1
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Kudo F. Biosynthesis of macrolactam antibiotics with β-amino acid polyketide starter units. J Antibiot (Tokyo) 2024; 77:486-498. [PMID: 38816450 PMCID: PMC11284099 DOI: 10.1038/s41429-024-00742-2] [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: 01/31/2024] [Revised: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Macrolactam antibiotics incorporating β-amino acid polyketide starter units, isolated primarily from Actinomycetes species, show significant biological activities. This review provides a detailed analysis into the biosynthetic studies of vicenistatin, a macrolactam antibiotic with a 3-aminoisobutyrate starter unit, as well as biosynthetic research on related macrolactam compounds. Firstly, the elucidation of a common mechanism for the incorporation of β-amino acid starter units into the polyketide synthase (PKS) is described. Secondly, the unique biosynthetic mechanisms of the β-amino acids that are used to supply the main macrolactam biosynthetic pathways with starter units are discussed. Thirdly, some distinctive post-PKS modification mechanisms that complete macrolactam antibiotic biosynthesis are summarized. Finally, future directions for creating new macrolactam compounds through engineered biosynthesis pathways are described.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan.
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2
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Jia K, Sun H, Zhou Y, Zhang W. Biosynthesis of isonitrile lipopeptides. Curr Opin Chem Biol 2024; 81:102470. [PMID: 38788523 PMCID: PMC11323250 DOI: 10.1016/j.cbpa.2024.102470] [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: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Isonitrile lipopeptides discovered from Actinobacteria have attracted wide attention due to their fascinating biosynthetic pathways and relevance to the virulence of many human pathogens including Mycobacterium tuberculosis. Specifically, the identification of the new class of isonitrile-forming enzymes that belong to non-heme iron (II) and α-ketoglutarate dependent dioxygenases has intrigued several research groups to investigate their catalytic mechanism. Here we summarize the recent studies on the biosynthesis of isonitrile lipopeptides from Streptomyces and Mycobacterium. The latest research on the core and tailoring enzymes involved in the pathway as well as the isonitrile metabolic enzymes are discussed in this review.
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Affiliation(s)
- Kaimin Jia
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, United States
| | - Helen Sun
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States
| | - Yiyan Zhou
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, United States.
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3
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Khamkar SL, Handore KL, Shinde HM, Reddy DS. Highly Stereoselective Diels-Alder-Based Strategy for the Synthesis of 3- epi-Formicin A and 1- epi-Formicin B. Org Lett 2024; 26:3961-3965. [PMID: 38679880 DOI: 10.1021/acs.orglett.4c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The first enantioselective approach based on a highly stereoselective Diels-Alder reaction for the synthesis of 3-epi-formicin A and 1-epi-formicin B with rare N-acetylcysteamine-containing indenone thioesters is reported. The strategy utilizes a key Diels-Alder reaction to form the core hydrindane system with three contiguous stereocenters in very high levels of diastereo- and regioselectivity and one-pot oxidation/isomerization/dehydrogenation. The scope of this method was tested with different substrates to give cycloadducts in a highly diastereoselective manner.
