1
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Du Z, Li Y, Liu Y, Shi T. Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism. Chemistry 2023; 29:e202203420. [PMID: 36464909 DOI: 10.1002/chem.202203420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol-1 and 24.5 kcal mol-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.
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Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yongzhen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yihan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ting Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, P. R. China
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2
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Linne Y, Bonandi E, Tabet C, Geldsetzer J, Kalesse M. The Total Synthesis of Chondrochloren A. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yannick Linne
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Elisa Bonandi
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Christopher Tabet
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Jan Geldsetzer
- Helmholtz Centre for Infection Research (HZI) Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Markus Kalesse
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
- Centre of Biomolecular Drug Research (BMWZ) Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Helmholtz Centre for Infection Research (HZI) Inhoffenstrasse 7 38124 Braunschweig Germany
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3
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Linne Y, Bonandi E, Tabet C, Geldsetzer J, Kalesse M. The Total Synthesis of Chondrochloren A. Angew Chem Int Ed Engl 2021; 60:6938-6942. [PMID: 33450788 PMCID: PMC8048958 DOI: 10.1002/anie.202016072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/13/2021] [Indexed: 12/01/2022]
Abstract
The first total synthesis of chondrochloren A is accomplished using a 1,2‐metallate rearrangement addition as an alternative for the Nozaki‐Hiyama‐Kishi reaction. This transformation also avoids the inherent challenges of this polyketide segment and provides a new, unprecedented strategy to assemble polyketidal frameworks. The formation of the Z‐enamide is accomplished using a Z‐selective cross coupling of the corresponding amide to a Z‐vinyl bromide.
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Affiliation(s)
- Yannick Linne
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Elisa Bonandi
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Christopher Tabet
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jan Geldsetzer
- Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany.,Centre of Biomolecular Drug Research (BMWZ), Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
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4
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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5
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Wu WJ, Li MM, Liu B, Wu Y. Racemization of α-Alkyl-β-Keto Esters and Enantioselective Total Synthesis of Two C-2′′′Epimers of Plant Glycerolipid Santinol C. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wen-Ju Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Mei-Mei Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Bo Liu
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Yikang Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
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6
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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7
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Sundaram S, Kim HJ, Bauer R, Thongkongkaew T, Heine D, Hertweck C. On-Line Polyketide Cyclization into Diverse Medium-Sized Lactones by a Specialized Ketosynthase Domain. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804991] [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)
- Srividhya Sundaram
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hak Joong Kim
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Ruth Bauer
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Tawatchai Thongkongkaew
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Daniel Heine
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
- Chair for Natural Product Chemistry; Friedrich Schiller University; Jena Germany
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8
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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9
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Sundaram S, Kim HJ, Bauer R, Thongkongkaew T, Heine D, Hertweck C. On-Line Polyketide Cyclization into Diverse Medium-Sized Lactones by a Specialized Ketosynthase Domain. Angew Chem Int Ed Engl 2018; 57:11223-11227. [PMID: 29897642 DOI: 10.1002/anie.201804991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Indexed: 12/15/2022]
Abstract
Ketosynthase (KS) domains of modular type I polyketide synthases (PKSs) typically catalyze the Claisen condensation of acyl and malonyl units to form linear chains. In stark contrast, the KS of the rhizoxin PKS branching module mediates a Michael addition, which sets the basis for a pharmacophoric δ-lactone moiety. The precise role of the KS was evaluated by site-directed mutagenesis, chemical probes, and biotransformations. Biochemical and kinetic analyses helped to dissect branching and lactonization reactions and unequivocally assign the entire sequence to the KS. Probing the range of accepted substrates with diverse synthetic surrogates in vitro, we found that the KS tolerates defined acyl chain lengths to produce five- to seven-membered lactones. These results show that the KS is multifunctional, as it catalyzes β-branching and lactonization. Information on the increased product portfolio of the unusual, TE-independent on-line cyclization is relevant for synthetic biology approaches.
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Affiliation(s)
- Srividhya Sundaram
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hak Joong Kim
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Ruth Bauer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Tawatchai Thongkongkaew
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Daniel Heine
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany.,Chair for Natural Product Chemistry, Friedrich Schiller University, Jena, Germany
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10
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Hemmerling F, Lebe KE, Wunderlich J, Hahn F. An Unusual Fatty Acyl:Adenylate Ligase (FAAL)-Acyl Carrier Protein (ACP) Didomain in Ambruticin Biosynthesis. Chembiochem 2018. [DOI: 10.1002/cbic.201800084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Karen E. Lebe
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Johannes Wunderlich
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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11
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Einblicke in die duale Aktivität einer bifunktionalen Dehydratase-Cyclase-Domäne. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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12
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Insights into the Dual Activity of a Bifunctional Dehydratase-Cyclase Domain. Angew Chem Int Ed Engl 2017; 57:343-347. [PMID: 29084363 DOI: 10.1002/anie.201707774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are a common structural motif in polyketide natural products and contribute significantly to their biological activity. Here, we report structural and mechanistic investigations on AmbDH3, a polyketide synthase domain with dual activity as dehydratase (DH) and pyran-forming cyclase in ambruticin biosynthesis. AmbDH3 is similar to monofunctional DH domains, using H51 and D215 for dehydration. V173 was confirmed as a diagnostic residue for cyclization activity by a mutational study and enzymatic in vitro experiments. Similar motifs were observed in the seemingly monofunctional AmbDH2, which also shows an unexpected cyclase activity. Our results pave the way for mining of hidden cyclases in biosynthetic pathways. They also open interesting prospects for the generation of novel biocatalysts for chemoenzymatic synthesis and pyran-polyketides by combinatorial biosynthesis.
