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Liu B, Wang W, Qiu J, Huang X, Qiu S, Bao Y, Xu S, Ruan L, Ran T, He J. Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity. Nat Commun 2023; 14:4343. [PMID: 37468532 DOI: 10.1038/s41467-023-40103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
SulE, an esterase, which detoxifies a variety of sulfonylurea herbicides through de-esterification, provides an attractive approach to remove environmental sulfonylurea herbicides and develop herbicide-tolerant crops. Here, we determined the crystal structures of SulE and an activity improved mutant P44R. Structural analysis revealed that SulE is a dimer with spacious binding pocket accommodating the large sulfonylureas substrate. Particularly, SulE contains a protruding β hairpin with a lid loop covering the active site of the other subunit of the dimer. The lid loop participates in substrate recognition and binding. P44R mutation altered the lid loop flexibility, resulting in the sulfonylurea heterocyclic ring repositioning to a relative stable conformation thus leading to dramatically increased activity. Our work provides important insights into the molecular mechanism of SulE, and establish a solid foundation for further improving the enzyme activity to various sulfonylurea herbicides through rational design.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Weiwu Wang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Huang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shenshen Qiu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siqiong Xu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Luyao Ruan
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Ran
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Nazarian Z, Arab SS. Discovery of carboxylesterases via metagenomics: Putative enzymes that contribute to chemical kinetic resolution. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhu C, Chen Y, Isupov MN, Littlechild JA, Sun L, Liu X, Wang Q, Gong H, Dong P, Zhang N, Wu Y. Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1079-1090. [PMID: 33445864 DOI: 10.1021/acs.jafc.0c06338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipolytic enzymes are essential biocatalysts in food processing as well as pharmaceutical and pesticide industries, catalyzing the cleavage of ester bonds in a variety of acyl chain substrates. Here, we report the crystal structure of an esterase from the deep-sea hydrothermal vent of the East Pacific Rise (EprEst). The X-ray structure of EprEst in complex with the ligand, acetate, has been determined at 2.03 Å resolution. The structure reveals a unique spatial arrangement and orientation of the helix cap domain and α/β hydrolase domain, which form a substrate pocket with preference for short-chain acyl groups. Molecular docking analysis further demonstrated that the active site pocket could accommodate p-nitrophenyl (pNP) carboxyl ligands of varying lengths (≤6 C atoms), with pNP-butyrate ester predicted to have the highest binding affinity. Additionally, the semirational design was conducted to improve the thermostability of EprEst by enzyme engineering based on the established structure and multiple sequence alignment. A mutation, K114P, introduced in the hinge region of the esterase, which displayed increased thermostability and enzyme activity. Collectively, the structural and functional data obtained herein could be used as basis for further protein engineering to ultimately expand the scope of industrial applications of marine-derived lipolytic enzymes.
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Affiliation(s)
- Chunhua Zhu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yayu Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Xiaodong Liu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Na Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
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Kim HJ, Lee BJ, Kwon AR. The grease trap: uncovering the mechanism of the hydrophobic lid in Cutibacterium acnes lipase. J Lipid Res 2020; 61:722-733. [PMID: 32165394 PMCID: PMC7193963 DOI: 10.1194/jlr.ra119000279] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 03/05/2020] [Indexed: 01/07/2023] Open
Abstract
Acne is one of the most common dermatological conditions, but the details of its pathology are unclear, and current management regimens often have adverse effects. Cutibacterium acnes is known as a major acne-associated bacterium that derives energy from lipase-mediated sebum lipid degradation. C. acnes is commensal, but lipase activity has been observed to differ among C. acnes types. For example, higher populations of the type IA strains are present in acne lesions with higher lipase activity. In the present study, we examined a conserved lipase in types IB and II that was truncated in type IA C. acnes strains. Closed, blocked, and open structures of C. acnes ATCC11828 lipases were elucidated by X-ray crystallography at 1.6-2.4 Å. The closed crystal structure, which is the most common form in aqueous solution, revealed that a hydrophobic lid domain shields the active site. By comparing closed, blocked, and open structures, we found that the lid domain-opening mechanisms of C. acnes lipases (CAlipases) involve the lid-opening residues, Phe-179 and Phe-211. To the best of our knowledge, this is the first structure-function study of CAlipases, which may help to shed light on the mechanisms involved in acne development and may aid in future drug design.
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Affiliation(s)
- Hyo Jung Kim
- College of Pharmacy,Woosuk University, Wanju 55338, Republic of Korea,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Ae-Ran Kwon
- Department of Beauty Care, College of Medical Science, Deagu Haany University, Gyeongsan 38610, Republic of Korea,To whom correspondence should be addressed. e-mail:
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Abstract
Hydrolytic enantioselective cleavage of different racemic non-steroidal anti-inflammatory drugs (NSAIDs) ester derivatives has been studied. An engineered esterase form Bacillus subtilis (BS2m) significantly outperformed homologous enzymes from Halomonas elongata (HeE) and Bacillus coagulants (BCE) in the enantioselective hydrolysis of naproxen esters. Structural analysis of the three active sites highlighted key differences which explained the substrate preference. Immobilization of a chimeric BS2m-T4 lysozyme fusion (BS2mT4L1) was improved by resin screening achieving twice the recovered activity (22.1 ± 5 U/g) with respect to what had been previously reported, and was utilized in a packed bed reactor. Continuous hydrolysis of α-methyl benzene acetic acid butyl ester as a model substrate was easily achieved, albeit at low concentration (1 mM). However, the high degree of insolubility of the naproxen butyl ester resulted in a slurry which could not be efficiently bioconverted, despite the addition of co-solvents and lower substrate concentration (1 mM). Addition of Triton® X-100 to the substrate mix yielded 24% molar conversion and 80% e.e. at a 5 mM scale with 5 min residence time and sufficient retention of catalytic efficiency after 6 h of use.
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Preparation of Sterically Demanding 2,2-Disubstituted-2-Hydroxy Acids by Enzymatic Hydrolysis. Catalysts 2019. [DOI: 10.3390/catal9020113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Preparation of optically-pure derivatives of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid of general structure 2 was accomplished by enzymatic hydrolysis of the correspondent esters. A screening with commercial hydrolases using the methyl ester of 2-hydroxy-2-(3-hydroxyphenyl)-2-phenylacetic acid (1a) showed that crude pig liver esterase (PLE) was the only preparation with catalytic activity. Low enantioselectivity was observed with substrates 1a–d, whereas PLE-catalysed hydrolysis of 1e proceeded with good enantioselectivity (E = 28), after optimization. Enhancement of the enantioselectivity was obtained by chemical re-esterification of enantiomerically enriched 2e, followed by sequential enzymatic hydrolysis with PLE. The preparation of optically-pure (S)-2e was validated on multi-milligram scale.
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