1
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Zheng C, Wei W, Wen J, Song W, Wu J, Wang R, Yin D, Chen X, Gao C, Liu J, Liu L. Rational Design of the Spatial Effect in a Fe(II)/α-Ketoglutarate-Dependent Dioxygenase Reverses the Regioselectivity of C(sp 3)-H Bond Hydroxylation in Aliphatic Amino Acids. Angew Chem Int Ed Engl 2024:e202406060. [PMID: 38789390 DOI: 10.1002/anie.202406060] [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: 03/29/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024]
Abstract
The hydroxylation of remote C(sp3)-H bonds in aliphatic amino acids yields crucial precursors for the synthesis of high-value compounds. However, accurate regulation of the regioselectivity of remote C(sp3)-H bonds hydroxylation in aliphatic amino acids continues to be a common challenge in chemosynthesis and biosynthesis. In this study, the Fe(II)/α-ketoglutarate-dependent dioxygenase from Bacillus subtilis (BlAH) was mined and found to catalyze hydroxylation at the γ and δ sites of aliphatic amino acids. Crystal structure analysis, molecular dynamics simulations, and quantum chemical calculations revealed that regioselectivity was regulated by the spatial effect of BlAH. Based on these results, the spatial effect of BlAH was reconstructed to stabilize the transition state at the δ site of aliphatic amino acids, thereby successfully reversing the γ site regioselectivity to the δ site. For example, the regioselectivity of L-Homoleucine (5 a) was reversed from the γ site (1 : 12) to the δ site (>99 : 1). The present study not only expands the toolbox of biocatalysts for the regioselective functionalization of remote C(sp3)-H bonds, but also provides a theoretical guidance for the precision-driven modification of similarly remote C(sp3)-H bonds in complex molecules.
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Affiliation(s)
- Chenni Zheng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Ran Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Dejing Yin
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
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2
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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3
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Guan J, Lu Y, Dai Z, Zhao S, Xu Y, Nie Y. R97 at "Handlebar" Binding Mode in Active Pocket Plays an Important Role in Fe(II)/α-Ketoglutaric Acid-Dependent Dioxygenase cis-P3H-Mediated Selective Synthesis of (2S,3R)-3-Hydroxypipecolic Acid. Molecules 2023; 28:molecules28041854. [PMID: 36838840 PMCID: PMC9968057 DOI: 10.3390/molecules28041854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Pipecolic acid (Pip) and its derivative hydroxypipecolic acids, such as (2S,3R)-3-hydroxypipecolic acid (cis-3-L-HyPip), are components of many natural and synthetic bioactive molecules. Fe(II)/α-ketoglutaric acid (Fe(II)/2-OG)-dependent dioxygenases can catalyze the hydroxylation of pipecolic acid. However, the available enzymes with desired activity and selectivity are limited. Herein, we compare the possible candidates in the Fe(II)/2-OG-dependent dioxygenase family, and cis-P3H is selected for potentially catalyzing selective hydroxylation of L-Pip. cis-P3H was further engineered to increase its catalytic efficiency toward L-Pip. By analyzing the structural confirmation and residue composition in substrate-binding pocket, a "handlebar" mode of molecular interactions is proposed. Using molecular docking, virtual mutation analysis, and dynamic simulations, R97, E112, L57, and G282 were identified as the key residues for subsequent site-directed saturation mutagenesis of cis-P3H. Consequently, the variant R97M showed an increased catalytic efficiency toward L-Pip. In this study, the kcat/Km value of the positive mutant R97M was about 1.83-fold that of the wild type. The mutation R97M would break the salt bridge between R97 and L-Pip and weaken the positive-positive interaction between R97 and R95. Therefore, the force on the amino and carboxyl groups of L-Pip was lightly balanced, allowing the molecule to be stabilized in the active pocket. These results provide a potential way of improving cis-P3H catalytic activity through rational protein engineering.
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Affiliation(s)
- Jiaojiao Guan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yilei Lu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Zixuan Dai
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Songyin Zhao
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China
- Correspondence:
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4
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Wu L, An J, Jing X, Chen CC, Dai L, Xu Y, Liu W, Guo RT, Nie Y. Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lunjie Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianhong An
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Ophthalmology and Optometry, and Eye Hospital, Wenzhou Medical University, State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang 325000, China
| | - Xiaoran Jing
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
- Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, Jiangsu 223814, China
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5
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Zhang X, Ma W, Zhang J, Tang W, Xue D, Xiao J, Sun H, Wang C. Asymmetric Ruthenium‐Catalyzed Hydroalkylation of Racemic Allylic Alcohols for the Synthesis of Chiral Amino Acid Derivatives. Angew Chem Int Ed Engl 2022; 61:e202203244. [DOI: 10.1002/anie.202203244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 01/07/2023]
Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Wei Ma
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
- School of Basic Medical Science Ningxia Medical University Yinchuan 750004 China
| | - Jinyu Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Weijun Tang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Dong Xue
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Jianliang Xiao
- Department of Chemistry University of Liverpool Liverpool L69 7ZD UK
| | - Huaming Sun
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Chao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
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6
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Charlton SN, Hayes MA. Oxygenating Biocatalysts for Hydroxyl Functionalisation in Drug Discovery and Development. ChemMedChem 2022; 17:e202200115. [PMID: 35385205 PMCID: PMC9323455 DOI: 10.1002/cmdc.202200115] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Indexed: 11/12/2022]
Abstract
C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.