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Affiliation(s)
- Sunil L Khamkar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- BASF Innovation Campus Mumbai, BASF Chemicals India Pvt. Ltd., Plot No. 12, TTC Area Thane Belapur Road, Turbhe, Navi Mumbai 400705, India
| | - Kishor L Handore
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Harish M Shinde
- BASF Innovation Campus Mumbai, BASF Chemicals India Pvt. Ltd., Plot No. 12, TTC Area Thane Belapur Road, Turbhe, Navi Mumbai 400705, India
| | - D Srinivasa Reddy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
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4
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Deng Z, Liu C, Wang F, Song N, Liu J, Li H, Liu S, Li T, Liu Z, Xiao F, Li W. A Versatile Thioesterase Involved in Dimerization during Cinnamoyl Lipid Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202402010. [PMID: 38462490 DOI: 10.1002/anie.202402010] [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: 01/28/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
The cinnamoyl lipid compound youssoufene A1 (1), featuring a unique dearomatic carbon-bridged dimeric skeleton, exhibits increased inhibition against multidrug resistant Enterococcus faecalis as compared to monomeric youssoufenes. However, the formation process of this intriguing dearomatization/dimerization remains unknown. In this study, an unusual "gene-within-gene" thioesterase (TE) gene ysfF was functionally characterized. The gene was found to naturally encodes two proteins, an entire YsfF with α/β-hydrolase and 4-hydroxybenzoyl-CoA thioesterase (4-HBT)-like enzyme domains, and a nested YsfFHBT (4-HBT-like enzyme). Using an intracellular tagged carrier-protein tracking (ITCT) strategy, in vitro reconstitution and in vivo experiments, we found that: i) both domains of YsfF displayed thioesterase activities; ii) YsfF/YsfFHBT could accomplish the 6π-electrocyclic ring closure for benzene ring formation; and iii) YsfF and cyclase YsfX together were responsible for the ACP-tethered dearomatization/dimerization process, possibly through an unprecedented Michael-type addition reaction. Moreover, site-directed mutagenesis experiments demonstrated that N301, E483 and H566 of YsfF are critical residues for both the 6π-electrocyclization and dimerization processes. This study enhances our understanding of the multifunctionality of the TE protein family.
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Affiliation(s)
- Zirong Deng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Chunni Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Fang Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Ni Song
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Jing Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Siyu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Wenli Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
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5
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Chen TY, Chen J, Ruszczycky MW, Hilovsky D, Hostetler T, Liu X, Zhou J, Chang WC. Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces. ACS Catal 2024; 14:4975-4983. [PMID: 38895101 PMCID: PMC11185824 DOI: 10.1021/acscatal.4c00645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A number of bacteria are known to produce isonitrile-containing peptides (INPs) that facilitate metal transport and are important for cell survival; however, considerable structural variation is observed among INPs depending on the producing organism. While non-heme iron 2-oxoglutarate dependent isonitrilases catalyze isonitrile formation, how the natural variation in INP structure is controlled and its implications for INP bioactivity remain open questions. Herein, total chemical synthesis is utilized with X-Ray crystallographic analysis of mycobacterial isonitrilases to provide a structural model of substrate specificity that explains the longer alkyl chains observed in mycobacterial versus Streptomyces INPs. Moreover, proton NMR titration experiments demonstrate that INPs regardless of alkyl chain length are specific for binding copper instead of zinc. These results suggest that isonitrilases may act as gatekeepers in modulating the observed biological distribution of INP structures and this distribution may be primarily related to differing metal transport requirements among the producing strains.
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Affiliation(s)
- Tzu-Yu Chen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dalton Hilovsky
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Tyler Hostetler
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, United States
| | - Jiahai Zhou
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
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6
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Manasra S, Kajava AV. Why does the first protein repeat often become the only one? J Struct Biol 2023; 215:108014. [PMID: 37567371 DOI: 10.1016/j.jsb.2023.108014] [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: 04/30/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023]
Abstract
Proteins with two similar motifs in tandem are one of the most common cases of tandem repeat proteins. The question arises: why is the first emerged repeat frequently fixed in the process of evolution, despite the ample opportunities to continue its multiplication at the DNA level? To answer this question, we systematically analyzed the structure and function of these proteins. Our analysis showed that, in the vast majority of cases, the structural repetitive units have a two-fold (C2) internal symmetry. These closed structures provide an internal structural limitation for the subsequent growth of the repeat number. Frequently, the units "swap" their secondary structure elements with each other. Moreover, the duplicated domains, in contrast to other tandem repeat proteins, form binding sites for small molecules around the axis of C2 symmetry. Thus, the closure of the C2 structures and the emergence of new functional sites around the axis of C2 symmetry provide plausible explanations for why a repeat, once appeared, becomes fixed in the evolutionary process. We have placed these structures within the general structural classification of tandem repeat proteins, classifying them as either Class IV or V depending on the size of the repetitive unit.
