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Cao ZQ, Wang GQ, Luo R, Gao YH, Lv JM, Qin SY, Chen GD, Awakawa T, Bao XF, Mei QH, Yao XS, Hu D, Abe I, Gao H. Biosynthesis of Enfumafungin-type Antibiotic Reveals an Unusual Enzymatic Fusion Pattern and Unprecedented C-C Bond Cleavage. J Am Chem Soc 2024; 146:12723-12733. [PMID: 38654452 DOI: 10.1021/jacs.4c02415] [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: 04/26/2024]
Abstract
Enfumafungin-type antibiotics, represented by enfumafungin and fuscoatroside, belong to a distinct group of triterpenoids derived from fungi. These compounds exhibit significant antifungal properties with ibrexafungerp, a semisynthetic derivative of enfumafungin, recently gaining FDA's approval as the first oral antifungal drug for treating invasive vulvar candidiasis. Enfumafungin-type antibiotics possess a cleaved E-ring with an oxidized carboxyl group and a reduced methyl group at the break site, suggesting unprecedented C-C bond cleavage chemistry involved in their biosynthesis. Here, we show that a 4-gene (fsoA, fsoD, fsoE, fsoF) biosynthetic gene cluster is sufficient to yield fuscoatroside by heterologous expression in Aspergillus oryzae. Notably, FsoA is an unheard-of terpene cyclase-glycosyltransferase fusion enzyme, affording a triterpene glycoside product that relies on enzymatic fusion. FsoE is a P450 enzyme that catalyzes successive oxidation reactions at C19 to facilitate a C-C bond cleavage, producing an oxidized carboxyl group and a reduced methyl group that have never been observed in known P450 enzymes. Our study thus sets the important foundation for the manufacture of enfumafungin-type antibiotics using biosynthetic approaches.
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Affiliation(s)
- Zhi-Qin Cao
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Integrated Chinese and Western Medicine Postdoctoral Research Station, School of Medicine, Jinan University, Guangzhou 510317, China
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Rui Luo
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Yao-Hui Gao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Sheng-Ying Qin
- Clinical Experimental Center, First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Xue-Feng Bao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Qing-Hua Mei
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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2
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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3
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Li RN, Chen SL. Mechanistic Insights into the N-Hydroxylations Catalyzed by the Binuclear Iron Domain of SznF Enzyme: Key Piece in the Synthesis of Streptozotocin. Chemistry 2024; 30:e202303845. [PMID: 38212866 DOI: 10.1002/chem.202303845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/13/2024]
Abstract
SznF, a member of the emerging family of heme-oxygenase-like (HO-like) di-iron oxidases and oxygenases, employs two distinct domains to catalyze the conversion of Nω-methyl-L-arginine (L-NMA) into N-nitroso-containing product, which can subsequently be transformed into streptozotocin. Using unrestricted density functional theory (UDFT) with the hybrid functional B3LYP, we have mechanistically investigated the two sequential hydroxylations of L-NMA catalyzed by SznF's binuclear iron central domain. Mechanism B primarily involves the O-O bond dissociation, forming Fe(IV)=O, induced by the H+/e- introduction to the FeA side of μ-1,2-peroxo-Fe2(III/III), the substrate hydrogen abstraction by Fe(IV)=O, and the hydroxyl rebound to the substrate N radical. The stochastic addition of H+/e- to the FeB side (mechanism C) can transition to mechanism B, thereby preventing enzyme deactivation. Two other competing mechanisms, involving the direct O-O bond dissociation (mechanism A) and the addition of H2O as a co-substrate (mechanism D), have been ruled out.
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Affiliation(s)
- Rui-Ning Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
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4
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Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
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Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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5
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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6
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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7
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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8
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Chen KL, Lai CY, Pham MT, Chein RJ, Tang Y, Lin HC. Enzyme-Catalyzed Azepinoindole Formation in Clavine Alkaloid Biosynthesis. Org Lett 2020; 22:3302-3306. [PMID: 32243182 PMCID: PMC8092377 DOI: 10.1021/acs.orglett.0c01132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
(-)-Aurantioclavine (1), which contains a characteristic seven-membered ring fused to an indole ring, belongs to the azepinoindole class of fungal clavine alkaloids. Here we show that starting from a 4-dimethylallyl-l-tryptophan precursor, a flavin adenine dinucleotide (FAD)-binding oxidase and a catalase-like heme-containing protein are involved in the biosynthesis of 1. The function of these two enzymes was characterized by heterologous expression, in vitro characterization, and deuterium labeling experiments.