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Affiliation(s)
- Sacha N. Charlton
- School of ChemistryUniversity of Bristol, Cantock's CloseBristolBS8 1TSUK
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery SciencesBiopharmaceuticals R&DAstraZenecaGothenburgSweden
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7
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Zhang X, Ma W, Zhang J, Tang W, Xue D, Xiao J, Sun H, Wang C. Asymmetric Ruthenium‐Catalyzed Hydroalkylation of Racemic Allylic Alcohols for the Synthesis of Chiral Amino Acid Derivatives. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Wei Ma
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
- School of Basic Medical Science Ningxia Medical University Yinchuan 750004 China
| | - Jinyu Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Weijun Tang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Dong Xue
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Jianliang Xiao
- Department of Chemistry University of Liverpool Liverpool L69 7ZD UK
| | - Huaming Sun
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
| | - Chao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 China
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8
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Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nat Commun 2022; 13:1595. [PMID: 35332143 PMCID: PMC8948231 DOI: 10.1038/s41467-022-29216-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/02/2022] [Indexed: 11/09/2022] Open
Abstract
Diols encompass important bulk and fine chemicals for the chemical, pharmaceutical and cosmetic industries. During the past decades, biological production of C3-C5 diols from renewable feedstocks has received great interest. Here, we elaborate a general principle for effectively synthesizing structurally diverse diols by expanding amino acid metabolism. Specifically, we propose to combine oxidative and reductive formations of hydroxyl groups from amino acids in a thermodynamically favorable order of four reactions catalyzed by amino acid hydroxylase, L-amino acid deaminase, α-keto acid decarboxylase and aldehyde reductase consecutively. The oxidative formation of hydroxyl group from an alkyl group is energetically more attractive than the reductive pathway, which is exclusively used in the synthetic pathways of diols reported so far. We demonstrate this general route for microbial production of branched-chain diols in E. coli. Ten C3-C5 diols are synthesized. Six of them, namely isopentyldiol (IPDO), 2-methyl-1,3-butanediol (2-M-1,3-BDO), 2-methyl-1,4-butanediol (2-M-1,4-BDO), 2-methyl-1,3-propanediol (MPO), 2-ethyl-1,3-propanediol (2-E-1,3-PDO), 1,4-pentanediol (1,4-PTD), have not been biologically synthesized before. This work opens up opportunities for synthesizing structurally diverse diols and triols, especially by genome mining, rational design or directed evolution of proper enzymes. Diols are important bulk and fine chemicals, but bioproduciton of branch-chain diols is hampered by the unknown biological route. Here, the authors report the expanding of amino acid metabolism for biosynthesis of branch-chain diols via a general route of combined oxidative and reductive formations of hydroxyl groups.
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9
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Cui Z, Nguyen H, Bhardwaj M, Wang X, Büschleb M, Lemke A, Schütz C, Rohrbacher C, Junghanns P, Koppermann S, Ducho C, Thorson JS, Van Lanen SG. Enzymatic C β-H Functionalization of l-Arg and l-Leu in Nonribosomally Derived Peptidyl Natural Products: A Tale of Two Oxidoreductases. J Am Chem Soc 2021; 143:19425-19437. [PMID: 34767710 DOI: 10.1021/jacs.1c08177] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Muraymycins are peptidyl nucleoside antibiotics that contain two Cβ-modified amino acids, (2S,3S)-capreomycidine and (2S,3S)-β-OH-Leu. The former is also a component of chymostatins, which are aldehyde-containing peptidic protease inhibitors that─like muraymycin─are derived from nonribosomal peptide synthetases (NRPSs). Using feeding experiments and in vitro characterization of 12 recombinant proteins, the biosynthetic mechanism for both nonproteinogenic amino acids is now defined. The formation of (2S,3S)-capreomycidine is shown to involve an FAD-dependent dehydrogenase:cyclase that requires an NRPS-bound pathway intermediate as a substrate. This cryptic dehydrogenation strategy is both temporally and mechanistically distinct in comparison to the biosynthesis of other capreomycidine diastereomers, which has previously been shown to proceed by Cβ-hydroxylation of free l-Arg catalyzed by a member of the nonheme Fe2+- and α-ketoglutarate (αKG)-dependent dioxygenase family and (eventually) a dehydration-mediated cyclization process catalyzed by a distinct enzyme(s). Contrary to our initial expectation, the sole nonheme Fe2+- and αKG-dependent dioxygenase candidate Mur15 encoded within the muraymycin gene cluster is instead demonstrated to catalyze specific Cβ hydroxylation of the Leu residue to generate (2S,3S)-β-OH-Leu that is found in most muraymycin congeners. Importantly, and in contrast to known l-Arg-Cβ-hydroxylases, the Mur15-catalyzed reaction occurs after the NRPS-mediated assembly of the peptide scaffold. This late-stage functionalization affords the opportunity to exploit Mur15 as a biocatalyst, proof of concept of which is provided.