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Affiliation(s)
- Simona Manasra
- Institute of Bioengineering, ITMO University, Kronverksky Pr. 49, 197101 Saint Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France.
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7
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Patel HN, Haines BE, Stauffacher CV, Helquist P, Wiest O. Computational Study of Base-Catalyzed Thiohemiacetal Decomposition in Pseudomonas mevalonii HMG-CoA Reductase. J Phys Chem B 2023; 127:4931-4938. [PMID: 37219997 PMCID: PMC11607680 DOI: 10.1021/acs.jpcb.2c08969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Thiohemiacetals are key intermediates in the active sites of many enzymes catalyzing a variety of reactions. In the case of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase (PmHMGR), this intermediate connects the two hydride transfer steps where a thiohemiacetal is the product of the first hydride transfer and its breakdown forms the substrate of the second one, serving as the intermediate during cofactor exchange. Despite the many examples of thiohemiacetals in a variety of enzymatic reactions, there are few studies that detail their reactivity. Here, we present computational studies on the decomposition of the thiohemiacetal intermediate in PmHMGR using both QM-cluster and QM/MM models. This reaction mechanism involves a proton transfer from the substrate hydroxyl to an anionic Glu83 followed by a C-S bond elongation stabilized by a cationic His381. The reaction provides insight into the varying roles of the residues in the active site that favor this multistep mechanism.
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Affiliation(s)
- Himani N. Patel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Brandon E. Haines
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Cynthia V. Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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8
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Del Rio Flores A, Narayanamoorthy M, Cai W, Zhai R, Yang S, Shen Y, Seshadri K, De Matias K, Xue Z, Zhang W. Biosynthesis of Isonitrile Lipopeptide Metallophores from Pathogenic Mycobacteria. Biochemistry 2023; 62:824-834. [PMID: 36638317 PMCID: PMC9905339 DOI: 10.1021/acs.biochem.2c00611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Isonitrile lipopeptides (INLPs) are known to be related to the virulence of pathogenic mycobacteria by mediating metal transport, but their biosynthesis remains obscure. In this work, we use in vitro biochemical assays, site-directed mutagenesis, chemical synthesis, and spectroscopy techniques to scrutinize the activity of core enzymes required for INLP biosynthesis in mycobacteria. Compared to environmental Streptomyces, pathogenic Mycobacterium employ a similar chemical logic and enzymatic machinery in INLP biosynthesis, differing mainly in the fatty-acyl chain length, which is controlled by multiple enzymes in the pathway. Our in-depth study on the non-heme iron(II) and α-ketoglutarate-dependent dioxygenase for isonitrile generation, including Rv0097 from Mycobacterium tuberculosis (Mtb), demonstrates that it recognizes a free-standing small molecule substrate, different from the recent hypothesis that a carrier protein is required for Rv0097 in Mtb. A key residue in Rv0097 is further identified to dictate the varied fatty-acyl chain length specificity between Streptomyces and Mycobacterium.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Siyue Yang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kyle De Matias
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Zhaoqiang Xue
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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9
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Wang X, Dong ZB. A Recent Progress for the Synthesis of Thioester Compounds. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xi Wang
- Wuhan Institute of Technology School of Chemistry and Environmental Engineering 430205 Wuhan CHINA
| | - Zhi-Bing Dong
- Wuhan Institute of Technology School of Chemistry and Environmental Engeering Liufang Campus, No. 206, Guanggu 1st Road 430205 Wuhan CHINA
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10
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Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Thioesterase enzyme families: Functions, structures, and mechanisms. Protein Sci 2022; 31:652-676. [PMID: 34921469 PMCID: PMC8862431 DOI: 10.1002/pro.4263] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.
