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Ding W, Zhou M, Li H, Li M, Qiu Y, Yin Y, Pan L, Yang W, Du Y, Zhang X, Tang Z, Liu W. Biocatalytic Fluoroalkylation Using Fluorinated S-Adenosyl-l-methionine Cofactors. Org Lett 2023; 25:5650-5655. [PMID: 37490590 DOI: 10.1021/acs.orglett.3c02028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Modification of organic molecules with fluorine functionalities offers a critical approach to develop new pharmaceuticals. Here, we report a multienzyme strategy for biocatalytic fluoroalkylation using S-adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs) and fluorinated SAM cofactors prepared from ATP and fluorinated l-methionine analogues by an engineered human methionine adenosyltransferase hMAT2AI322A. This work introduces the first example of biocatalytic 3,3-difluoroallylation. Importantly, this strategy can be applied to late-stage site-selective fluoroalkylation of complex molecule vancomycin with conversions up to 99%.
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Affiliation(s)
- Wenping Ding
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Minqi Zhou
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Huayu Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yanping Qiu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yu Yin
- School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wenchao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xingang Zhang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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2
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Neupane T, Chambers LR, Godfrey AJ, Monlux MM, Jacobs EJ, Whitworth S, Spawn JE, Clingman SHK, Vergunst KL, Niven FM, Townley JJ, Orion IW, Goodspeed CR, Cooper KA, Cronk JD, Shepherd JN, Langelaan DN. Microbial rhodoquinone biosynthesis proceeds via an atypical RquA-catalyzed amino transfer from S-adenosyl-L-methionine to ubiquinone. Commun Chem 2022; 5:89. [PMID: 36697674 PMCID: PMC9814641 DOI: 10.1038/s42004-022-00711-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/20/2022] [Indexed: 01/28/2023] Open
Abstract
Rhodoquinone (RQ) is a close analogue of ubiquinone (UQ) that confers diverse bacterial and eukaryotic taxa the ability to utilize fumarate as an electron acceptor in hypoxic conditions. The RquA protein, identified in a Rhodospirillum rubrum RQ-deficient mutant, has been shown to be required for RQ biosynthesis in bacteria. In this report, we demonstrate that RquA, homologous to SAM-dependent methyltransferases, is necessary and sufficient to catalyze RQ biosynthesis from UQ in vitro. Remarkably, we show that RquA uses SAM as the amino group donor in a substitution reaction that converts UQ to RQ. In contrast to known aminotransferases, RquA does not use pyridoxal 5'-phosphate (PLP) as a coenzyme, but requires the presence of Mn2+ as a cofactor. As these findings reveal, RquA provides an example of a non-canonical SAM-dependent enzyme that does not catalyze methyl transfer, instead it uses SAM in an atypical amino transfer mechanism.
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Affiliation(s)
- Trilok Neupane
- grid.55602.340000 0004 1936 8200Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS Canada
| | - Lydia R. Chambers
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Alexander J. Godfrey
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Melina M. Monlux
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Evan J. Jacobs
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Sophia Whitworth
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Jamie E. Spawn
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Seo Hee K. Clingman
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Kathleen L. Vergunst
- grid.55602.340000 0004 1936 8200Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS Canada
| | - Fair M. Niven
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - James J. Townley
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Iris W. Orion
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Carly R. Goodspeed
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Kathryn A. Cooper
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Jeff D. Cronk
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - Jennifer N. Shepherd
- grid.256410.40000 0001 0668 7980Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA USA
| | - David N. Langelaan
- grid.55602.340000 0004 1936 8200Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS Canada
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3
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Wilkinson IVL, Pfanzelt M, Sieber SA. Functionalised Cofactor Mimics for Interactome Discovery and Beyond. Angew Chem Int Ed Engl 2022; 61:e202201136. [PMID: 35286003 PMCID: PMC9401033 DOI: 10.1002/anie.202201136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Cofactors are required for almost half of all enzyme reactions, but their functions and binding partners are not fully understood even after decades of research. Functionalised cofactor mimics that bind in place of the unmodified cofactor can provide answers, as well as expand the scope of cofactor activity. Through chemical proteomics approaches such as activity-based protein profiling, the interactome and localisation of the native cofactor in its physiological environment can be deciphered and previously uncharacterised proteins annotated. Furthermore, cofactors that supply functional groups to substrate biomolecules can be hijacked by mimics to site-specifically label targets and unravel the complex biology of post-translational protein modification. The diverse activity of cofactors has inspired the design of mimics for use as inhibitors, antibiotic therapeutics, and chemo- and biosensors, and cofactor conjugates have enabled the generation of novel enzymes and artificial DNAzymes.