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Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Han Nguyen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Xiachang Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Martin Büschleb
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University, GöTammannstr. 2, 37077 Göttingen, Germany
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Schütz
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Rohrbacher
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Pierre Junghanns
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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Enzymatic Synthesis of l- threo-β-Hydroxy-α-Amino Acids via Asymmetric Hydroxylation Using 2-Oxoglutarate-Dependent Hydroxylase from Sulfobacillus thermotolerans Y0017. Appl Environ Microbiol 2021; 87:e0133521. [PMID: 34347519 DOI: 10.1128/aem.01335-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
β-Hydroxy-α-amino acids are useful compounds for pharmaceutical development. Enzymatic synthesis of β-hydroxy-α-amino acids has attracted considerable interest as a selective, sustainable, and environmentally benign process. In this study, we identified a novel amino acid hydroxylase, AEP14369, from Sulfobacillus thermotolerans Y0017, which is included in a previously constructed CAS-like superfamily protein library, to widen the variety of amino acid hydroxylases. The detailed structures determined by nuclear magnetic resonance and X-ray crystallography analysis of the enzymatically produced compounds revealed that AEP14369 catalyzed threo-β-selective hydroxylation of l-His and l-Gln in a 2-oxoglutarate-dependent manner. Furthermore, the production of l-threo-β-hydroxy-His and l-threo-β-hydroxy-Gln was achieved using Escherichia coli expressing the gene encoding AEP14369 as a whole-cell biocatalyst. Under optimized reaction conditions, 137 mM (23.4 g L-1) l-threo-β-hydroxy-His and 150 mM l-threo-β-hydroxy-Gln (24.3 g L-1) were obtained, indicating that the enzyme is applicable for preparative-scale production. AEP14369, an l-His/l-Gln threo-β-hydroxylase, increases the availability of 2-oxoglutarate-dependent hydroxylase and opens the way for the practical production of β-hydroxy-α-amino acids in the future. The amino acids produced in this study would also contribute to the structural diversification of pharmaceuticals that affect important bioactivities. Importance Owing to an increasing concern for sustainability, enzymatic approaches for producing industrially useful compounds have attracted considerable attention as a powerful complement to chemical synthesis for environment-friendly synthesis. In this study, we developed a bioproduction method for β-hydroxy-α-amino acid synthesis using a newly discovered enzyme. AEP14369 from the moderate thermophilic bacterium Sulfobacillus thermotolerans Y0017 catalyzed the hydroxylation of l-His and l-Gln in a regioselective and stereoselective fashion. Furthermore, we biotechnologically synthesized both l-threo-β-hydroxy-His and l-threo-β-hydroxy-Gln with a titer of over 20 g L-1 through whole-cell bioconversion using recombinant Escherichia coli cells. As β-hydroxy-α-amino acids are important compounds for pharmaceutical development, this achievement would facilitate future sustainable and economical industrial applications.
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11
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Heinilä LMP, Fewer DP, Jokela JK, Wahlsten M, Ouyang X, Permi P, Jortikka A, Sivonen K. The structure and biosynthesis of heinamides A1-A3 and B1-B5, antifungal members of the laxaphycin lipopeptide family. Org Biomol Chem 2021; 19:5577-5588. [PMID: 34085692 DOI: 10.1039/d1ob00772f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Laxaphycins are a family of cyclic lipopeptides with synergistic antifungal and antiproliferative activities. They are produced by multiple cyanobacterial genera and comprise two sets of structurally unrelated 11- and 12-residue macrocyclic lipopeptides. Here, we report the discovery of new antifungal laxaphycins from Nostoc sp. UHCC 0702, which we name heinamides, through antimicrobial bioactivity screening. We characterized the chemical structures of eight heinamide structural variants A1-A3 and B1-B5. These variants contain the rare non-proteinogenic amino acids 3-hydroxy-4-methylproline, 4-hydroxyproline, 3-hydroxy-d-leucine, dehydrobutyrine, 5-hydroxyl β-amino octanoic acid, and O-carbamoyl-homoserine. We obtained an 8.6-Mb complete genome sequence from Nostoc sp. UHCC 0702 and identified the 93 kb heinamide biosynthetic gene cluster. The structurally distinct heinamides A1-A3 and B1-B5 variants are synthesized using an unusual branching biosynthetic pathway. The heinamide biosynthetic pathway also encodes several enzymes that supply non-proteinogenic amino acids to the heinamide synthetase. Through heterologous expression, we showed that (2S,4R)-4-hydroxy-l-proline is supplied through the action of a novel enzyme LxaN, which hydroxylates l-proline. 11- and 12-residue heinamides have the characteristic synergistic activity of laxaphycins against Aspergillus flavus FBCC 2467. Structural and genetic information of heinamides may prove useful in future discovery of natural products and drug development.
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Affiliation(s)
| | - David Peter Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Jouni Kalevi Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Xiaodan Ouyang
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland and Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Anna Jortikka
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
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12
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Stout CN, Renata H. Reinvigorating the Chiral Pool: Chemoenzymatic Approaches to Complex Peptides and Terpenoids. Acc Chem Res 2021; 54:1143-1156. [PMID: 33543931 DOI: 10.1021/acs.accounts.0c00823] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biocatalytic transformations that leverage the selectivity and efficiency of enzymes represent powerful tools for the construction of complex natural products. Enabled by innovations in genome mining, bioinformatics, and enzyme engineering, synthetic chemists are now more than ever able to develop and employ enzymes to solve outstanding chemical problems, one of which is the reliable and facile generation of stereochemistry within natural product scaffolds. In recognition of this unmet need, our group has sought to advance novel chemoenzymatic strategies to both expand and reinvigorate the chiral pool. Broadly defined, the chiral pool comprises cheap, enantiopure feedstock chemicals that serve as popular foundations for asymmetric total synthesis. Among these building blocks, amino acids and enantiopure terpenes, whose core structures can be mapped onto several classes of structurally and pharmaceutically intriguing natural products, are of particular interest to the synthetic community.In this Account, we summarize recent efforts from our group in leveraging biocatalytic transformations to expand the chiral pool, as well as efforts toward the efficient application of these transformations in natural products total synthesis, the ultimate testing ground for any novel methodology. First, we describe several examples of enzymatic generation of noncanonical amino acids as means to simplify the synthesis of peptide natural products. By extracting amino acid hydroxylases from native biosynthetic pathways, we obtain efficient access to hydroxylated variants of proline, lysine, arginine, and their derivatives. The newly installed hydroxyl moiety then becomes a chemical handle that can facilitate additional complexity generation, thereby expanding the pool of amino acid-derived building blocks available for peptide synthesis. Next, we present our efforts in enzymatic C-H oxidations of diverse terpene scaffolds, in which traditional chemistry can be combined with strategic applications of biocatalysis to selectively and efficiently derivatize several commercial terpenoid skeletons. The synergistic logic of this approach enables a small handful of synthetic intermediates to provide access to a plethora of terpenoid natural product families. Taken together, these findings demonstrate the advantages of applying enzymes in total synthesis in conjunction with established methodologies, as well as toward the expansion of the chiral pool to enable facile incorporation of stereochemistry during synthetic campaigns.
