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Huening KA, Jiang R, Krzycki JA. Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri. FEMS Microbiol Lett 2020; 367:5896951. [PMID: 32840570 DOI: 10.1093/femsle/fnaa128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/27/2020] [Indexed: 12/30/2022] Open
Abstract
In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.
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Affiliation(s)
- Katherine A Huening
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ruisheng Jiang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph A Krzycki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Kountz DJ, Behrman EJ, Zhang L, Krzycki JA. MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase. J Biol Chem 2020; 295:11971-11981. [PMID: 32571881 PMCID: PMC7443480 DOI: 10.1074/jbc.ra120.012934] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/18/2020] [Indexed: 12/22/2022] Open
Abstract
The trimethylamine methyltransferase MttB is the first described member of a superfamily comprising thousands of microbial proteins. Most members of the MttB superfamily are encoded by genes that lack the codon for pyrrolysine characteristic of trimethylamine methyltransferases, raising questions about the activities of these proteins. The superfamily member MtcB is found in the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that can grow by demethylation of l-carnitine. Here, we demonstrate that MtcB catalyzes l-carnitine demethylation. When growing on l-carnitine, E. limosum excreted the unusual biological product norcarnitine as well as acetate, butyrate, and caproate. Cellular extracts of E. limosum grown on l-carnitine, but not lactate, methylated cob-(I)alamin or tetrahydrofolate using l-carnitine as methyl donor. MtcB, along with the corrinoid protein MtqC and the methylcorrinoid:tetrahydrofolate methyltransferase MtqA, were much more abundant in E. limosum cells grown on l-carnitine than on lactate. Recombinant MtcB methylates either cob(I)alamin or Co(I)-MtqC in the presence of l-carnitine and, to a much lesser extent, γ-butyrobetaine. Other quaternary amines were not substrates. Recombinant MtcB, MtqC, and MtqA methylated tetrahydrofolate via l-carnitine, forming a key intermediate in the acetogenic Wood-Ljungdahl pathway. To our knowledge, MtcB methylation of cobalamin or Co(I)-MtqC represents the first described mechanism of biological l-carnitine demethylation. The conversion of l-carnitine and its derivative γ-butyrobetaine to trimethylamine by the gut microbiome has been linked to cardiovascular disease. The activities of MtcB and related proteins in E. limosum might demethylate proatherogenic quaternary amines and contribute to the perceived health benefits of this human gut symbiont.
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Affiliation(s)
- Duncan J Kountz
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Edward J Behrman
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Liwen Zhang
- Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility, Ohio State University, Columbus, Ohio, USA
| | - Joseph A Krzycki
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA; Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio, USA.
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Kißling L, Greiser Y, Dürichen H, Studenik S. Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors. FEBS J 2020; 287:4971-4981. [PMID: 32160390 DOI: 10.1111/febs.15290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/31/2020] [Accepted: 03/10/2020] [Indexed: 12/01/2022]
Abstract
Corrinoid-dependent enzyme systems rely on the super-reduced state of the protein-bound corrinoid cofactor to be functional, for example, in methyl transfer reactions. Due to the low redox potential of the [CoII ]/[CoI ] couple, autoxidation of the corrinoid cofactor occurs and leads to the formation of the inactive [CoII ]-state. For the reactivation, which is an energy-demanding process, electrons have to be transferred from a physiological donor to the corrinoid cofactor by the help of a reductive activator protein. In this study, we identified reduced flavodoxin as electron donor for the ATP-dependent reduction of protein-bound corrinoid cofactors of bacterial O-demethylase enzyme systems. Reduced flavodoxin was generated enzymatically using pyruvate:ferredoxin/flavodoxin oxidoreductase rather than hydrogenase. Two of the four flavodoxins identified in Acetobacterium dehalogenans and Desulfitobacterium hafniense DCB-2 were functional in supplying electrons for corrinoid reduction. They exhibited a midpoint potential of about -400 mV (ESHE , pH 7.5) for the semiquinone/hydroquinone transition. Reduced flavodoxin could be replaced by reduced clostridial ferredoxin. It was shown that the low-potential electrons of reduced flavodoxin are first transferred to the iron-sulfur cluster of the reductive activator and finally to the protein-bound corrinoid cofactor. This study further highlights the importance of reduced flavodoxin, which allows maintaining a variety of enzymatic reaction cycles by delivering low-potential electrons.
