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Chen G, Wang ZX, Yang Y, Li Y, Zhang T, Ouyang S, Zhang L, Chen Y, Ruan X, Miao M. Elucidation of the mechanism underlying the sequential catalysis of inulin by fructotransferase. Int J Biol Macromol 2024; 277:134446. [PMID: 39098696 DOI: 10.1016/j.ijbiomac.2024.134446] [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: 05/17/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
Glycoside hydrolase family 91 (GH91) inulin fructotransferase (IFTases) enables biotransformation of fructans into sugar substitutes for dietary intervention in metabolic syndrome. However, the catalytic mechanism underlying the sequential biodegradation of inulin remains unelusive during the biotranformation of fructans. Herein we present the crystal structures of IFTase from Arthrobacter aurescens SK 8.001 in apo form and in complexes with kestose, nystose, or fructosyl nystose, respectively. Two kinds of conserved noncatalytic binding regions are first identified for IFTase-inulin interactions. The conserved interactions of substrates were revealed in the catalytic center that only contained a catalytic residue E205. A switching scaffold was comprised of D194 and Q217 in the catalytic channel, which served as the catalytic transition stabilizer through side chain displacement in the cycling of substrate sliding in/out the catalytic pocket. Such features in GH91 contribute to the catalytic model for consecutive cutting of substrate chain as well as product release in IFTase, and thus might be extended to other exo-active enzymes with an enclosed bottom of catalytic pocket. The study expands the current general catalytic principle in enzyme-substrate complexes and shed light on the rational design of IFTase for fructan biotransformation.
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Affiliation(s)
- Gang Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Zhao-Xi Wang
- Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Yuqi Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yungao Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Songying Ouyang
- Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Liang Zhang
- Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei 230027, China.
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Xinglin Ruan
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road Gulou District, Fuzhou 350001, China.
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Cheng M, Hou X, Huang Z, Chen Z, Ni D, Zhang W, Rao Y, Mu W. Structural Insights into the Catalytic Cycle of Inulin Fructotransferase: From Substrate Anchoring to Product Releasing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17030-17040. [PMID: 39034843 DOI: 10.1021/acs.jafc.4c03615] [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: 07/23/2024]
Abstract
Carbohydrate degradation is crucial for living organisms due to their essential functions in providing energy and composing various metabolic pathways. Nevertheless, in the catalytic cycle of polysaccharide degradation, the details of how the substrates bind and how the products release need more case studies. Here, we choose an inulin fructotransferase (SpIFTase) as a model system, which can degrade inulin into functionally difructose anhydride I. At first, the crystal structures of SpIFTase in the absence of carbohydrates and complex with fructosyl-nystose (GF4), difructose anhydride I, and fructose are obtained, giving the substrate trajectory and product path of SpIFTase, which are further supported by steered molecular dynamics simulations (MDSs) along with mutagenesis. Furthermore, structural topology variations at the active centers of inulin fructotransferases are suggested as the structural base for product release, subsequently proven by substitution mutagenesis and MDSs. Therefore, this study provides a case in point for a deep understanding of the catalytic cycle with substrate trajectory and product path.
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Affiliation(s)
- Mei Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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3
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Yu S, Li Q, Wang Z, Zhao W. Innovative application of a novel and thermostable inulin fructotransferase from Arthrobacter sp. ISL-85 to fructan inulin in burdock root to improve nutrition. Food Chem 2024; 441:138336. [PMID: 38183723 DOI: 10.1016/j.foodchem.2023.138336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
Inulin fructotransferase converts prebiotic polysaccharide inulin to difructose anhydride III, known for its numerous beneficial physiological effects. While previous studies focused on using inulin extracts under optimal conditions, this study delves into the enzyme's behavior when dealing with more complex food materials, inulin-rich burdock root, which possesses greater nutritional value but may influence the enzymatic reaction. An inulin fructotransferase from Arthrobacter sp. ISL-85 was identified and characterized, which has the highest activity of 783 U mg-1 at pH 6.5 and 65 °C and remains stable even up to 80 °C. When applied to inulin-rich burdock root (pH 4.7) at 80 °C for 2 h, the enzyme yielded 4.1 g of difructose anhydride III, concurrently increasing fructo-oligosaccharides. This study demonstrates the potential of this enzyme as a valuable tool for efficiently processing inulin within whole food materials under high temperatures. Such an approach could pave the way for enhancing nutrition and promoting health benefits.