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Affiliation(s)
- Isabel V L Wilkinson
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Martin Pfanzelt
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
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4
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Wilkinson IVL, Pfanzelt M, Sieber SA. Funktionalisierte Cofaktor‐Analoga für die Erforschung von Interaktomen und darüber hinaus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel V. L. Wilkinson
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Martin Pfanzelt
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Stephan A. Sieber
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
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5
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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6
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McKean IJW, Hoskisson PA, Burley GA. Biocatalytic Alkylation Cascades: Recent Advances and Future Opportunities for Late‐Stage Functionalization. Chembiochem 2020; 21:2890-2897. [DOI: 10.1002/cbic.202000187] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/22/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Iain J. W. McKean
- Department of Pure & Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy & Biomedical Sciences University of Strathclyde 161 Cathedral Street Glasgow G4 0RE United Kingdom
| | - Glenn A. Burley
- Department of Pure & Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL United Kingdom
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7
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Weickhmann AK, Keller H, Wurm JP, Strebitzer E, Juen MA, Kremser J, Weinberg Z, Kreutz C, Duchardt-Ferner E, Wöhnert J. The structure of the SAM/SAH-binding riboswitch. Nucleic Acids Res 2019; 47:2654-2665. [PMID: 30590743 PMCID: PMC6411933 DOI: 10.1093/nar/gky1283] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/26/2018] [Indexed: 12/16/2022] Open
Abstract
S-adenosylmethionine (SAM) is a central metabolite since it is used as a methyl group donor in many different biochemical reactions. Many bacteria control intracellular SAM concentrations using riboswitch-based mechanisms. A number of structurally different riboswitch families specifically bind to SAM and mainly regulate the transcription or the translation of SAM-biosynthetic enzymes. In addition, a highly specific riboswitch class recognizes S-adenosylhomocysteine (SAH)—the product of SAM-dependent methyl group transfer reactions—and regulates enzymes responsible for SAH hydrolysis. High-resolution structures are available for many of these riboswitch classes and illustrate how they discriminate between the two structurally similar ligands SAM and SAH. The so-called SAM/SAH riboswitch class binds both ligands with similar affinities and is structurally not yet characterized. Here, we present a high-resolution nuclear magnetic resonance structure of a member of the SAM/SAH-riboswitch class in complex with SAH. Ligand binding induces pseudoknot formation and sequestration of the ribosome binding site. Thus, the SAM/SAH-riboswitches are translational ‘OFF’-switches. Our results establish a structural basis for the unusual bispecificity of this riboswitch class. In conjunction with genomic data our structure suggests that the SAM/SAH-riboswitches might be an evolutionary late invention and not a remnant of a primordial RNA-world as suggested for other riboswitches.
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Affiliation(s)
- A Katharina Weickhmann
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Heiko Keller
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jan P Wurm
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Bavaria, Germany
| | - Elisabeth Strebitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Institute of Informatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
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8
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Wicks SL, Hargrove AE. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods 2019; 167:3-14. [PMID: 31051253 DOI: 10.1016/j.ymeth.2019.04.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.
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Affiliation(s)
- Sarah L Wicks
- Duke University, Department of Chemistry, Durham, NC 27705, United States
| | - Amanda E Hargrove
- Duke University, Department of Chemistry, Durham, NC 27705, United States.