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Affiliation(s)
- Lena Kißling
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Yvonne Greiser
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hendrike Dürichen
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Studenik
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Goetzl S, Teutloff C, Werther T, Hennig SE, Jeoung JH, Bittl R, Dobbek H. Protein Dynamics in the Reductive Activation of a B12-Containing Enzyme. Biochemistry 2017; 56:5496-5502. [DOI: 10.1021/acs.biochem.7b00477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Goetzl
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Werther
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra E. Hennig
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robert Bittl
- Fachbereich
Physik, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
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Gao Y, Jin L, Shi H, Chu Z. Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8381-8390. [PMID: 26368393 DOI: 10.1021/acs.jafc.5b03326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacillus sp. strain hys-1, which was isolated from active sludge, could degrade >90% butachlor at a concentration of 100 mg/L within 7 days. The present work revealed that strain hys-1 could mineralize butachlor via the following pathway: butachlor was initially metabolized to 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide by debutoxylation and then transformed to form 2-chloro-N-(2,6-diethylphenyl)acetamide by N-demethylation. Subsequently, it was converted to 2,6-diethylaniline and further mineralized into CO2 and H2O. In addition, the catalytic efficiency of crude cell extracts descended as follows: alachlor > acetochlor > butachlor. Furthermore, a novel 744 bp gene responsible for transforming butachlor into 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide was cloned from strain hys-1 and the encoding debutoxylase was designated Dbo. Then Dbo was expressed in Escherichia coli BL21 (DE3) and purified using Ni-nitrilotriacetic acid affinity chromatography. Dbo displayed the highest activity against butachlor at pH 6.5 and 30 °C. Metal ions played an important role in Dbo activity. To the best of the authors' knowledge, this is the first report that strain hys-1 can mineralize butachlor by a novel metabolic mechanism and the first identification of a gene encoding butachlor debutoxylase.
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Affiliation(s)
- Yang Gao
- Zhejiang Ocean University , Zhoushan 316000, China
| | - Lei Jin
- Zhejiang Ocean University , Zhoushan 316000, China
- Marine Fishery Research Institute of Zhejiang Province , Zhoushan 316021, China
| | - Hui Shi
- Marine Fishery Research Institute of Zhejiang Province , Zhoushan 316021, China
| | - Zhangjie Chu
- Zhejiang Ocean University , Zhoushan 316000, China
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Sjuts H, Dunstan MS, Fisher K, Leys D. Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation. ACTA ACUST UNITED AC 2015; 71:1900-8. [PMID: 26327380 DOI: 10.1107/s1399004715013061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022]
Abstract
O-Demethylation by acetogenic or organohalide-respiring bacteria leads to the formation of methyltetrahydrofolate from aromatic methyl ethers. O-Demethylases, which are cobalamin-dependent, three-component enzyme systems, catalyse methyl-group transfers from aromatic methyl ethers to tetrahydrofolate via methylcobalamin intermediates. In this study, crystal structures of the tetrahydrofolate-binding methyltransferase module from a Desulfitobacterium hafniense DCB-2 O-demethylase were determined both in complex with tetrahydrofolate and the product methyltetrahydrofolate. While these structures are similar to previously determined methyltransferase structures, the position of key active-site residues is subtly altered. A strictly conserved Asn is displaced to establish a putative proton-transfer network between the substrate N5 and solvent. It is proposed that this supports the efficient catalysis of methyltetrahydrofolate formation, which is necessary for efficient O-demethylation.
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Affiliation(s)
- Hanno Sjuts
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - Mark S Dunstan
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - Karl Fisher
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - David Leys
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
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Mingo FS, Studenik S, Diekert G. Conversion of phenyl methyl ethers byDesulfitobacteriumspp. and screening for the genes involved. FEMS Microbiol Ecol 2014; 90:783-90. [DOI: 10.1111/1574-6941.12433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/09/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Felix S. Mingo
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
| | - Sandra Studenik
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University Jena; Jena Germany
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Sperfeld M, Diekert G, Studenik S. Kinetic regulation of a corrinoid-reducing metallo-ATPase by its substrates. Mol Microbiol 2014; 92:598-608. [PMID: 24646146 DOI: 10.1111/mmi.12582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2014] [Indexed: 02/06/2023]
Abstract
Corrinoid cofactors play a crucial role as methyl group carriers in the C1 metabolism of anaerobes, e.g. in the cleavage of phenyl methyl ethers by O-demethylases. For the methylation, the protein-bound corrinoid has to be in the super-reduced [Co(I) ]-state, which is highly sensitive to autoxidation. The reduction of inadvertently oxidized corrinoids ([Co(II) ]-state) is catalysed in an ATP-dependent reaction by RACE proteins, the reductive activators of corrinoid-dependent enzymes. In this study, a reductive activator of O-demethylase corrinoid proteins was characterized with respect to its ATPase and corrinoid reduction activity. The reduction of the corrinoid cofactor was dependent on the presence of potassium or ammonium ions. In the absence of the corrinoid protein, a basal slow ATP hydrolysis was observed which was obviously not coupled to corrinoid reduction. ATP hydrolysis was significantly stimulated by the corrinoid protein in the [Co(II) ]-state of the corrinoid cofactor. The stoichiometry of ATP hydrolysed per mol corrinoid reduced was near 1:1. Site-directed mutagenesis was applied to study the impact of a highly conserved region possibly involved in nucleotide binding of RACE proteins, indicating that an aspartate and a glycine residue may play an essential role for the function of the enzyme.
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Affiliation(s)
- Martin Sperfeld
- Institut für Mikrobiologie, Friedrich-Schiller-Universität Jena, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, Philosophenweg 12, 07743, Jena, Germany
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