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Affiliation(s)
- Carter N. Stout
- Department of Chemistry, Scripps Research, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, Scripps Research, 110 Scripps Way, Jupiter, Florida 33458, United States
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13
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Renata H. Exploration of Iron- and a-Ketoglutarate-Dependent Dioxygenases as Practical Biocatalysts in Natural Product Synthesis. Synlett 2021; 32:775-784. [PMID: 34413574 PMCID: PMC8372184 DOI: 10.1055/s-0040-1707320] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Catalytic C─H oxidation is a powerful transformation with enormous promise to streamline access to complex molecules. In recent years, biocatalytic C─H oxidation strategies have received tremendous attention due to their potential to address unmet regio- and stereoselectivity challenges that are often encountered with the use of small-molecule-based catalysts. This Account provides an overview of recent contributions from our laboratory in this area, specifically in the use of iron- and α-ketoglutarate-dependent dioxygenases in the chemoenzymatic synthesis of complex natural products.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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14
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Cha L, Milikisiyants S, Davidson M, Xue S, Smirnova T, Smirnov A, Guo Y, Chang WC. Alternative Reactivity of Leucine 5-Hydroxylase Using an Olefin-Containing Substrate to Construct a Substituted Piperidine Ring. Biochemistry 2020; 59:1961-1965. [PMID: 32401494 DOI: 10.1021/acs.biochem.0c00289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Applying enzymatic reactions to produce useful molecules is a central focus of chemical biology. Iron and 2-oxoglutarate (Fe/2OG) enzymes are found in all kingdoms of life and catalyze a broad array of oxidative transformations. Herein, we demonstrate that the activity of an Fe/2OG enzyme can be redirected when changing the targeted carbon hybridization from sp3 to sp2. During leucine 5-hydroxylase catalysis, installation of an olefin group onto the substrate redirects the Fe(IV)-oxo species reactivity from hydroxylation to asymmetric epoxidation. The resulting epoxide subsequently undergoes intramolecular cyclization to form the substituted piperidine, 2S,5S-hydroxypipecolic acid.
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Affiliation(s)
- Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Madison Davidson
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shan Xue
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Tatyana Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alex Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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15
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Hara R, Kino K. Enzymatic reactions and microorganisms producing the various isomers of hydroxyproline. Appl Microbiol Biotechnol 2020; 104:4771-4779. [PMID: 32291491 DOI: 10.1007/s00253-020-10603-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023]
Abstract
Hydroxyproline is an industrially important compound with applications in the pharmaceutical, nutrition, and cosmetic industries. trans-4-Hydroxy-L-proline is recognized as the most abundant of the eight possible isomers (hydroxy group at C-3 or C-4, cis- or trans-configuration, and L- or D-form). However, little attention has been paid to the rare isomers, probably due to their limited availability. This mini-review provides an overview of recent advances in microbial and enzymatic processes to develop practical production strategies for various hydroxyprolines. Here, we introduce three screening strategies, namely, activity-, sequence-, and metabolite-based approaches, allowing identification of diverse proline-hydroxylating enzymes with different product specificities. All naturally occurring hydroxyproline isomers can be produced by using suitable hydroxylases in a highly regio- and stereo-selective manner. Furthermore, crystal structures of relevant hydroxylases provide much insight into their functional roles. Since hydroxylases acting on free L-proline belong to the 2-oxoglutarate-dependent dioxygenase superfamily, cellular metabolism of Escherichia coli coupled with a hydroxylase is a valuable source of 2-oxoglutarate, which is indispensable as a co-substrate in L-proline hydroxylation. Further, microbial hydroxyproline 2-epimerase may serve as a highly adaptable tool to convert L-hydroxyproline into D-hydroxyproline. KEY POINTS: • Proline hydroxylases serve as powerful tools for selectivel-proline hydroxylation. • Engineered Escherichia coli are a robust platform for hydroxyproline production. • Hydroxyproline epimerase convertsl-hydroxyproline intod-hydroxyproline.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan. .,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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16