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9
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Weickhmann AK, Keller H, Duchardt-Ferner E, Strebitzer E, Juen MA, Kremser J, Wurm JP, Kreutz C, Wöhnert J. NMR resonance assignments for the SAM/SAH-binding riboswitch RNA bound to S-adenosylhomocysteine. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:329-334. [PMID: 30051308 DOI: 10.1007/s12104-018-9834-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
Riboswitches are structured RNA elements in the 5'-untranslated regions of bacterial mRNAs that are able to control the transcription or translation of these mRNAs in response to the specific binding of small molecules such as certain metabolites. Riboswitches that bind with high specificity to either S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) are widespread in bacteria. Based on differences in secondary structure and sequence these riboswitches can be grouped into a number of distinct classes. X-ray structures for riboswitch RNAs in complex with SAM or SAH established a structural basis for understanding ligand recognition and discrimination in many of these riboswitch classes. One class of riboswitches-the so-called SAM/SAH riboswitch class-binds SAM and SAH with similar affinity. However, this class of riboswitches is structurally not yet characterized and the structural basis for its unusual bispecificity is not established. In order to understand the ligand recognition mode that enables this riboswitch to bind both SAM and SAH with similar affinities, we are currently determining its structure in complex with SAH using NMR spectroscopy. Here, we present the NMR resonance assignment of the SAM/SAH binding riboswitch (env9b) in complex with SAH as a prerequisite for a solution NMR-based high-resolution structure determination.
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Affiliation(s)
- A Katharina Weickhmann
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Heiko Keller
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elisabeth Strebitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Jan Philip Wurm
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Jens Wöhnert
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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10
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Burgos ES, Walters RO, Huffman DM, Shechter D. A simplified characterization of S-adenosyl-l-methionine-consuming enzymes with 1-Step EZ-MTase: a universal and straightforward coupled-assay for in vitro and in vivo setting. Chem Sci 2017; 8:6601-6612. [PMID: 29449933 PMCID: PMC5676521 DOI: 10.1039/c7sc02830j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/25/2017] [Indexed: 01/02/2023] Open
Abstract
Methyltransferases use S-adenosyl-l-methionine (SAM) to deposit methyl marks. Many of these epigenetic 'writers' are associated with gene regulation. As cancer etiology is highly correlated with misregulated methylation patterns, methyltransferases are emerging therapeutic targets. Successful assignment of methyltransferases' roles within intricate biological networks relies on (1) the access to enzyme mechanistic insights and (2) the efficient screening of chemical probes against these targets. To characterize methyltransferases in vitro and in vivo, we report a highly-sensitive one-step deaminase-linked continuous assay where the S-adenosyl-l-homocysteine (SAH) enzyme-product is rapidly and quantitatively catabolized to S-inosyl-l-homocysteine (SIH). To highlight the broad capabilities of this assay, we established enzymatic characteristics of two protein arginine methyltransferases (PRMT5 and PRMT7), a histone-lysine N-methyltransferase (DIM-5) and a sarcosine/dimethylglycine N-methyltransferase (SDMT). Since the coupling deaminase TM0936 displays robust activity over a broad pH-range we determined the pH dependence of SDMT reaction rates. TM0936 reactions are monitored at 263 nm, so a drawback may arise when methyl acceptor substrates absorb within this UV-range. To overcome this limitation, we used an isosteric fluorescent SAM-analog: S-8-aza-adenosyl-l-methionine. Most enzymes tolerated this probe and sustained methyltransfers were efficiently monitored through loss of fluorescence at 360 nm. Unlike discontinuous radioactive- and antibody-based assays, our assay provides a simple, versatile and affordable approach towards the characterization of methyltransferases. Supported by three logs of linear dynamic range, the 1-Step EZ-MTase can detect methylation rates as low as 2 μM h-1, thus making it possible to quantify low nanomolar concentrations of glycine N-methyltransferase within crude biological samples. With Z'-factors above 0.75, this assay is well suited to high-throughput screening and may promote the identification of novel therapeutics.