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Affiliation(s)
- Kuan-Lin Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Chen-Yu Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Mai-Truc Pham
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan R.O.C
| | - Rong-Jie Chein
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Yi Tang
- Departments of Chemical and Biomolecular Engineering and Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
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9
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Yee DA, Kakule TB, Cheng W, Chen M, Chong CTY, Hai Y, Hang LF, Hung YS, Liu N, Ohashi M, Okorafor IC, Song Y, Tang M, Zhang Z, Tang Y. Genome Mining of Alkaloidal Terpenoids from a Hybrid Terpene and Nonribosomal Peptide Biosynthetic Pathway. J Am Chem Soc 2020; 142:710-714. [PMID: 31885262 DOI: 10.1021/jacs.9b13046] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Biosynthetic pathways containing multiple core enzymes have potential to produce structurally complex natural products. Here we mined a fungal gene cluster that contains two predicted terpene cyclases (TCs) and a nonribosomal peptide synthetase (NRPS). We showed the flv pathway produces flavunoidine 1, an alkaloidal terpenoid. The core of 1 is a tetracyclic, cage-like, and oxygenated sesquiterpene that is connected to dimethylcadaverine via a C-N bond and is acylated with 5,5-dimethyl-l-pipecolate. The roles of all flv enzymes are established on the basis of metabolite analysis from heterologous expression.
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Affiliation(s)
| | | | - Wei Cheng
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
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10
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Song H, Naowarojna N, Cheng R, Lopez J, Liu P. Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:1-61. [PMID: 31564305 DOI: 10.1016/bs.apcsb.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.
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Affiliation(s)
- Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, People's Republic of China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, United States
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11
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Deng Q, Liu Y, Chen L, Xu M, Naowarojna N, Lee N, Chen L, Zhu D, Hong X, Deng Z, Liu P, Zhao C. Biochemical Characterization of a Multifunctional Mononuclear Nonheme Iron Enzyme (PtlD) in Neopentalenoketolactone Biosynthesis. Org Lett 2019; 21:7592-7596. [DOI: 10.1021/acs.orglett.9b02872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qian Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Yang Liu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Meiling Xu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Norman Lee
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dongqing Zhu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Xuechuan Hong
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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12
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Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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13
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Rabe P, Kamps JJAG, Schofield CJ, Lohans CT. Roles of 2-oxoglutarate oxygenases and isopenicillin N synthase in β-lactam biosynthesis. Nat Prod Rep 2018; 35:735-756. [PMID: 29808887 PMCID: PMC6097109 DOI: 10.1039/c8np00002f] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/01/2023]
Abstract
Covering: up to 2017 2-Oxoglutarate (2OG) dependent oxygenases and the homologous oxidase isopenicillin N synthase (IPNS) play crucial roles in the biosynthesis of β-lactam ring containing natural products. IPNS catalyses formation of the bicyclic penicillin nucleus from a tripeptide. 2OG oxygenases catalyse reactions that diversify the chemistry of β-lactams formed by both IPNS and non-oxidative enzymes. Reactions catalysed by the 2OG oxygenases of β-lactam biosynthesis not only involve their typical hydroxylation reactions, but also desaturation, epimerisation, rearrangement, and ring-forming reactions. Some of the enzymes involved in β-lactam biosynthesis exhibit remarkable substrate and product selectivities. We review the roles of 2OG oxygenases and IPNS in β-lactam biosynthesis, highlighting opportunities for application of knowledge of their roles, structures, and mechanisms.
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Affiliation(s)
- Patrick Rabe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jos J A G Kamps
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher T Lohans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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14
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Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL, Chang WC. Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation. Angew Chem Int Ed Engl 2018; 57:1831-1835. [PMID: 29314482 DOI: 10.1002/anie.201710567] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/04/2017] [Indexed: 11/08/2022]
Abstract
AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epimer are reported. Meanwhile, a detailed mechanistic study was carried out to decipher the desaturation mechanism. These findings suggest that a pathway involving hydrogen atom abstraction at the C10 position of the substrate by a short-lived FeIV -oxo species and the subsequent formation of a carbocation or a hydroxylated intermediate is preferred during AsqJ-catalyzed desaturation.
