1
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T Waffo AF, Lorent C, Katz S, Schoknecht J, Lenz O, Zebger I, Caserta G. Structural Determinants of the Catalytic Ni a-L Intermediate of [NiFe]-Hydrogenase. J Am Chem Soc 2023. [PMID: 37328284 DOI: 10.1021/jacs.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
[NiFe]-hydrogenases catalyze the reversible cleavage of H2 into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H2/H- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Nia-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Nia-L1, Nia-L2, and the hydride-binding Nia-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Nia-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.
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Affiliation(s)
- Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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2
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Kulka-Peschke CJ, Schulz AC, Lorent C, Rippers Y, Wahlefeld S, Preissler J, Schulz C, Wiemann C, Bernitzky CCM, Karafoulidi-Retsou C, Wrathall SLD, Procacci B, Matsuura H, Greetham GM, Teutloff C, Lauterbach L, Higuchi Y, Ishii M, Hunt NT, Lenz O, Zebger I, Horch M. Reversible Glutamate Coordination to High-Valent Nickel Protects the Active Site of a [NiFe] Hydrogenase from Oxygen. J Am Chem Soc 2022; 144:17022-17032. [PMID: 36084022 DOI: 10.1021/jacs.2c06400] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NAD+-reducing [NiFe] hydrogenases are valuable biocatalysts for H2-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O2 and elevated temperatures, the soluble NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O2-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O2 levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O2 that could protect the enzyme from oxidative damage.
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Affiliation(s)
- Catharina J Kulka-Peschke
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Christine Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Stefan Wahlefeld
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Janina Preissler
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Claudia Schulz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Charlotte Wiemann
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | | | - Chara Karafoulidi-Retsou
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Solomon L D Wrathall
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Barbara Procacci
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN/SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, U.K
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Lars Lauterbach
- Institute of Applied Microbiology, Synthetic Microbiology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Masaharu Ishii
- Graduate School of Agricultural and Life Sciences / Faculty of Agriculture, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Neil T Hunt
- Department of Chemistry & York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Marius Horch
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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3
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Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study. Catalysts 2022. [DOI: 10.3390/catal12090988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.
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4
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Fan Q, Caserta G, Lorent C, Zebger I, Neubauer P, Lenz O, Gimpel M. High-Yield Production of Catalytically Active Regulatory [NiFe]-Hydrogenase From Cupriavidus necator in Escherichia coli. Front Microbiol 2022; 13:894375. [PMID: 35572669 PMCID: PMC9100943 DOI: 10.3389/fmicb.2022.894375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrogenases are biotechnologically relevant metalloenzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. The O2-tolerant [NiFe]-hydrogenases from Cupriavidus necator (formerly Ralstonia eutropha) are of particular interest as they maintain catalysis even in the presence of molecular oxygen. However, to meet the demands of biotechnological applications and scientific research, a heterologous production strategy is required to overcome the low production yields in their native host. We have previously used the regulatory hydrogenase (RH) from C. necator as a model for the development of such a heterologous hydrogenase production process in E. coli. Although high protein yields were obtained, the purified enzyme was inactive due to the lack of the catalytic center, which contains an inorganic nickel-iron cofactor. In the present study, we significantly improved the production process to obtain catalytically active RH. We optimized important factors such as O2 content, metal availability, production temperature and time as well as the co-expression of RH-specific maturase genes. The RH was successfully matured during aerobic cultivation of E. coli by co-production of seven hydrogenase-specific maturases and a nickel permease, which was confirmed by activity measurements and spectroscopic investigations of the purified enzyme. The improved production conditions resulted in a high yield of about 80 mg L–1 of catalytically active RH and an up to 160-fold space-time yield in E. coli compared to that in the native host C. necator [<0.1 U (L d) –1]. Our strategy has important implications for the use of E. coli K-12 and B strains in the recombinant production of complex metalloenzymes, and provides a blueprint for the production of catalytically active [NiFe]-hydrogenases in biotechnologically relevant quantities.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Giorgio Caserta
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christian Lorent
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Ingo Zebger
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Oliver Lenz
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Matthias Gimpel,
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5
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Abstract
The role of deuterium in disentangling key steps of the mechanisms of H2 activation by mimics of hydrogenases is presented. These studies have allowed to a better understanding of the mode of action of the natural enzymes and their mimics.