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Affiliation(s)
- Emmanuel S Burgos
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA . ; ; ; Tel: +1-718-430-4120 ; Tel: +1-718-430-4128
| | - Ryan O Walters
- Department of Molecular Pharmacology , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Medicine , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Institute for Aging Research , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA
| | - Derek M Huffman
- Department of Molecular Pharmacology , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Medicine , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA.,Department of Institute for Aging Research , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA
| | - David Shechter
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , USA . ; ; ; Tel: +1-718-430-4120 ; Tel: +1-718-430-4128
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11
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Fuchs AL, Neu A, Sprangers R. A general method for rapid and cost-efficient large-scale production of 5' capped RNA. RNA (NEW YORK, N.Y.) 2016; 22:1454-66. [PMID: 27368341 PMCID: PMC4986899 DOI: 10.1261/rna.056614.116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/03/2023]
Abstract
The eukaryotic mRNA 5' cap structure is indispensible for pre-mRNA processing, mRNA export, translation initiation, and mRNA stability. Despite this importance, structural and biophysical studies that involve capped RNA are challenging and rare due to the lack of a general method to prepare mRNA in sufficient quantities. Here, we show that the vaccinia capping enzyme can be used to produce capped RNA in the amounts that are required for large-scale structural studies. We have therefore designed an efficient expression and purification protocol for the vaccinia capping enzyme. Using this approach, the reaction scale can be increased in a cost-efficient manner, where the yields of the capped RNA solely depend on the amount of available uncapped RNA target. Using a large number of RNA substrates, we show that the efficiency of the capping reaction is largely independent of the sequence, length, and secondary structure of the RNA, which makes our approach generally applicable. We demonstrate that the capped RNA can be directly used for quantitative biophysical studies, including fluorescence anisotropy and high-resolution NMR spectroscopy. In combination with (13)C-methyl-labeled S-adenosyl methionine, the methyl groups in the RNA can be labeled for methyl TROSY NMR spectroscopy. Finally, we show that our approach can produce both cap-0 and cap-1 RNA in high amounts. In summary, we here introduce a general and straightforward method that opens new means for structural and functional studies of proteins and enzymes in complex with capped RNA.
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Affiliation(s)
- Anna-Lisa Fuchs
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ancilla Neu
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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12
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Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
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Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
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13
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Vranken C, Fin A, Tufar P, Hofkens J, Burkart MD, Tor Y. Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase. Org Biomol Chem 2016; 14:6189-92. [PMID: 27270873 DOI: 10.1039/c6ob00844e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SalL, an enzyme that catalyzes the synthesis of SAM from l-methionine and 5'-chloro-5'-deoxyoadenosine, is shown to accept 5'-chloro-5'-deoxythienoadenosine as a substrate and facilitate the synthesis of a synthetic SAM analog with an unnatural nucleobase. This synthetic cofactor is demonstrated to replace SAM in the DNA methylation reaction with M.TaqI.
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Affiliation(s)
- C Vranken
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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14
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Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
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Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
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15
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Abstract
In eukaryotic DNA, cytosine can be enzymatically modified to yield up to four epigenetic base variants. DNA methyltransferases convert cytosine to 5-methylcytosine (mC), which plays critical roles in gene regulation during development. Ten-eleven translocation (TET) enzymes can sequentially oxidize mC to three products: 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized bases have been found in numerous mammalian cell types, where they potentially carry out independent epigenetic functions and aid in DNA demethylation. To gain insight into the mechanisms and functions of TET family enzymes, rigorous approaches are needed to quantify genomic cytosine modifications in cells and track TET enzyme activity in vitro. Here, we present tools developed by our lab and others to report on each of the five forms of cytosine (unmodified, mC, hmC, fC, and caC) with high specificity and sensitivity. We provide detailed protocols for qualitative and quantitative analysis of cytosine modifications in genomic DNA by dot blotting and LC-MS/MS. We then describe methods for generating synthetic oligonucleotide substrates for biochemical studies, provide optimized reaction conditions, and introduce several chemoenzymatic assays, as well as HPLC, mass spectrometry, and scintillation counting methods to quantify cytosine modifications in vitro. These approaches enable mechanistic studies of TET activity, which are key to understanding the role of these enzymes in epigenetic regulation.