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Affiliation(s)
- Hsuan-Jen Liao
- Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, 100, Taiwan
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Jhih-Liang Huang
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Madison Davidson
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Igor Kurnikov
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, 100, Taiwan
| | - Justin L Lee
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Maria Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, 100, Taiwan
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
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15
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Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL, Chang WC. Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hsuan-Jen Liao
- Institute of Biochemistry and Molecular Biology; College of Medicine; National (Taiwan) University; Taipei 100 Taiwan
| | - Jikun Li
- Department of Chemistry; Carnegie Mellon University; Pittsburgh PA 15213 USA
| | - Jhih-Liang Huang
- Department of Chemistry; North Carolina State University; Raleigh NC 27695 USA
| | - Madison Davidson
- Department of Chemistry; North Carolina State University; Raleigh NC 27695 USA
| | - Igor Kurnikov
- Department of Chemistry; Carnegie Mellon University; Pittsburgh PA 15213 USA
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology; College of Medicine; National (Taiwan) University; Taipei 100 Taiwan
| | - Justin L. Lee
- Department of Chemistry; Carnegie Mellon University; Pittsburgh PA 15213 USA
| | - Maria Kurnikova
- Department of Chemistry; Carnegie Mellon University; Pittsburgh PA 15213 USA
| | - Yisong Guo
- Department of Chemistry; Carnegie Mellon University; Pittsburgh PA 15213 USA
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology; College of Medicine; National (Taiwan) University; Taipei 100 Taiwan
| | - Wei-chen Chang
- Department of Chemistry; North Carolina State University; Raleigh NC 27695 USA
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16
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Tichy EM, Hardwick SW, Luisi BF, Salmond GPC. 1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:549-556. [PMID: 28695855 DOI: 10.1107/s2059798317002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022]
Abstract
The natural production of the β-lactam antibiotic carbapenem in bacteria involves a group of enzymes that form a synthetic pathway as well as proteins that protect the cell from self-intoxification by the products. Here, the crystal structure of CarF, one of the two proteins that confer resistance to synthesis of the antibiotic in the host organism, is reported. The CarF fold places it within a widely occurring structural family, indicating an ancient structural origin from which the resistance function has been derived.
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Affiliation(s)
- Evelyn M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, England
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17
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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18
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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19
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The facial triad in the α-ketoglutarate dependent oxygenase FIH: A role for sterics in linking substrate binding to O 2 activation. J Inorg Biochem 2016; 166:26-33. [PMID: 27815979 DOI: 10.1016/j.jinorgbio.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023]
Abstract
The factor inhibiting hypoxia inducible factor-1α (FIH) is a nonheme Fe(II)/αKG oxygenase using a 2-His-1-Asp facial triad. FIH activates O2 via oxidative decarboxylation of α-ketoglutarate (αKG) to generate an enzyme-based oxidant which hydroxylates the Asn803 residue within the C-terminal transactivation domain (CTAD) of HIF-1α. Tight coupling of these two sequential reactions requires a structural linkage between the Fe(II) and the substrate binding site to ensure that O2 activation occurs after substrate binds. We tested the hypothesis that the facial triad carboxylate (Asp201) of FIH linked substrate binding and O2 binding sites. Asp201 variants of FIH were constructed and thoroughly characterized in vitro using steady-state kinetics, crystallography, autohydroxylation, and coupling measurements. Our studies revealed each variant activated O2 with a catalytic efficiency similar to that of wild-type (WT) FIH (kcataKM(O2)=0.17μM-1min-1), but led to defects in the coupling of O2 activation to substrate hydroxylation. Steady-state kinetics showed similar catalytic efficiencies for hydroxylation by WT-FIH (kcat/KM(CTAD)=0.42μM-1min-1) and D201G (kcat/KM(CTAD)=0.34μM-1min-1); hydroxylation by D201E was greatly impaired, while hydroxylation by D201A was undetectable. Analysis of the crystal structure of the D201E variant revealed steric crowding near the diffusible ligand site supporting a role for sterics from the facial triad carboxylate in the O2 binding order. Our data support a model in which the facial triad carboxylate Asp201 provides both steric and polar contacts to favor O2 access to the Fe(II) only after substrate binds, leading to coupled turnover in FIH and other αKG oxygenases.