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The ADEP Biosynthetic Gene Cluster in Streptomyces hawaiiensis NRRL 15010 Reveals an Accessory clpP Gene as a Novel Antibiotic Resistance Factor. Appl Environ Microbiol 2019; 85:AEM.01292-19. [PMID: 31399403 DOI: 10.1128/aem.01292-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023] Open
Abstract
The increasing threat posed by multiresistant bacterial pathogens necessitates the discovery of novel antibacterials with unprecedented modes of action. ADEP1, a natural compound produced by Streptomyces hawaiiensis NRRL 15010, is the prototype for a new class of acyldepsipeptide (ADEP) antibiotics. ADEP antibiotics deregulate the proteolytic core ClpP of the bacterial caseinolytic protease, thereby exhibiting potent antibacterial activity against Gram-positive bacteria, including multiresistant pathogens. ADEP1 and derivatives, here collectively called ADEP, have been previously investigated for their antibiotic potency against different species, structure-activity relationship, and mechanism of action; however, knowledge on the biosynthesis of the natural compound and producer self-resistance have remained elusive. In this study, we identified and analyzed the ADEP biosynthetic gene cluster in S. hawaiiensis NRRL 15010, which comprises two NRPSs, genes necessary for the biosynthesis of (4S,2R)-4-methylproline, and a type II polyketide synthase (PKS) for the assembly of highly reduced polyenes. While no resistance factor could be identified within the gene cluster itself, we discovered an additional clpP homologous gene (named clpP ADEP) located further downstream of the biosynthetic genes, separated from the biosynthetic gene cluster by several transposable elements. Heterologous expression of ClpPADEP in three ADEP-sensitive Streptomyces species proved its role in conferring ADEP resistance, thereby revealing a novel type of antibiotic resistance determinant.IMPORTANCE Antibiotic acyldepsipeptides (ADEPs) represent a promising new class of potent antibiotics and, at the same time, are valuable tools to study the molecular functioning of their target, ClpP, the proteolytic core of the bacterial caseinolytic protease. Here, we present a straightforward purification procedure for ADEP1 that yields substantial amounts of the pure compound in a time- and cost-efficient manner, which is a prerequisite to conveniently study the antimicrobial effects of ADEP and the operating mode of bacterial ClpP machineries in diverse bacteria. Identification and characterization of the ADEP biosynthetic gene cluster in Streptomyces hawaiiensis NRRL 15010 enables future bioinformatics screenings for similar gene clusters and/or subclusters to find novel natural compounds with specific substructures. Most strikingly, we identified a cluster-associated clpP homolog (named clpP ADEP) as an ADEP resistance gene. ClpPADEP constitutes a novel bacterial resistance factor that alone is necessary and sufficient to confer high-level ADEP resistance to Streptomyces across species.
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Abstract
C–H functionalization is a chemically challenging but highly desirable transformation. 2-oxoglutarate-dependent oxygenases (2OGXs) are remarkably versatile biocatalysts for the activation of C–H bonds. In nature, they have been shown to accept both small and large molecules carrying out a plethora of reactions, including hydroxylations, demethylations, ring formations, rearrangements, desaturations, and halogenations, making them promising candidates for industrial manufacture. In this review, we describe the current status of 2OGX use in biocatalytic applications concentrating on 2OGX-catalyzed oxyfunctionalization of amino acids and synthesis of antibiotics. Looking forward, continued bioinformatic sourcing will help identify additional, practical useful members of this intriguing enzyme family, while enzyme engineering will pave the way to enhance 2OGX reactivity for non-native substrates.
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18
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Davidson M, McNamee M, Fan R, Guo Y, Chang WC. Repurposing Nonheme Iron Hydroxylases To Enable Catalytic Nitrile Installation through an Azido Group Assistance. J Am Chem Soc 2019; 141:3419-3423. [PMID: 30759343 DOI: 10.1021/jacs.8b13906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three mononuclear nonheme iron and 2-oxoglutarate dependent enzymes, l-Ile 4-hydroxylase, l-Leu 5-hydroxylase and polyoxin dihydroxylase, are previously reported to catalyze the hydroxylation of l-isoleucine, l-leucine, and l-α-amino-δ-carbamoylhydroxyvaleric acid (ACV). In this study, we showed that these enzymes can accommodate leucine isomers and catalyze regiospecific hydroxylation. On the basis of these results, as a proof-of-concept, we demonstrated that the outcome of the reaction can be redirected by installation of an assisting group within the substrate. Specifically, instead of canonical hydroxylation, these enzymes can catalyze non-native nitrile group installation when an azido group is introduced. The reaction is likely to proceed through C-H bond activation by an Fe(IV)-oxo species, followed by azido-directed C≡N bond formation. These results offer a unique opportunity to investigate and expand the reaction repertoire of Fe/2OG enzymes.