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Affiliation(s)
- Mar Gómez-Gallego
- Departamento de Química Orgánica I and Center for Innovation in Advanced Chemistry (ORFEO-CINQA). Facultad de Química
- Universidad Complutense
- 28040-Madrid
- Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica I and Center for Innovation in Advanced Chemistry (ORFEO-CINQA). Facultad de Química
- Universidad Complutense
- 28040-Madrid
- Spain
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6
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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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7
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Schulz AC, Frielingsdorf S, Pommerening P, Lauterbach L, Bistoni G, Neese F, Oestreich M, Lenz O. Formyltetrahydrofolate Decarbonylase Synthesizes the Active Site CO Ligand of O2-Tolerant [NiFe] Hydrogenase. J Am Chem Soc 2019; 142:1457-1464. [DOI: 10.1021/jacs.9b11506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Anne-Christine Schulz
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Phillip Pommerening
- Institut für Chemie, Organische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Lars Lauterbach
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Giovanni Bistoni
- Department of Molecular Theory and Spectroscopy, Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy, Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Martin Oestreich
- Institut für Chemie, Organische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
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8
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Xia W, Li H, Sun H. Nickel Metallochaperones: Structure, Function, and Nickel-Binding Properties. THE BIOLOGICAL CHEMISTRY OF NICKEL 2017. [DOI: 10.1039/9781788010580-00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nickel-containing enzymes catalyze a series of important biochemical processes in both prokaryotes and eukaryotes. The maturation of the enzymes requires the proper assembly of the nickel-containing active sites, which involves a battery of nickel metallochaperones that exert metal delivery and storage functions. “Cross-talk” also exists between different nickel enzyme maturation processes. This chapter summarizes the updated knowledge about the nickel chaperones based on biochemical and structural biology research, and discusses the possible nickel delivery mechanisms.
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Affiliation(s)
- Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
| | - Hongzhe Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry Sun Yat-sen University Guangzhou 510275 China
- Department of Chemistry, The University of Hong Kong Hong Kong SAR China
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9
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CO synthesized from the central one-carbon pool as source for the iron carbonyl in O2-tolerant [NiFe]-hydrogenase. Proc Natl Acad Sci U S A 2016; 113:14722-14726. [PMID: 27930319 DOI: 10.1073/pnas.1614656113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogenases are nature's key catalysts involved in both microbial consumption and production of molecular hydrogen. H2 exhibits a strongly bonded, almost inert electron pair and requires transition metals for activation. Consequently, all hydrogenases are metalloenzymes that contain at least one iron atom in the catalytic center. For appropriate interaction with H2, the iron moiety demands for a sophisticated coordination environment that cannot be provided just by standard amino acids. This dilemma has been overcome by the introduction of unprecedented chemistry-that is, by ligating the iron with carbon monoxide (CO) and cyanide (or equivalent) groups. These ligands are both unprecedented in microbial metabolism and, in their free form, highly toxic to living organisms. Therefore, the formation of the diatomic ligands relies on dedicated biosynthesis pathways. So far, biosynthesis of the CO ligand in [NiFe]-hydrogenases was unknown. Here we show that the aerobic H2 oxidizer Ralstonia eutropha, which produces active [NiFe]-hydrogenases in the presence of O2, employs the auxiliary protein HypX (hydrogenase pleiotropic maturation X) for CO ligand formation. Using genetic engineering and isotope labeling experiments in combination with infrared spectroscopic investigations, we demonstrate that the α-carbon of glycine ends up in the CO ligand of [NiFe]-hydrogenase. The α-carbon of glycine is a building block of the central one-carbon metabolism intermediate, N10-formyl-tetrahydrofolate (N10-CHO-THF). Evidence is presented that the multidomain protein, HypX, converts the formyl group of N10-CHO-THF into water and CO, thereby providing the carbonyl ligand for hydrogenase. This study contributes insights into microbial biosynthesis of metal carbonyls involving toxic intermediates.