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20
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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21
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Ma G, Zhu W, Su H, Cheng N, Liu Y. Uncoupled Epimerization and Desaturation by Carbapenem Synthase: Mechanistic Insights from QM/MM Studies. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01275] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangcai Ma
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Hao Su
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Na Cheng
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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23
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Cochrane RVK, Vederas JC. Highly selective but multifunctional oxygenases in secondary metabolism. Acc Chem Res 2014; 47:3148-61. [PMID: 25250512 DOI: 10.1021/ar500242c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biosynthesis of bioactive natural products frequently features oxidation at multiple sites. Starting from a relatively reduced chemical scaffold that is assembled by controlled polymerization of small precursors, for example, acetate or amino acids, a diverse range of redox reactions can generate very complex and highly oxygenated structures. Their formation often involves C-H activation reactions catalyzed by oxygenase enzymes, either monooxygenases or dioxygenases. The former category includes the cytochrome P450s and flavin-dependent oxygenases, whereas examples of the latter are the non-heme iron α-ketoglutarate-dependent oxygenases. Oxygenases can catalyze a plethora of reactions ranging from hydroxylations and epoxidations to dehydrogenations, cyclizations, and rearrangements. The specific transformations are usually possible only with the use of these enzymatic catalysts. Aside from the ability of oxygenases to specifically oxidize unactivated carbon skeletons, some have recently been demonstrated to possess a fascinating ability to catalyze multiple reactions in a highly ordered fashion at different sites starting with a single substrate molecule. In the past, oxygenases associated with secondary metabolite pathways were considered to be highly regio-, stereo-, and substrate specific, with one oxidizing enzyme encoded in the gene cluster corresponding to one oxidation location in the natural product itself. However, it is becoming progressively clear that this "one oxygenase, one oxidation site" relationship is not necessarily a valid assumption. Multifunctional oxidases are known to occur in higher plants, fungi, and bacteria. Natural product gene clusters that contain multifunctional oxidase enzymes are responsible for production of lovastatin (a cholesterol-lowering agent and precursor to simvastatin), scopolamine (an anticholinergic drug), and cytochalasin E (an angiogenesis inhibitor), among many others. As opposed to simply being substrate promiscuous, these enzymes show very high substrate specificity and catalyze several oxidative reactions in a single pathway, with each oxidation being a prerequisite for the next. The basis for their specificity and highly ordered sequence is not yet well understood. In the lovastatin pathway, LovA is a cytochrome P450 that introduces a double bond and a hydroxyl group. H6H is an α-ketoglutarate-dependent oxygenase that hydroxylates (-)-atropine and then closes the newly introduced oxygen onto a neighboring methylene to generate the epoxide of scopolamine. CcsB is a flavin-dependent Baeyer-Villigerase that converts a ketone to a carbonate by double oxidation, a reaction not possible without enzymes. Recent crystallographic studies of other multifunctional oxygenases, such as AurH, a cytochrome P450 from Streptomyces thioluteus involved in aureothin biosynthesis, have indicated a steric switch mechanism. After the initial hydroxylation reaction catalyzed by AurH, the enzyme is thought to undergo a substrate-induced conformational change. In this Account, advances in our knowledge of these fascinating multifunctional enzymes and their potential will be explored.
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Affiliation(s)
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
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24
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Tichy EM, Luisi BF, Salmond GPC. Crystal structure of the carbapenem intrinsic resistance protein CarG. J Mol Biol 2014; 426:1958-70. [PMID: 24583229 PMCID: PMC4361734 DOI: 10.1016/j.jmb.2014.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
In the Gram-negative enterobacterium Erwinia (Pectobacterium) and Serratia sp. ATCC 39006, intrinsic resistance to the carbapenem antibiotic 1-carbapen-2-em-3-carboxylic acid is mediated by the CarF and CarG proteins, by an unknown mechanism. Here, we report a high-resolution crystal structure for the Serratia sp. ATCC 39006 carbapenem resistance protein CarG. This structure of CarG is the first in the carbapenem intrinsic resistance (CIR) family of resistance proteins from carbapenem-producing bacteria. The crystal structure shows the protein to form a homodimer, in agreement with results from analytical gel filtration. The structure of CarG does not show homology with any known antibiotic resistance proteins nor does it belong to any well-characterised protein structural family. However, it is a close structural homologue of the bacterial inhibitor of invertebrate lysozyme, PliI-Ah, with some interesting structural variations, including the absence of the catalytic site responsible for lysozyme inhibition. Both proteins show a unique β-sandwich fold with short terminal α-helices. The core of the protein is formed by stacked anti-parallel sheets that are individually very similar in the two proteins but differ in their packing interface, causing the splaying of the two sheets in CarG. Furthermore, a conserved cation binding site identified in CarG is absent from the homologue.
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Affiliation(s)
- E M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - G P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
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25
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Chang WC, Guo Y, Wang C, Butch SE, Rosenzweig AC, Boal AK, Krebs C, Bollinger JM. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics. Science 2014; 343:1140-4. [PMID: 24604200 PMCID: PMC4160820 DOI: 10.1126/science.1248000] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.
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Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan E. Butch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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26
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Cele ZED, Pawar SA, Naicker T, Maguire GEM, Arvidsson PI, Kruger HG, Govender T. Organocatalytic Mannich Reactions on a Carbapenem Core - Synthesis of Mannich Bases and Bicyclic Diazanonanes. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301823] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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