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Affiliation(s)
- Madison Davidson
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Meredith McNamee
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Ruixi Fan
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Yisong Guo
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Wei-Chen Chang
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695 , United States
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19
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Sun D, Gao D, Liu X, Zhu M, Li C, Chen Y, Zhu Z, Lu F, Qin HM. Redesign and engineering of a dioxygenase targeting biocatalytic synthesis of 5-hydroxyl leucine. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00110g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The protein engineering and metabolic engineering strategies are performed to solve rate-limiting steps in the biosynthesis of 5-HLeu.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Dengke Gao
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Xin Liu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Menglu Zhu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Chao Li
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Ying Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
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20
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Correia Cordeiro RS, Enoki J, Busch F, Mügge C, Kourist R. Cloning and characterization of a new delta-specific l-leucine dioxygenase from Anabaena variabilis. J Biotechnol 2018; 284:68-74. [DOI: 10.1016/j.jbiotec.2018.07.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 11/24/2022]
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21
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Sun D, Gao D, Xu P, Guo Q, Zhu Z, Cheng X, Bai S, Qin HM, Lu F. A novel l -leucine 5-hydroxylase from Nostoc piscinale unravels unexpected sulfoxidation activity toward l -methionine. Protein Expr Purif 2018; 149:1-6. [DOI: 10.1016/j.pep.2018.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/13/2018] [Indexed: 01/21/2023]
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22
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Zwick CR, Renata H. Evolution of Biocatalytic and Chemocatalytic C–H Functionalization Strategy in the Synthesis of Manzacidin C. J Org Chem 2018; 83:7407-7415. [DOI: 10.1021/acs.joc.8b00248] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christian R. Zwick
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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23
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Zwick CR, Renata H. Remote C-H Hydroxylation by an α-Ketoglutarate-Dependent Dioxygenase Enables Efficient Chemoenzymatic Synthesis of Manzacidin C and Proline Analogs. J Am Chem Soc 2018; 140:1165-1169. [PMID: 29283572 DOI: 10.1021/jacs.7b12918] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective C-H functionalization at distal positions remains a highly challenging problem in organic synthesis. Though Nature has evolved a myriad of enzymes capable of such feat, their synthetic utility has largely been overlooked. Here, we functionally characterize an α-ketoglutarate-dependent dioxygenase (Fe/αKG) that selectively hydroxylates the δ position of various aliphatic amino acids. Kinetic analysis and substrate profiling of the enzyme show superior catalytic efficiency and substrate promiscuity relative to other Fe/αKGs that catalyze similar reactions. We demonstrate the practical utility of this transformation in the concise syntheses of a rare alkaloid, manzacidin C, and densely substituted amino acid derivatives with remarkable step efficiency. This work provides a blueprint for future applications of Fe/αKG hydroxylation in complex molecule synthesis and the development of powerful synthetic paradigms centered on enzymatic C-H functionalization logic.
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Affiliation(s)
- Christian R Zwick
- Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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24
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Lukat P, Katsuyama Y, Wenzel S, Binz T, König C, Blankenfeldt W, Brönstrup M, Müller R. Biosynthesis of methyl-proline containing griselimycins, natural products with anti-tuberculosis activity. Chem Sci 2017; 8:7521-7527. [PMID: 29163906 PMCID: PMC5676206 DOI: 10.1039/c7sc02622f] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
Griselimycins (GMs) are depsidecapeptides with superb anti-tuberculosis activity. They contain up to three (2S,4R)-4-methyl-prolines (4-MePro), of which one blocks oxidative degradation and increases metabolic stability in animal models. The natural congener with this substitution is only a minor component in fermentation cultures. We showed that this product can be significantly increased by feeding the reaction with 4-MePro and we investigated the molecular basis of 4-MePro biosynthesis and incorporation. We identified the GM biosynthetic gene cluster as encoding a nonribosomal peptide synthetase and a sub-operon for 4-MePro formation. Using heterologous expression, gene inactivation, and in vitro experiments, we showed that 4-MePro is generated by leucine hydroxylation, oxidation to an aldehyde, and ring closure with subsequent reduction. The crystal structures of the leucine hydroxylase GriE have been determined in complex with substrates and products, providing insight into the stereospecificity of the reaction.
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Affiliation(s)
- Peer Lukat
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbrücken , Germany . .,Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstr. 7 , 38124 Braunschweig , Germany
| | - Yohei Katsuyama
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbrücken , Germany . .,German Centre for Infection Research Association (DZIF) , Partner site Hannover-Braunschweig , Germany
| | - Silke Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbrücken , Germany . .,German Centre for Infection Research Association (DZIF) , Partner site Hannover-Braunschweig , Germany
| | - Tina Binz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbrücken , Germany . .,German Centre for Infection Research Association (DZIF) , Partner site Hannover-Braunschweig , Germany
| | - Claudia König
- Sanofi Aventis Deutschland , Industriepark Höchst , 65926 Frankfurt , Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstr. 7 , 38124 Braunschweig , Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics , Technische Universität Braunschweig , Spielmannstr. 7 , 38106 Braunschweig , Germany
| | - Mark Brönstrup
- Department for Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstr. 7 , 38124 Braunschweig , Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbrücken , Germany . .,German Centre for Infection Research Association (DZIF) , Partner site Hannover-Braunschweig , Germany
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25
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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26
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Enoki J, Meisborn J, Müller AC, Kourist R. A Multi-Enzymatic Cascade Reaction for the Stereoselective Production of γ-Oxyfunctionalyzed Amino Acids. Front Microbiol 2016; 7:425. [PMID: 27092111 PMCID: PMC4823265 DOI: 10.3389/fmicb.2016.00425] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/16/2016] [Indexed: 11/26/2022] Open
Abstract
A stereoselective three-enzyme cascade for synthesis of diasteromerically pure γ-oxyfunctionalized α-amino acids was developed. By coupling a dynamic kinetic resolution (DKR) using an N-acylamino acid racemase (NAAAR) and an L-selective aminoacylase from Geobacillus thermoglucosidasius with a stereoselective isoleucine dioxygenase from Bacillus thuringiensis, diastereomerically pure oxidized amino acids were produced from racemic N-acetylamino acids. The three enzymes differed in their optimal temperature and pH-spectra. Their different metal cofactor dependencies led to inhibitory effects. Under optimized conditions, racemic N-acetylmethionine was quantitatively converted into L-methionine-(S)-sulfoxide with 97% yield and 95% de. The combination of these three different biocatalysts allowed the direct synthesis of diastereopure oxyfunctionalized amino acids from inexpensive racemic starting material.
