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Schaupp S, Arriaza-Gallardo FJ, Pan HJ, Kahnt J, Angelidou G, Paczia N, Costa K, Hu X, Shima S. In Vitro Biosynthesis of the [Fe]-Hydrogenase Cofactor Verifies the Proposed Biosynthetic Precursors. Angew Chem Int Ed Engl 2022; 61:e202200994. [PMID: 35286742 PMCID: PMC9314073 DOI: 10.1002/anie.202200994] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Indexed: 02/06/2023]
Abstract
In the FeGP cofactor of [Fe]‐hydrogenase, low‐spin FeII is in complex with two CO ligands and a pyridinol derivative; the latter ligates the iron with a 6‐acylmethyl substituent and the pyridinol nitrogen. A guanylylpyridinol derivative, 6‐carboxymethyl‐3,5‐dimethyl‐4‐guanylyl‐2‐pyridinol (3), is produced by the decomposition of the FeGP cofactor under irradiation with UV‐A/blue light and is also postulated to be a precursor of FeGP cofactor biosynthesis. HcgC and HcgB catalyze consecutive biosynthesis steps leading to 3. Here, we report an in vitro biosynthesis assay of the FeGP cofactor using the cell extract of the ΔhcgBΔhcgC strain of Methanococcus maripaludis, which does not biosynthesize 3. We chemically synthesized pyridinol precursors 1 and 2, and detected the production of the FeGP cofactor from 1, 2 and 3. These results indicated that 1, 2 and 3 are the precursors of the FeGP cofactor, and the carboxy group of 3 is converted to the acyl ligand.
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Affiliation(s)
- Sebastian Schaupp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | | | - Hui-Jie Pan
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Georgia Angelidou
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Kyle Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, USA
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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Schaupp S, Arriaza‐Gallardo FJ, Pan H, Kahnt J, Angelidou G, Paczia N, Costa K, Hu X, Shima S. In Vitro Biosynthesis of the [Fe]‐Hydrogenase Cofactor Verifies the Proposed Biosynthetic Precursors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Schaupp
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | | | - Hui‐jie Pan
- Laboratory of Inorganic Synthesis and Catalysis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305 1015 Lausanne Switzerland
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Georgia Angelidou
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Kyle Costa
- Department of Plant and Microbial Biology University of Minnesota Twin Cities St. Paul, MN USA
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne (EPFL) ISIC-LSCI, BCH 3305 1015 Lausanne Switzerland
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch-Straße 10 35043 Marburg Germany
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Yang Z, Liu F, Steeves AH, Kulik HJ. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. J Phys Chem Lett 2019; 10:3779-3787. [PMID: 31244268 DOI: 10.1021/acs.jpclett.9b01555] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fang Liu
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Adam H Steeves
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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Watanabe T, Wagner T, Huang G, Kahnt J, Ataka K, Ermler U, Shima S. The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates. Angew Chem Int Ed Engl 2019; 58:3506-3510. [PMID: 30600878 DOI: 10.1002/anie.201813465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Indexed: 11/11/2022]
Abstract
[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H4 MPT+ ) with H2 . H4 MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog, termed HmdII, and the HcgA-G proteins. The latter are required for the biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H4 MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the hydrogenation of derivatives of tetrahydrofolate, the bacterial C1-carrier, albeit with low enzymatic activities. The crystal structures show how Hmd recognizes tetrahydrofolate derivatives. These findings have an impact on future biotechnology by identifying a bacterial Hmd paralog.
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Affiliation(s)
- Tomohiro Watanabe
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
| | - Tristan Wagner
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany.,Current address: Microbial Metabolism group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Gangfeng Huang
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectrometry and Proteomics Unit, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Ulrich Ermler
- Department of Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438, Frankfurt/Main, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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Watanabe T, Wagner T, Huang G, Kahnt J, Ataka K, Ermler U, Shima S. The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tomohiro Watanabe
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch Straße 10 35043 Marburg Germany
| | - Tristan Wagner
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch Straße 10 35043 Marburg Germany
- Current address: Microbial Metabolism group; Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 28359 Bremen Germany
| | - Gangfeng Huang
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch Straße 10 35043 Marburg Germany
| | - Jörg Kahnt
- Mass Spectrometry and Proteomics Unit; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch Straße 10 35043 Marburg Germany
| | - Kenichi Ataka
- Department of Physics; Freie Universität Berlin; 14195 Berlin Germany
| | - Ulrich Ermler
- Department of Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt/Main Germany
| | - Seigo Shima
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch Straße 10 35043 Marburg Germany
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