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10
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Abstract
[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario, Canada M5S 3H6.,Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada M5S 1A8
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11
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Lauterbach L, Wang H, Horch M, Gee LB, Yoda Y, Tanaka Y, Zebger I, Lenz O, Cramer SP. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O 2-tolerant NAD +-reducing [NiFe] hydrogenase. Chem Sci 2015; 6:1055-1060. [PMID: 25678951 PMCID: PMC4321745 DOI: 10.1039/c4sc02982h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy is used to characterize all Fe-containing cofactors in a complex multicofactor enzyme.
Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.
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Affiliation(s)
- Lars Lauterbach
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany ; Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
| | - Marius Horch
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Leland B Gee
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- RIKEN, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Ingo Zebger
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Stephen P Cramer
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
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12
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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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13
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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14
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15
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Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc Natl Acad Sci U S A 2013; 110:20485-90. [PMID: 24297906 PMCID: PMC3870729 DOI: 10.1073/pnas.1313620110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hydrogenase pleiotropically acting protein (Hyp)E plays a role in biosynthesis of the cyano groups for the NiFe(CN)2CO center of [NiFe] hydrogenases by catalyzing the ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, until now there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. Here, we report the crystal structures of the carbamoylated and cyanated forms of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53- and 1.64-Å resolution, respectively. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. In the presence of ATP, the thiocarboxamide of Cys338 is successfully dehydrated into the thiocyanate. In the carbamoylated state, the thiocarboxamide nitrogen atom of Cys338 is close to a conserved glutamate residue (Glu272), but the spatial position of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. The close contact of Lys134 with an arginine residue lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively.
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Affiliation(s)
- Taiga Tominaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Watanabe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Rie Matsumi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan; and
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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16
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Kothari A, Vaughn M, Garcia-Pichel F. Comparative genomic analyses of the cyanobacterium, Lyngbya aestuarii BL J, a powerful hydrogen producer. Front Microbiol 2013; 4:363. [PMID: 24376438 PMCID: PMC3858816 DOI: 10.3389/fmicb.2013.00363] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 11/15/2013] [Indexed: 11/13/2022] Open
Abstract
The filamentous, non-heterocystous cyanobacterium Lyngbya aestuarii is an important contributor to marine intertidal microbial mats system worldwide. The recent isolate L. aestuarii BL J, is an unusually powerful hydrogen producer. Here we report a morphological, ultrastructural, and genomic characterization of this strain to set the basis for future systems studies and applications of this organism. The filaments contain circa 17 μm wide trichomes, composed of stacked disk-like short cells (2 μm long), encased in a prominent, laminated exopolysaccharide sheath. Cellular division occurs by transversal centripetal growth of cross-walls, where several rounds of division proceed simultaneously. Filament division occurs by cell self-immolation of one or groups of cells (necridial cells) at the breakage point. Short, sheath-less, motile filaments (hormogonia) are also formed. Morphologically and phylogenetically L. aestuarii belongs to a clade of important cyanobacteria that include members of the marine Trichodesmiun and Hydrocoleum genera, as well as terrestrial Microcoleus vaginatus strains, and alkalyphilic strains of Arthrospira. A draft genome of strain BL J was compared to those of other cyanobacteria in order to ascertain some of its ecological constraints and biotechnological potential. The genome had an average GC content of 41.1%. Of the 6.87 Mb sequenced, 6.44 Mb was present as large contigs (>10,000 bp). It contained 6515 putative protein-encoding genes, of which, 43% encode proteins of known functional role, 26% corresponded to proteins with domain or family assignments, 19.6% encode conserved hypothetical proteins, and 11.3% encode apparently unique hypothetical proteins. The strain's genome reveals its adaptations to a life of exposure to intense solar radiation and desiccation. It likely employs the storage compounds, glycogen, and cyanophycin but no polyhydroxyalkanoates, and can produce the osmolytes, trehalose, and glycine betaine. According to its genome, BL J strain also has the potential to produce a plethora of products of biotechnological interest such as Curacin A, Barbamide, Hemolysin-type calcium-binding toxin, the suncreens scytonemin, and mycosporines, as well as heptadecane and pentadecane alkanes. With respect to hydrogen production, initial comparisons of the genetic architecture and sequence of relevant genes and loci, and a comparative model of protein structure of the NiFe bidirectional hydrogenase, did not reveal conspicuous differences that could explain its unusual hydrogen producing capacity.