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Affiliation(s)
- Junichi Enoki
- Faculty of Biology and Biotechnology, Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Jaqueline Meisborn
- Faculty of Biology and Biotechnology, Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Ann-Christin Müller
- Faculty of Biology and Biotechnology, Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
| | - Robert Kourist
- Faculty of Biology and Biotechnology, Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum Bochum, Germany
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27
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Novel Enzyme Family Found in Filamentous Fungi Catalyzing trans-4-Hydroxylation of L-Pipecolic Acid. Appl Environ Microbiol 2016; 82:2070-2077. [PMID: 26801577 DOI: 10.1128/aem.03764-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/19/2016] [Indexed: 11/20/2022] Open
Abstract
Hydroxypipecolic acids are bioactive compounds widely distributed in nature and are valuable building blocks for the organic synthesis of pharmaceuticals. We have found a novel hydroxylating enzyme with activity toward L-pipecolic acid (L-Pip) in a filamentous fungus, Fusarium oxysporum c8D. The enzyme L-Pip trans-4-hydroxylase (Pip4H) of F. oxysporum (FoPip4H) belongs to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily, catalyzes the regio- and stereoselective hydroxylation of L-Pip, and produces optically pure trans-4-hydroxy-L-pipecolic acid (trans-4-L-HyPip). Amino acid sequence analysis revealed several fungal enzymes homologous with FoPip4H, and five of these also had L-Pip trans-4-hydroxylation activity. In particular, the homologous Pip4H enzyme derived from Aspergillus nidulans FGSC A4 (AnPip4H) had a broader substrate specificity spectrum than other homologues and reacted with the L and D forms of various cyclic and aliphatic amino acids. Using FoPip4H as a biocatalyst, a system for the preparative-scale production of chiral trans-4-L-HyPip was successfully developed. Thus, we report a fungal family of L-Pip hydroxylases and the enzymatic preparation of trans-4-L-HyPip, a bioactive compound and a constituent of secondary metabolites with useful physiological activities.
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Hibi M, Kasahara T, Kawashima T, Yajima H, Kozono S, Smirnov SV, Kodera T, Sugiyama M, Shimizu S, Yokozeki K, Ogawa J. Multi-Enzymatic Synthesis of Optically Pure β-Hydroxy α-Amino Acids. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400672] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kimura T, Ishikawa C, Osorio-Lozada A, Robins KT, Hibi M, Ogawa J. Production of a pharmaceutical intermediate via biohydroxylation using whole cells of Rhodococcus rubropertinctus N82. Biosci Biotechnol Biochem 2014; 78:1772-6. [DOI: 10.1080/09168451.2014.925781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Rhodococcus rubropertinctus N82 possesses unique regiospecific hydroxylation activity in biotransformation of compounds. In this study, the ability of whole cells of the strain R. rubropertinctus N82 in biotransformation was studied. The hydroxylation activity resulted in transforming 6,7-dihydro-4H-thieno[3,2-c]-pyridine-5-carboxylic acid tert-butyl ester (LS1) into 2-hydroxy-6,7-dihydro-4H-thieno[3,2-c]-pyridine-5-carboxylic acid tert-butyl ester (LP1), a pharmaceutical intermediate. By optimizing conditions for the hydroxylating biotransformation using whole cells of R. rubropertinctus N82 as biocatalyst, 3.3 mM LP1 was successfully produced from 4 mM LS1 with a molar yield of 83%. Thus, effective method was newly developed to produce LP1, which is a synthetic intermediate of a platelet inhibitor active pharmaceutical ingredient drug, prasugrel.
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Affiliation(s)
- Takatoshi Kimura
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Chihiro Ishikawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Makoto Hibi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Baud D, Saaidi PL, Monfleur A, Harari M, Cuccaro J, Fossey A, Besnard M, Debard A, Mariage A, Pellouin V, Petit JL, Salanoubat M, Weissenbach J, de Berardinis V, Zaparucha A. Synthesis of Mono- and Dihydroxylated Amino Acids with New α-Ketoglutarate-Dependent Dioxygenases: Biocatalytic Oxidation of CH Bonds. ChemCatChem 2014. [DOI: 10.1002/cctc.201402498] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Qin HM, Miyakawa T, Nakamura A, Hibi M, Ogawa J, Tanokura M. Structural optimization of SadA, an Fe(II)- and α-ketoglutarate-dependent dioxygenase targeting biocatalytic synthesis of N-succinyl-L-threo-3,4-dimethoxyphenylserine. Biochem Biophys Res Commun 2014; 450:1458-61. [PMID: 25017911 DOI: 10.1016/j.bbrc.2014.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/02/2014] [Indexed: 11/27/2022]
Abstract
L-threo-3,4-Dihydroxyphenylserine (l-DOPS, Droxidopa) is a psychoactive drug and synthetic amino acid precursor that acts as a prodrug to the neurotransmitters. SadA, a dioxygenase from Burkholderia ambifaria AMMD, is an Fe(II)- and α-ketoglutarate (KG)-dependent enzyme that catalyzes N-substituted branched-chain or aromatic l-amino acids. SadA is able to produce N-succinyl-l-threo-3,4-dimethoxyphenylserine (NSDOPS), which is a precursor of l-DOPS, by catalyzing the hydroxylation of N-succinyl-3,4-dimethoxyphenylalanine (NSDOPA). However, the catalytic activity of SadA toward NSDOPS is much lower than that toward N-succinyl branched-chain l-amino acids. Here, we report an improved biocatalytic synthesis of NSDOPS with SadA. Structure-based protein engineering was applied to improve the α-KG turnover activity for the synthesis of NSDOPS. The G79A, G79A/F261W or G79A/F261R mutant showed a more than 6-fold increase in activity compared to that of the wild-type enzyme. The results provide a new insight into the substrate specificity toward NSDOPA and will be useful for the rational design of SadA mutants as a target of industrial biocatalysts.