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Affiliation(s)
- Benjamin T. Caswell
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Caio C. de Carvalho
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Hung Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Monikrishna Roy
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Tin Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - David C. Cantu
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
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11
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Chen TY, Zheng Z, Zhang X, Chen J, Cha L, Tang Y, Guo Y, Zhou J, Wang B, Liu HW, Chang WC. Deciphering the Reaction Pathway of Mononuclear Iron Enzyme-Catalyzed N≡C Triple Bond Formation in Isocyanide Lipopeptide and Polyketide Biosynthesis. ACS Catal 2022; 12:2270-2279. [PMID: 35992736 PMCID: PMC9390461 DOI: 10.1021/acscatal.1c04869] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite the diversity of reactions catalyzed by 2-oxoglutarate-dependent nonheme iron (Fe/2OG) enzymes identified in recent years, only a limited number of these enzymes have been investigated in mechanistic detail. In particular, several Fe/2OG-dependent enzymes capable of catalyzing isocyanide formation have been reported. While the glycine moiety has been identified as a biosynthon for the isocyanide group, how the actual conversion is effected remains obscure. To elucidate the catalytic mechanism, we characterized two previously unidentified (AecA and AmcA) along with two known (ScoE and SfaA) Fe/2OG-dependent enzymes that catalyze N≡C triple bond installation using synthesized substrate analogues and potential intermediates. Our results indicate that isocyanide formation likely entails a two-step sequence involving an imine intermediate that undergoes decarboxylation-assisted desaturation to yield the isocyanide product. Results obtained from the in vitro experiments are further supported by mutagenesis, the product-bound enzyme structure, and in silico analysis.
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Affiliation(s)
| | | | | | - Jinfeng Chen
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jiahai Zhou
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hung-wen Liu
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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13
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Chen TY, Chen J, Tang Y, Zhou J, Guo Y, Chang WC. Current Understanding toward Isonitrile Group Biosynthesis and Mechanism. CHINESE J CHEM 2021; 39:463-472. [PMID: 34658601 PMCID: PMC8519408 DOI: 10.1002/cjoc.202000448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022]
Abstract
Isonitrile group has been identified in many natural products. Due to the broad reactivity of N≡C triple bond, these natural products have valuable pharmaceutical potentials. This review summarizes the current biosynthetic pathways and the corresponding enzymes that are responsible for isonitrile-containing natural product generation. Based on the strategies utilized, two fundamentally distinctive approaches are discussed. In addition, recent progress in elucidating isonitrile group formation mechanisms is also presented.
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Affiliation(s)
- Tzu-Yu Chen
- Department of Chemistry, North Carolina State University Raleigh, NC 27695, U.S.A
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, U.S.A
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, U.S.A
| | - Wei-chen Chang
- Department of Chemistry, North Carolina State University Raleigh, NC 27695, U.S.A
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14
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Cui Z, Overbay J, Wang X, Liu X, Zhang Y, Bhardwaj M, Lemke A, Wiegmann D, Niro G, Thorson JS, Ducho C, Van Lanen SG. Pyridoxal-5'-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis. Nat Chem Biol 2020; 16:904-911. [PMID: 32483377 PMCID: PMC7377962 DOI: 10.1038/s41589-020-0548-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/10/2020] [Indexed: 11/09/2022]
Abstract
Several nucleoside antibiotics are structurally characterized by a 5′′-amino-5′′-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside, (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origins of which have yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR-GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phophosate (PLP)-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to utilizing a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway.
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Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Xiaodong Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Yinan Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.