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Affiliation(s)
- Ankita Kothari
- School of Life Sciences, Arizona State University Tempe, AZ, USA
| | - Michael Vaughn
- Department of Chemistry and Biochemistry, Arizona State University Tempe, AZ, USA
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17
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18
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Albareda M, Manyani H, Imperial J, Brito B, Ruiz-Argüeso T, Böck A, Palacios JM. Dual role of HupF in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum. BMC Microbiol 2012; 12:256. [PMID: 23136881 PMCID: PMC3534401 DOI: 10.1186/1471-2180-12-256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/24/2012] [Indexed: 11/16/2022] Open
Abstract
Background [NiFe] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use H2 as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. Biosynthesis of [NiFe] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. The endosymbiotic bacterium Rhizobium leguminosarum requires the products of eighteen genes (hupSLCDEFGHIJKhypABFCDEX) to synthesize an active hydrogenase. hupF and hupK genes are found only in hydrogenase clusters from bacteria expressing hydrogenase in the presence of oxygen. Results HupF is a HypC paralogue with a similar predicted structure, except for the C-terminal domain present only in HupF. Deletion of hupF results in the inability to process the hydrogenase large subunit HupL, and also in reduced stability of this subunit when cells are exposed to high oxygen tensions. A ΔhupF mutant was fully complemented for hydrogenase activity by a C-terminal deletion derivative under symbiotic, ultra low-oxygen tensions, but only partial complementation was observed in free living cells under higher oxygen tensions (1% or 3%). Co-purification experiments using StrepTag-labelled HupF derivatives and mass spectrometry analysis indicate the existence of a major complex involving HupL and HupF, and a less abundant HupF-HupK complex. Conclusions The results indicate that HupF has a dual role during hydrogenase biosynthesis: it is required for hydrogenase large subunit processing and it also acts as a chaperone to stabilize HupL when hydrogenase is synthesized in the presence of oxygen.
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Affiliation(s)
- Marta Albareda
- Centro de Biotecnología y Genómica de Plantas-CBGP, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40- km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain
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19
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Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation. Structure 2012; 20:2124-37. [PMID: 23123111 DOI: 10.1016/j.str.2012.09.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/03/2012] [Accepted: 09/27/2012] [Indexed: 12/22/2022]
Abstract
[NiFe] hydrogenase maturation represents one of the most dynamic and sophisticated processes in metallocenter assembly. The Fe(CN)(2)CO moiety of [NiFe] hydrogenases is assembled via unknown transient interactions among specific maturation proteins HypC (metallochaperone), HypD (redox protein), and HypE (cyanide synthesis/donor). Here, we report the structures of the HypC-HypD and HypC-HypD-HypE complexes, providing a view of the transient interactions that take place during the maturation process. HypC binds to the conserved region of HypD through extensive hydrophobic interactions. The ternary complex formation between HypE and the HypCD complex involves both HypC and HypD, rendering the HypE conformation favorable for cyanide transfer. In the complex, the conserved cysteines of HypC and HypD form an Fe binding site. The conserved C-terminal cysteine of HypE can access the thiol redox cascade of HypD. These results provide structural insights into the Fe atom cyanation in the HypCDE complex.
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Affiliation(s)
- Satoshi Watanabe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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20
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Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1153-7. [PMID: 23027738 PMCID: PMC3497970 DOI: 10.1107/s1744309112036421] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/21/2012] [Indexed: 12/27/2022]
Abstract
HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (ACP) domain interacts with the zinc-finger domain with some flexibility in its relative position. Molecular-surface analysis shows that a deep pocket formed between the ACP and zinc-finger domains is highly conserved and has positive potential. These results suggest that the positively charged pocket identified is involved in the hydrolysis of carbamoyl phosphate and the formation of a carbamoyl intermediate.
