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Bhoite A, Gaur NK, Palange M, Kontham R, Gupta V, Kulkarni K. Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant epoxide hydrolases. Biochem Biophys Res Commun 2024; 733:150444. [PMID: 39067247 DOI: 10.1016/j.bbrc.2024.150444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Epoxide hydrolases (EHs) are a group of ubiquitous enzymes that catalyze hydrolysis of chemically reactive epoxides to yield corresponding dihydrodiols. Despite extensive studies on EHs from different clades, generic rules governing their substrate specificity determinants have remained elusive. Here, we present structural, biochemical and molecular dynamics simulation studies on MiEH2, a plant epoxide hydrolase from Mangifera indica. Comparative structure-function analysis of nine homologs of MiEH2, which include a few AlphaFold structural models, show that the two conserved tyrosines (MiEH2Y152 and MiEH2Y232) from the lid domain dissect substrate binding tunnel into two halves, forming substrate-binding-pocket one (BP1) and two (BP2). This compartmentalization offers diverse binding modes to their substrates, as exemplified by the binding of smaller aromatic substrates, such as styrene oxide (SO). Docking and molecular dynamics simulations reveal that the linear epoxy fatty acid substrates predominantly occupy BP1, while the aromatic substrates can bind to either BP1 or BP2. Furthermore, SO preferentially binds to BP2, by stacking against catalytically important histidine (MiEH2H297) with the conserved lid tyrosines engaging its epoxide oxygen. Residue (MiEH2L263) next to the catalytic aspartate (MiEH2D262) modulates substrate binding modes. Thus, the divergent binding modes correlate with the differential affinities of the EHs for their substrates. Furthermore, long-range dynamical coupling between the lid and core domains critically influences substrate enantioselectivity in plant EHs.
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Affiliation(s)
- Ashwini Bhoite
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Neeraj K Gaur
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Megha Palange
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Ravindar Kontham
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Vidya Gupta
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune- 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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Wang P, Li D, Sun M, Yin J, Zheng T. Microalgae enhanced co-metabolism of sulfamethoxazole using aquacultural feedstuff components: Co-metabolic pathways and enzymatic mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134279. [PMID: 38613960 DOI: 10.1016/j.jhazmat.2024.134279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
The application of antibiotics in freshwater aquaculture leads to increased contamination of aquatic environments. However, limited information is available on the co-metabolic biodegradation of antibiotics by microalgae in aquaculture. Feedstuffs provide multiple organic substrates for microalgae-mediated co-metabolism. Herein, we investigated the co-metabolism of sulfamethoxazole (SMX) by Chlorella pyrenoidosa when adding main components of feedstuff (glucose and lysine). Results showed that lysine had an approximately 1.5-fold stronger enhancement on microalgae-mediated co-metabolism of SMX than glucose, with the highest removal rate (68.77% ± 0.50%) observed in the 9-mM-Lys co-metabolic system. Furthermore, we incorporated reactive sites predicted by density functional theory calculations, 14 co-metabolites identified by mass spectrometry, and the roles of 18 significantly activated enzymes to reveal the catalytic reaction mechanisms underlying the microalgae-mediated co-metabolism of SMX. In lysine- and glucose-treated groups, five similar co-metabolic pathways were proposed, including bond breaking on the nucleophilic sulfur atom, ring cleavage and hydroxylation at multiple free radical reaction sites, together with acylation and glutamyl conjugation on electrophilic nitrogen atoms. Cytochrome P450, serine hydrolase, and peroxidase play crucial roles in catalyzing hydroxylation, bond breaking, and ring cleavage of SMX. These findings provide theoretical support for better utilization of microalgae-driven co-metabolism to reduce sulfonamide antibiotic residues in aquaculture.