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15
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Kawasaki D, Miyanaga A, Chisuga T, Kudo F, Eguchi T. Functional and Structural Analyses of the Split-Dehydratase Domain in the Biosynthesis of Macrolactam Polyketide Cremimycin. Biochemistry 2019; 58:4799-4803. [DOI: 10.1021/acs.biochem.9b00897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Kawasaki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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16
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Kawasaki D, Chisuga T, Miyanaga A, Kudo F, Eguchi T. Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a β-Amino Acid Starter Unit in Cremimycin Biosynthesis. Biochemistry 2019; 58:2706-2709. [PMID: 31154757 DOI: 10.1021/acs.biochem.9b00444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The flavin adenine dinucleotide-dependent oxidase CmiS2 catalyzes the oxidation of N-carboxymethyl-3-aminononanoic acid to produce a 3-aminononanoic acid starter unit for the biosynthesis of cremimycin, a macrolactam polyketide. Although the sequence of CmiS2 is similar with that of the well-characterized glycine oxidase ThiO, the chemical structure of the substrate of CmiS2 is different from that of ThiO substrate glycine. Here, we present the biochemical and structural characterization of CmiS2. Kinetic analysis revealed that CmiS2 has a strong preference for N-carboxymethyl-3-aminononanoic acid over other substrates such as N-carboxymethyl-3-aminobutanoic acid and glycine, suggesting that CmiS2 recognizes the nonanoic acid moiety of the substrate as well as the glycine moiety. We determined the crystal structure of CmiS2 in complex with a substrate analogue, namely, S-carboxymethyl-3-thiononanoic acid, which enabled the identification of key amino acid residues involved in substrate recognition. We discovered that Asn49, Arg243, and Arg334 interact with the carboxyl group of the nonanoic acid moiety, while Pro46, Leu52, and Ile335 recognize the alkyl chain of the nonanoic acid moiety via hydrophobic interaction. These residues are highly conserved in CmiS2 homologues involved in the biosynthesis of related macrolactam polyketides but are not conserved in glycine oxidases such as ThiO. These results suggest that CmiS2-type enzymes employ a distinct mechanism of substrate recognition for the synthesis of β-amino acids.
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Affiliation(s)
- Daisuke Kawasaki
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Taichi Chisuga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Fumitaka Kudo
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Tadashi Eguchi
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
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17
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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18
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Harris NC, Born DA, Cai W, Huang Y, Martin J, Khalaf R, Drennan CL, Zhang W. Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase. Angew Chem Int Ed Engl 2018; 57:9707-9710. [PMID: 29906336 DOI: 10.1002/anie.201804307] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 01/11/2023]
Abstract
The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.
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Affiliation(s)
- Nicholas C Harris
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - David A Born
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Yaobing Huang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Joelle Martin
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Ryan Khalaf
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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19
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Harris NC, Born DA, Cai W, Huang Y, Martin J, Khalaf R, Drennan CL, Zhang W. Isonitrile Formation by a Non‐Heme Iron(II)‐Dependent Oxidase/Decarboxylase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nicholas C. Harris
- Department of Plant and Microbial Biology University of California Berkeley Berkeley CA 94720 USA
| | - David A. Born
- Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 USA
- Graduate Program in Biophysics Harvard University Cambridge MA 02138 USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley CA 94720 USA
| | - Yaobing Huang
- Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley CA 94720 USA
| | - Joelle Martin
- Department of Chemistry University of California Berkeley Berkeley CA 94720 USA
| | - Ryan Khalaf
- Department of Chemistry University of California Berkeley Berkeley CA 94720 USA
| | - Catherine L. Drennan
- Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 USA
- Howard Hughes Medical Institute Massachusetts Institute of Technology Cambridge MA 02139 USA
- Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley CA 94720 USA
- Chan Zuckerberg Biohub San Francisco CA 94158 USA
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20
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Miyanaga A. Structure and function of polyketide biosynthetic enzymes: various strategies for production of structurally diverse polyketides. Biosci Biotechnol Biochem 2017; 81:2227-2236. [DOI: 10.1080/09168451.2017.1391687] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Polyketides constitute a large family of natural products that display various biological activities. Polyketides exhibit a high degree of structural diversity, although they are synthesized from simple acyl building blocks. Recent biochemical and structural studies provide a better understanding of the biosynthetic logic of polyketide diversity. This review highlights the biosynthetic mechanisms of structurally unique polyketides, β-amino acid-containing macrolactams, enterocin, and phenolic lipids. Functional and structural studies of macrolactam biosynthetic enzymes have revealed the unique biosynthetic machinery used for selective incorporation of a rare β-amino acid starter unit into the polyketide skeleton. Biochemical and structural studies of cyclization enzymes involved in the biosynthesis of enterocin and phenolic lipids provide mechanistic insights into how these enzymes diversify the carbon skeletons of their products.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
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