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Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
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13
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Berkhan G, Merten C, Holec C, Hahn F. Das Zusammenspiel zwischen einer multifunktionalen Dehydratase-Domäne und einer C-Methyltransferase bewirkt die Doppelbindungsverschiebung in der Ambruticin-Biosynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Christian Merten
- Ruhr-Universität Bochum; Organische Chemie 2; Universitätsstraße 150 44801 Bochum Deutschland
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität, Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Deutschland
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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14
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Berkhan G, Merten C, Holec C, Hahn F. The Interplay between a Multifunctional Dehydratase Domain and a C-Methyltransferase Effects Olefin Shift in Ambruticin Biosynthesis. Angew Chem Int Ed Engl 2016; 55:13589-13592. [DOI: 10.1002/anie.201607827] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Christian Merten
- Ruhr Universität Bochum; Organische Chemie 2; Universitätsstrasse 150 44801 Bochum Germany
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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15
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Yang L, Lin Z, Huang SH, Hong R. Stereodivergent Synthesis of Functionalized Tetrahydropyrans Accelerated by Mechanism-Based Allylboration and Bioinspired Oxa-Michael Cyclization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lin Yang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Zuming Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Sha-Hua Huang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
- School of Chemical and Environmental Engineering; Shanghai Institute of Technology; 100 Haiquan Road Shanghai 201418 China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
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16
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Yang L, Lin Z, Huang SH, Hong R. Stereodivergent Synthesis of Functionalized Tetrahydropyrans Accelerated by Mechanism-Based Allylboration and Bioinspired Oxa-Michael Cyclization. Angew Chem Int Ed Engl 2016; 55:6280-4. [DOI: 10.1002/anie.201600558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/23/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Lin Yang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Zuming Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Sha-Hua Huang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
- School of Chemical and Environmental Engineering; Shanghai Institute of Technology; 100 Haiquan Road Shanghai 201418 China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
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17
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Cochrane RVK, Sanichar R, Lambkin GR, Reiz B, Xu W, Tang Y, Vederas JC. Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent. Angew Chem Int Ed Engl 2015; 55:664-8. [PMID: 26783060 DOI: 10.1002/anie.201509345] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/10/2022]
Abstract
The antimalarial agent cladosporin is a nanomolar inhibitor of the Plasmodium falciparum lysyl-tRNA synthetase, and exhibits activity against both blood- and liver-stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it is biosynthesized by a highly reducing (HR) and a non-reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism and subsequent heterologous expression of these enzymes in Saccharomyces cerevisiae produced cladosporin, confirming the identity of the putative gene cluster. Incorporation of a pentaketide intermediate analogue indicated a 5+3 assembly by the HR PKS Cla2 and the NR PKS Cla3 during cladosporin biosynthesis. Advanced-intermediate analogues were synthesized and incorporated by Cla3 to furnish new cladosporin analogues. A putative lysyl-tRNA synthetase resistance gene was identified in the cladosporin gene cluster. Analysis of the active site emphasizes key structural features thought to be important in resistance to cladosporin.
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Affiliation(s)
- Rachel V K Cochrane
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Randy Sanichar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Gareth R Lambkin
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada).
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Cochrane RVK, Sanichar R, Lambkin GR, Reiz B, Xu W, Tang Y, Vederas JC. Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. ACTA ACUST UNITED AC 2015; 127:13826-13829. [PMID: 27587902 PMCID: PMC4988243 DOI: 10.1002/ange.201507090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/25/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13622-5. [PMID: 26377145 PMCID: PMC4648038 DOI: 10.1002/anie.201507090] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 02/06/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK).
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Bis DM, Ban YH, James ED, Alqahtani N, Viswanathan R, Lane AL. Characterization of the nocardiopsin biosynthetic gene cluster reveals similarities to and differences from the rapamycin and FK-506 pathways. Chembiochem 2015; 16:990-7. [PMID: 25755076 DOI: 10.1002/cbic.201500007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 01/19/2023]
Abstract
Macrolide-pipecolate natural products, such as rapamycin (1) and FK-506 (2), are renowned modulators of FK506-binding proteins (FKBPs). The nocardiopsins, from Nocardiopsis sp. CMB-M0232, are the newest members of this structural class. Here, the biosynthetic pathway for nocardiopsins A-D (4-7) is revealed by cloning, sequencing, and bioinformatic analyses of the nsn gene cluster. In vitro evaluation of recombinant NsnL revealed that this lysine cyclodeaminase catalyzes the conversion of L-lysine into the L-pipecolic acid incorporated into 4 and 5. Bioinformatic analyses supported the conjecture that a linear nocardiopsin precursor is equipped with the hydroxy group required for macrolide closure in a previously unobserved manner by employing a P450 epoxidase (NsnF) and limonene epoxide hydrolase homologue (NsnG). The nsn cluster also encodes candidates for tetrahydrofuran group biosynthesis. The nocardiopsin pathway provides opportunities for engineering of FKBP-binding metabolites and for probing new enzymology in nature's polyketide tailoring arsenal.
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Affiliation(s)
- Dana M Bis
- Chemistry Department, University of North Florida, 1 UNF Drive, Jacksonville, FL 32224 (USA)
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