HYSCORE and 3p-ESEEM. J Phys Chem B 2015; 119:13680-9. [PMID: 25978307 DOI: 10.1021/acs.jpcb.5b03110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The catalytic site of [FeFe]-hydrogenase, the "H-cluster", composed of a [4Fe-4S] unit connected by a cysteinyl residue to a [2Fe] center coordinated by three CO, two CN(-), and a bridging dithiolate, is assembled in a complex maturation pathway, at present not fully characterized, involving three conserved proteins, HydG, HydE, and HydF. HydF is a complex enzyme, which is thought to act as a scaffold and carrier for the [2Fe] subunit of the H-cluster. This maturase protein contains itself a [4Fe-4S] cluster binding site, with three conserved cysteine residues and a noncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEM and HYSCORE spectroscopies to get insight into the structure and the chemical environment of the [4Fe-4S] cluster of HydF from the hyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility of the active site comprising the [4Fe-4S] cluster are discussed on the basis of the spectroscopic results obtained upon H/D exchange. We propose that the noncysteinyl ligated Fe atom of the [4Fe-4S] cluster is the site where the [2Fe] subcluster precursor is anchored and finally processed to be delivered to the hydrogenase (HydA).
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Affiliation(s)
- Marco Albertini
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Berto
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Francesca Vallese
- Department of Biomedical Sciences, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova , Viale G. Colombo 3, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy
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20
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Peters JW, Schut GJ, Boyd ES, Mulder DW, Shepard EM, Broderick JB, King PW, Adams MWW. [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1350-69. [PMID: 25461840 DOI: 10.1016/j.bbamcr.2014.11.021] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/10/2014] [Accepted: 11/16/2014] [Indexed: 11/29/2022]
Abstract
The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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21
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Shepard EM, Mus F, Betz JN, Byer AS, Duffus BR, Peters JW, Broderick JB. [FeFe]-hydrogenase maturation. Biochemistry 2014; 53:4090-104. [PMID: 24878200 DOI: 10.1021/bi500210x] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible reduction of protons at unusual metal centers. This Current Topic discusses recent advances in elucidating the steps involved in the biosynthesis of the complex metal cluster at the [FeFe]-hydrogenase (HydA) active site, known as the H-cluster. The H-cluster is composed of a 2Fe subcluster that is anchored within the active site by a bridging cysteine thiolate to a [4Fe-4S] cubane. The 2Fe subcluster contains carbon monoxide, cyanide, and bridging dithiolate ligands. H-cluster biosynthesis is now understood to occur stepwise; standard iron-sulfur cluster assembly machinery builds the [4Fe-4S] cubane of the H-cluster, while three specific maturase enzymes known as HydE, HydF, and HydG assemble the 2Fe subcluster. HydE and HydG are both radical S-adenosylmethionine enzymes that interact with an iron-sulfur cluster binding GTPase scaffold, HydF, during the construction of the 2Fe subcluster moiety. In an unprecedented biochemical reaction, HydG cleaves tyrosine and decomposes the resulting dehydroglycine into carbon monoxide and cyanide ligands. The role of HydE in the biosynthetic pathway remains undefined, although it is hypothesized to be critical for the synthesis of the bridging dithiolate. HydF is the site where the complete 2Fe subcluster is formed and ultimately delivered to the immature hydrogenase protein in the final step of [FeFe]-hydrogenase maturation. This work addresses the roles of and interactions among HydE, HydF, HydG, and HydA in the formation of the mature [FeFe]-hydrogenase.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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22
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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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