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16
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Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism. J Am Chem Soc 2016; 138:730-3. [PMID: 26734843 PMCID: PMC4762542 DOI: 10.1021/jacs.5b10554] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Modification of cytosine-guanine
dinucleotides (CpGs) is a key
part of mammalian epigenetic regulation and helps shape cellular identity.
Tet enzymes catalyze stepwise oxidation of 5-methylcytosine (mC) in
CpGs to 5-hydroxymethylcytosine (hmC), or onward to 5-formylcytosine
(fC) or 5-carboxylcytosine (caC). The multiple mC oxidation products,
while intricately linked, are postulated to play independent epigenetic
roles, making it critical to understand how the products of stepwise
oxidation are established and maintained. Using highly sensitive isotope-based
studies, we newly show that Tet2 can yield fC and caC by iteratively
acting in a single encounter with mC-containing DNA, without release
of the hmC intermediate, and that the modification state of the complementary
CpG has little impact on Tet2 activity. By revealing Tet2 as an iterative, de novo mC oxygenase, our study provides insight into how
features intrinsic to Tet2 shape the epigenetic landscape.
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Affiliation(s)
- Daniel J Crawford
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Monica Yun Liu
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christopher S Nabel
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Xing-Jun Cao
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A Garcia
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Rahul M Kohli
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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17
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Chatterjee D, Kudlinzki D, Linhard V, Saxena K, Schieborr U, Gande SL, Wurm JP, Wöhnert J, Abele R, Rogov VV, Dötsch V, Osiewacz HD, Sreeramulu S, Schwalbe H. Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina. J Biol Chem 2015; 290:16415-30. [PMID: 25979334 DOI: 10.1074/jbc.m115.660829] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Indexed: 11/06/2022] Open
Abstract
Low levels of reactive oxygen species (ROS) act as important signaling molecules, but in excess they can damage biomolecules. ROS regulation is therefore of key importance. Several polyphenols in general and flavonoids in particular have the potential to generate hydroxyl radicals, the most hazardous among all ROS. However, the generation of a hydroxyl radical and subsequent ROS formation can be prevented by methylation of the hydroxyl group of the flavonoids. O-Methylation is performed by O-methyltransferases, members of the S-adenosyl-l-methionine (SAM)-dependent O-methyltransferase superfamily involved in the secondary metabolism of many species across all kingdoms. In the filamentous fungus Podospora anserina, a well established aging model, the O-methyltransferase (PaMTH1) was reported to accumulate in total and mitochondrial protein extracts during aging. In vitro functional studies revealed flavonoids and in particular myricetin as its potential substrate. The molecular architecture of PaMTH1 and the mechanism of the methyl transfer reaction remain unknown. Here, we report the crystal structures of PaMTH1 apoenzyme, PaMTH1-SAM (co-factor), and PaMTH1-S-adenosyl homocysteine (by-product) co-complexes refined to 2.0, 1.9, and 1.9 Å, respectively. PaMTH1 forms a tight dimer through swapping of the N termini. Each monomer adopts the Rossmann fold typical for many SAM-binding methyltransferases. Structural comparisons between different O-methyltransferases reveal a strikingly similar co-factor binding pocket but differences in the substrate binding pocket, indicating specific molecular determinants required for substrate selection. Furthermore, using NMR, mass spectrometry, and site-directed active site mutagenesis, we show that PaMTH1 catalyzes the transfer of the methyl group from SAM to one hydroxyl group of the myricetin in a cation-dependent manner.