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Affiliation(s)
- Hui-Min Qin
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Nakamura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Hibi
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Hibi M, Ogawa J. Characteristics and biotechnology applications of aliphatic amino acid hydroxylases belonging to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily. Appl Microbiol Biotechnol 2014; 98:3869-76. [PMID: 24682483 DOI: 10.1007/s00253-014-5620-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/28/2022]
Abstract
The asymmetric hydroxylation of inactive carbon atoms is still an important reaction in the industrial synthesis of valuable chiral compounds such as pharmaceuticals and fine chemicals. Applications of monooxygenation enzymes, like cytochrome P450 monooxygenases, flavin-containing monooxygenases, and Fe(II)/α-ketoglutarate-dependent dioxygenases (Fe/αKG-DOs), are strongly desired as hydroxylation biocatalysts because they have great advantages in regio- and stereoselectivity of the reactions. Recently, several novel Fe/αKG-DOs have been found to catalyze the asymmetric hydroxylation of aliphatic amino acids. Depending on their amino acid sequences, these Fe/αKG-DOs catalyze different types of regioselective hydroxylations, or C3-, C4-, and C5-hydroxylation. Additionally, most also have stereoselective sulfoxidation activities. Here, we have reviewed the characterization and process development of this novel functioning group of Fe/αKG-DOs.
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Affiliation(s)
- Makoto Hibi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
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Du YL, Dalisay DS, Andersen RJ, Ryan KS. N-carbamoylation of 2,4-diaminobutyrate reroutes the outcome in padanamide biosynthesis. ACTA ACUST UNITED AC 2013; 20:1002-11. [PMID: 23911586 DOI: 10.1016/j.chembiol.2013.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 01/07/2023]
Abstract
Padanamides are linear tetrapeptides notable for the absence of proteinogenic amino acids in their structures. In particular, two unusual heterocycles, (S)-3-amino-2-oxopyrrolidine-1-carboxamide (S-Aopc) and (S)-3-aminopiperidine-2,6-dione (S-Apd), are found at the C-termini of padanamides A and B, respectively. Here we identify the padanamide biosynthetic gene cluster and carry out systematic gene inactivation studies. Our results show that padanamides are synthesized by highly dissociated hybrid nonribosomal peptide synthetase/polyketide synthase machinery. We further demonstrate that carbamoyltransferase gene padQ is critical to the formation of padanamide A but dispensable for biosynthesis of padanamide B. Biochemical investigations show that PadQ carbamoylates the rare biosynthetic precursor l-2,4-diaminobutyrate, generating l-2-amino-4-ureidobutyrate, the presumed precursor to the C-terminal residue of padanamide A. By contrast, the C-terminal residue of padanamide B may derive from glutamine. An unusual thioesterase-catalyzed cyclization is proposed to generate the S-Aopc/S-Apd heterocycles.
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Affiliation(s)
- Yi-Ling Du
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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Hüttel W. Biocatalytic Production of Chemical Building Blocks in Technical Scale with α-Ketoglutarate-Dependent Dioxygenases. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201300008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Cacho RA, Jiang W, Chooi YH, Walsh CT, Tang Y. Identification and characterization of the echinocandin B biosynthetic gene cluster from Emericella rugulosa NRRL 11440. J Am Chem Soc 2012; 134:16781-90. [PMID: 22998630 PMCID: PMC3482383 DOI: 10.1021/ja307220z] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Echinocandins are a family of fungal lipidated cyclic hexapeptide natural products. Due to their effectiveness as antifungal agents, three semisynthetic derivatives have been developed and approved for treatment of human invasive candidiasis. All six of the amino acid residues are hydroxylated, including 4R,5R-dihydroxy-L-ornithine, 4R-hydroxyl-L-proline, 3S,4S-dihydroxy-L-homotyrosine, and 3S-hydroxyl-4S-methyl-L-proline. We report here the biosynthetic gene cluster of echinocandin B 1 from Emericella rugulosa NRRL 11440 containing genes encoding for a six-module nonribosomal peptide synthetase EcdA, an acyl-AMP ligase EcdI, and oxygenases EcdG, EcdH, and EcdK. We showed EcdI activates linoleate as linoleyl-AMP and installs it on the first thiolation domain of EcdA. We have also established through ATP-PP(i) exchange assay that EcdA loads L-ornithine in the first module. A separate hty gene cluster encodes four enzymes for de novo generation of L-homotyrosine from acetyl-CoA and 4-hydroxyphenyl-pyruvate is found from the sequenced genome. Deletions in the ecdA, and htyA genes validate their essential roles in echinocandin B production. Five predicted iron-centered oxygenase genes, ecdG, ecdH, ecdK, htyE, and htyF, in the two separate ecd and hty clusters are likely to be the tailoring oxygenases for maturation of the nascent NRPS lipohexapeptidolactam product.
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Affiliation(s)
- Ralph A. Cacho
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
| | - Wei Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
| | - Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095
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