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Affiliation(s)
- Taiga Tominaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Watanabe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Rie Matsumi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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21
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Bürstel I, Siebert E, Winter G, Hummel P, Zebger I, Friedrich B, Lenz O. A universal scaffold for synthesis of the Fe(CN)2(CO) moiety of [NiFe] hydrogenase. J Biol Chem 2012; 287:38845-53. [PMID: 23019332 DOI: 10.1074/jbc.m112.376947] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogen-cycling [NiFe] hydrogenases harbor a dinuclear catalytic center composed of nickel and iron ions, which are coordinated by four cysteine residues. Three unusual diatomic ligands in the form of two cyanides (CN(-)) and one carbon monoxide (CO) are bound to the iron and apparently account for the complexity of the cofactor assembly process, which involves the function of at least six auxiliary proteins, designated HypA, -B, -C, -D, -E, and -F. It has been demonstrated previously that the HypC, -D, -E, and -F proteins participate in cyanide synthesis and transfer. Here, we show by infrared spectroscopic analysis that the purified HypCD complexes from Ralstonia eutropha and Escherichia coli carry in addition to both cyanides the CO ligand. We present experimental evidence that in vivo the attachment of the CN(-) ligands is a prerequisite for subsequent CO binding. With the aid of genetic engineering and subsequent mutant analysis, the functional role of conserved cysteine residues in HypD from R. eutropha was investigated. Our results demonstrate that the HypCD complex serves as a scaffold for the assembly of the Fe(CN)(2)(CO) entity of [NiFe] hydrogenase.
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Affiliation(s)
- Ingmar Bürstel
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117,10115 Berlin, Germany
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Shomura Y, Higuchi Y. Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases. J Biol Chem 2012; 287:28409-19. [PMID: 22740694 DOI: 10.1074/jbc.m112.387134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As a remarkable structural feature of hydrogenase active sites, [NiFe]-hydrogenases harbor one carbonyl and two cyano ligands, where HypE and HypF are involved in the biosynthesis of the nitrile group as a precursor of the cyano groups. HypF catalyzes S-carbamoylation of the C-terminal cysteine of HypE via three steps using carbamoylphosphate and ATP, producing two unstable intermediates: carbamate and carbamoyladenylate. Although the crystal structures of intact HypE homodimers and partial HypF have been reported, it remains unclear how the consecutive reactions occur without the loss of unstable intermediates during the proposed reaction scheme. Here we report the crystal structures of full-length HypF both alone and in complex with HypE at resolutions of 2.0 and 2.6 Å, respectively. Three catalytic sites of the structures of the HypF nucleotide- and phosphate-bound forms have been identified, with each site connected via channels inside the protein. This finding suggests that the first two consecutive reactions occur without the release of carbamate or carbamoyladenylate from the enzyme. The structure of HypF in complex with HypE revealed that HypF can associate with HypE without disturbing its homodimeric interaction and that the binding manner allows the C-terminal Cys-351 of HypE to access the S-carbamoylation active site in HypF, suggesting that the third step can also proceed without the release of carbamoyladenylate. A comparison of the structure of HypF with the recently reported structures of O-carbamoyltransferase revealed different reaction mechanisms for carbamoyladenylate synthesis and a similar reaction mechanism for carbamoyltransfer to produce the carbamoyl-HypE molecule.
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Affiliation(s)
- Yasuhito Shomura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
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23
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Schick M, Xie X, Ataka K, Kahnt J, Linne U, Shima S. Biosynthesis of the Iron-Guanylylpyridinol Cofactor of [Fe]-Hydrogenase in Methanogenic Archaea as Elucidated by Stable-Isotope Labeling. J Am Chem Soc 2012; 134:3271-80. [DOI: 10.1021/ja211594m] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Michael Schick
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| | - Xiulan Xie
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany
| | - Kenichi Ataka
- Department of Physics, Freie-Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
- PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
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