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Affiliation(s)
- Peifang Wang
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Dingxin Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Min Sun
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Tianming Zheng
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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Hu D, Jia XW, Lu JL, Lu ZY, Tang CD, Xue F, Huang C, Ren QG, He YC. Chemoenzymatic Asymmetric Synthesis of Chiral Triazole Fungicide ( R)-Tebuconazole in High Optical Purity Mediated by an Epoxide Hydrolase from Rhodotorula paludigensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10428-10438. [PMID: 38660720 DOI: 10.1021/acs.jafc.3c07949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Tebuconazole is a chiral triazole fungicide used globally in agriculture as a racemic mixture, but its enantiomers exhibit significant enantioselective dissimilarities in bioactivity and environmental behaviors. The steric hindrance caused by the tert-butyl group makes it a great challenge to synthesize tebuconazole enantiomers. Here, we designed a simple chemoenzymatic approach for the asymmetric synthesis of (R)-tebuconazole, which includes the biocatalytic resolution of racemic epoxy-precursor (2-tert-butyl-2-[2-(4-chlorophenyl)ethyl] oxirane, rac-1a) by Escherichia coli/Rpeh whole cells expressed epoxide hydrolase from Rhodotorula paludigensis (RpEH), followed by a one-step chemocatalytic synthesis of (R)-tebuconazole. It was observed that (S)-1a was preferentially hydrolyzed by E. coli/Rpeh, whereas (R)-1a was retained with a specific activity of 103.8 U/g wet cells and a moderate enantiomeric ratio (E value) of 13.4, which was remarkably improved to 43.8 after optimizing the reaction conditions. Additionally, a gram-scale resolution of 200 mM rac-1a was performed using 150 mg/mL E. coli/Rpeh wet cells, resulting in the retention of (R)-1a in a 97.0% ees, a 42.5% yields, and a 40.5 g/L/d space-time yield. Subsequently, the synthesis of highly optical purity (R)-tebuconazole (>99% ee) was easily achieved through the chemocatalytic ring-opening of the epoxy-precursor (R)-1a with 1,2,4-triazole. To elucidate insight into the enantioselectivity, molecular docking simulations revealed that the unique L-shaped substrate-binding pocket of RpEH plays a crucial role in the enantioselective recognition of bulky 2,2-disubstituted oxirane 1a.
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Affiliation(s)
- Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Xue-Wei Jia
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Jia-Lan Lu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Zhi-Yi Lu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, Henan, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No 1, Nanjing 210023, China
| | - Chao Huang
- Process Research Department, STA Pharmaceutical Co., Ltd, A WuXi AppTec Company, Changzhou 213164, China
| | - Qing-Gong Ren
- School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Yu-Cai He
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
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Bučko M, Kaniaková K, Hronská H, Gemeiner P, Rosenberg M. Epoxide Hydrolases: Multipotential Biocatalysts. Int J Mol Sci 2023; 24:ijms24087334. [PMID: 37108499 PMCID: PMC10138715 DOI: 10.3390/ijms24087334] [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: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Epoxide hydrolases are attractive and industrially important biocatalysts. They can catalyze the enantioselective hydrolysis of epoxides to the corresponding diols as chiral building blocks for bioactive compounds and drugs. In this review article, we discuss the state of the art and development potential of epoxide hydrolases as biocatalysts based on the most recent approaches and techniques. The review covers new approaches to discover epoxide hydrolases using genome mining and enzyme metagenomics, as well as improving enzyme activity, enantioselectivity, enantioconvergence, and thermostability by directed evolution and a rational design. Further improvements in operational and storage stabilization, reusability, pH stabilization, and thermal stabilization by immobilization techniques are discussed in this study. New possibilities for expanding the synthetic capabilities of epoxide hydrolases by their involvement in non-natural enzyme cascade reactions are described.
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Affiliation(s)
- Marek Bučko
- Department of Glycobiotechnology, Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Katarína Kaniaková
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Helena Hronská
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Peter Gemeiner
- Department of Glycobiotechnology, Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Michal Rosenberg
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
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Engineering the regiocomplementarity of an epoxide hydrolase from Rhodotorula paludigena by means of computer-aided design for the scale-up enantioconvergent hydrolysis of racemic m-nitrostyrene oxide. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Enantioconvergent hydrolysis of racemic epoxides at elevated concentrations in Tween-20/phosphate buffer by the corresponding epoxide hydrolases. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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