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Affiliation(s)
- Deep Chatterjee
- From the Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Denis Kudlinzki
- From the Institute for Organic Chemistry and Chemical Biology, the German Cancer Consortium (DKTK), Heidelberg D-69210, Germany, and the German Cancer Research Center (DKFZ), Heidelberg D-69210, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Verena Linhard
- From the Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Krishna Saxena
- From the Institute for Organic Chemistry and Chemical Biology, the German Cancer Consortium (DKTK), Heidelberg D-69210, Germany, and the German Cancer Research Center (DKFZ), Heidelberg D-69210, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Ulrich Schieborr
- From the Institute for Organic Chemistry and Chemical Biology, the German Cancer Consortium (DKTK), Heidelberg D-69210, Germany, and the German Cancer Research Center (DKFZ), Heidelberg D-69210, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Santosh L Gande
- From the Institute for Organic Chemistry and Chemical Biology, the German Cancer Consortium (DKTK), Heidelberg D-69210, Germany, and the German Cancer Research Center (DKFZ), Heidelberg D-69210, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Jan Philip Wurm
- the Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Jens Wöhnert
- the Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | | | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | | | - Sridhar Sreeramulu
- From the Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany,
| | - Harald Schwalbe
- From the Institute for Organic Chemistry and Chemical Biology, the German Cancer Consortium (DKTK), Heidelberg D-69210, Germany, and the German Cancer Research Center (DKFZ), Heidelberg D-69210, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany,
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18
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19
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Wang F, Singh S, Zhang J, Huber TD, Helmich KE, Sunkara M, Hurley KA, Goff RD, Bingman CA, Morris AJ, Thorson JS, Phillips GN. Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus. FEBS J 2014; 281:4224-39. [PMID: 24649856 DOI: 10.1111/febs.12784] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/06/2014] [Accepted: 03/12/2014] [Indexed: 12/28/2022]
Abstract
UNLABELLED Methionine adenosyltransferase (MAT) is a family of enzymes that utilizes ATP and methionine to produce S-adenosylmethionine (AdoMet), the most crucial methyl donor in the biological methylation of biomolecules and bioactive natural products. Here, we report that the MAT from Sulfolobus solfataricus (sMAT), an enzyme from a poorly explored class of the MAT family, has the ability to produce a range of differentially alkylated AdoMet analogs in the presence of non-native methionine analogs and ATP. To investigate the molecular basis for AdoMet analog production, we have crystallized the sMAT in the AdoMet bound, S-adenosylethionine (AdoEth) bound and unbound forms. Notably, among these structures, the AdoEth bound form offers the first MAT structure containing a non-native product, and cumulatively these structures add new structural insight into the MAT family and allow for detailed active site comparison with its homologs in Escherichia coli and human. As a thermostable MAT structure from archaea, the structures herein also provide a basis for future engineering to potentially broaden AdoMet analog production as reagents for methyltransferase-catalyzed 'alkylrandomization' and/or the study of methylation in the context of biological processes. DATABASES PDB IDs: 4HPV, 4L7I, 4K0B and 4L2Z. EC 2.5.1.6 STRUCTURED DIGITAL ABSTRACT: • sMAT and sMAT bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, USA
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20
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Singh S, Zhang J, Huber TD, Sunkara M, Hurley K, Goff RD, Wang G, Zhang W, Liu C, Rohr J, Van Lanen SG, Morris AJ, Thorson JS. Facile chemoenzymatic strategies for the synthesis and utilization of S-adenosyl-(L)-methionine analogues. Angew Chem Int Ed Engl 2014; 53:3965-9. [PMID: 24616228 PMCID: PMC4076696 DOI: 10.1002/anie.201308272] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/16/2013] [Indexed: 01/22/2023]
Abstract
A chemoenzymatic platform for the synthesis of S-adenosyl-L-methionine (SAM) analogues compatible with downstream SAM-utilizing enzymes is reported. Forty-four non-native S/Se-alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non-native SAM analogues. As a proof of concept for the feasibility of natural product "alkylrandomization", a small set of differentially-alkylated indolocarbazole analogues was generated by using a coupled hMAT2-RebM system (RebM is the sugar C4'-O-methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Jianjun Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Tyler D. Huber
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY 40536 (USA)
| | - Katherine Hurley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Randal D. Goff
- Western Wyoming Community College, 2500 College Dr. Rock Springs, WY 82902-0428
| | - Guojun Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Wen Zhang
- Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, University of Kentucky, Lexington, KY 40536 (USA)
| | - Chunming Liu
- Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, University of Kentucky, Lexington, KY 40536 (USA)
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY 40536 (USA)
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
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21
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Hickey SF, Hammond MC. Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs. CHEMISTRY & BIOLOGY 2014; 21:345-56. [PMID: 24560607 PMCID: PMC4074398 DOI: 10.1016/j.chembiol.2014.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/12/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022]
Abstract
Many classes of S-adenosylmethionine (SAM)-binding RNAs and proteins are of interest as potential drug targets in diverse therapeutic areas, from infectious diseases to cancer. In the former case, the SAM-I riboswitch is an attractive target because this structured RNA element is found only in bacterial mRNAs and regulates multiple genes in several human pathogens. Here, we describe the synthesis of stable and fluorescent analogs of SAM in which the fluorophore is introduced through a functionalizable linker to the ribose. A Cy5-labeled SAM analog was shown to bind several SAM-I riboswitches via in-line probing and fluorescence polarization assays, including one from Staphylococcus aureus that controls the expression of SAM synthetase in this organism. A fluorescent ligand displacement assay was developed and validated for high-throughput screening of compounds to target the SAM-I riboswitch class.
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Affiliation(s)
- Scott F Hickey
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Synthetic Biology Institute, University of California, Berkeley, Berkely, CA 94720, USA
| | - Ming C Hammond
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Synthetic Biology Institute, University of California, Berkeley, Berkely, CA 94720, USA.
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22
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Singh S, Zhang J, Huber TD, Sunkara M, Hurley K, Goff RD, Wang G, Zhang W, Liu C, Rohr J, Van Lanen SG, Morris AJ, Thorson JS. Facile Chemoenzymatic Strategies for the Synthesis and Utilization ofS-Adenosyl-L-Methionine Analogues. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308272] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Stachelska-Wierzchowska A, Wierzchowski J, Wielgus-Kutrowska B, Mikleušević G. Enzymatic synthesis of highly fluorescent 8-azapurine ribosides using a purine nucleoside phosphorylase reverse reaction: variable ribosylation sites. Molecules 2013; 18:12587-98. [PMID: 24126376 PMCID: PMC6270051 DOI: 10.3390/molecules181012587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022] Open
Abstract
Various forms of purine-nucleoside phosphorylase (PNP) were used as catalysts of enzymatic ribosylation of selected fluorescent 8-azapurines. It was found that the recombinant calf PNP catalyzes ribosylation of 2,6-diamino-8-azapurine in a phosphate-free medium, with ribose-1-phosphate as ribose donor, but the ribosylation site is predominantly N7 and N8, with the proportion of N8/N7 ribosylated products markedly dependent on the reaction conditions. Both products are fluorescent. Application of the E. coli PNP gave a mixture of N8 and N9-substituted ribosides. Fluorescence of the ribosylated 2,6-diamino-8-azapurine has been briefly characterized. The highest quantum yield, ~0.9, was obtained for N9-β-d-riboside (λmax 365 nm), while for N8-β-d-riboside, emitting at ~430 nm, the fluorescence quantum yield was found to be close to 0.4. Ribosylation of 8-azaguanine with calf PNP as a catalyst goes exclusively to N9. By contrast, the E. coli PNP ribosylates 8-azaGua predominantly at N9, with minor, but highly fluorescent products ribosylated at N8/N7.
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Affiliation(s)
- Alicja Stachelska-Wierzchowska
- Department of Biophysics, University of Varmia & Masuria, 4 Oczapowskiego St., 10-719 Olsztyn, Poland; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +48-5233406; Fax: +48-5234547
| | - Jacek Wierzchowski
- Department of Biophysics, University of Varmia & Masuria, 4 Oczapowskiego St., 10-719 Olsztyn, Poland; E-Mail:
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland; E-Mail:
| | - Goran Mikleušević
- Division of Physical Chemistry, Rudjer Bošković Institute, POB 180, HR-10002 Zagreb, Croatia; E-Mail:
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24
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Wierzchowski J, Mędza G, Szabelski M, Stachelska-Wierzchowska A. Properties of 2,6-diamino-8-azapurine, a highly fluorescent purine analog and its N-alkyl derivatives: Tautomerism and excited-state proton transfer reactions. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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