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Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China.
| | - Qiting Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China
| | - Zhenlong Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China
| | - Wei Zhao
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, PR China
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Li Q, Wang Z, Zhu M, Zhao W, Yu S. Metabolism of Inulin via Difructose Anhydride I Pathway in Microbacterium flavum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9647-9655. [PMID: 38629750 DOI: 10.1021/acs.jafc.4c00729] [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: 05/02/2024]
Abstract
Difructose anhydride I (DFA-I) can be produced from inulin, with DFA-I-forming inulin fructotransferase (IFTase-I). However, the metabolism of inulin through DFA-I remains unclear. To clarify this pathway, several genes of enzymes related to this pathway in the genome of Microbacterium flavum DSM 18909 were synthesized, and the corresponding enzymes were encoded, purified, and investigated in vitro. After inulin is decomposed to DFA-I by IFTase-I, DFA-I is hydrolyzed to inulobiose by DFA-I hydrolase. Inulobiose is then hydrolyzed by β-fructofuranosidase to form fructose. Finally, fructose enters glycolysis through fructokinase. A β-fructofuranosidase (MfFFase1) clears the byproducts (sucrose and fructo-oligosaccharides), which might be partially hydrolyzed by fructan β-(2,1)-fructosidase/1-exohydrolase and another fructofuranosidase (MfFFase2). Exploring the DFA-I pathway of inulin and well-studied enzymes in vitro extends our basic scientific knowledge of the energy-providing way of inulin, thereby paving the way for further investigations in vivo and offering a reference for further nutritional investigation of inulin and DFA-I in the future.
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Affiliation(s)
- Qiting Li
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Zhenlong Wang
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Mengyan Zhu
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Zhao
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
| | - Shuhuai Yu
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, P. R. China
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Yu S, Wang Z, Li Q, Wang T, Zhao W. Innovative application of a novel di-D-fructofuranose 1,2':2,3'-dianhydride hydrolase (DFA-IIIase) from Duffyella gerundensis A4 to burdock root to improve nutrition. Food Funct 2024; 15:1021-1030. [PMID: 38180053 DOI: 10.1039/d3fo03277a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Burdock is native to Europe and Asia and rich in many functional ingredients, including biomacromolecule polysaccharide inulin. The prebiotic fructan inulin can provide energy to organisms via several pathways. One pathway is that inulin fructotransferase (IFTase) first converts inulin to III-type difructose anhydride (DFA-III), which has many beneficial physiological functions. Then, DFA-III is hydrolyzed to inulobiose, which is a Fn-type prebiotic fructo-oligosaccharide, via difructose anhydride hydrolase (DFA-IIIase). However, there has been no study on the application of IFTase or DFA-IIIase to process burdock to increase DFA-III or inulobiose. Moreover, only five DFA-IIIases have been reported to date and all of them are from the Arthrobacter genus. Whether other microbes except for the Arthrobacter genus can utilize DFA-III through DFA-IIIase is unknown. In this work, a DFA-IIIase from Duffyella gerundensis A4 (D. gerundensis A4), abbreviated as DgDFA-IIIase, was identified and characterized in detail. DgDFA-IIIase is a bifunctional enzyme, that is, besides its hydrolytic ability to DFA-III, it has the same catalytic ability as IFTase to inulin. The enzyme was applied to the burdock root aiming at inulin and DFA-III, and inulobiose was produced with an increase in Gn-type fructo-oligosaccharide. The work verifies that microorganisms of the non-Arthrobacter genus also have the potential ability to use DFA-III by DFA-IIIase, and DFA-IIIase is feasible to increase functional substances of burdock root instead of IFTase and endo-inulinase, which paves the way for the production of functional food utilizing the polysaccharide inulin to improve nutrition and health.
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Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenlong Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Qiting Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tong Wang
- Microsoft Research AI4Science, Beijing 100080, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
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Feng Y, Lyu X, Cong Y, Miao T, Fang B, Zhang C, Shen Q, Matthews M, Fisher AJ, Zhang JZH, Zhang L, Yang R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int J Biol Macromol 2023; 253:127093. [PMID: 37758108 DOI: 10.1016/j.ijbiomac.2023.127093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-β1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.
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Affiliation(s)
- Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tingwei Miao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Shen
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Melissa Matthews
- Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan; Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China; Department of Chemistry, New York University, New York, NY 10003, United States
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
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7
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Kashima T, Ishiwata A, Fujita K, Fushinobu S. Identification and structural basis of an enzyme that degrades oligosaccharides in caramel. Biophys Physicobiol 2023; 20:e200017. [PMID: 38496246 PMCID: PMC10941961 DOI: 10.2142/biophysico.bppb-v20.0017] [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: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Cooking with fire produces foods containing carbohydrates that are not naturally occurring, such as α-d-fructofuranoside found in caramel. Each of the hundreds of compounds produced by caramelization reactions is considered to possess its own characteristics. Various studies from the viewpoints of biology and biochemistry have been conducted to elucidate some of the scientific characteristics. Here, we review the composition of caramelized sugars and then describe the enzymatic studies that have been conducted and the physiological functions of the caramelized sugar components that have been elucidated. In particular, we recently identified a glycoside hydrolase (GH), GH172 difructose dianhydride I synthase/hydrolase (αFFase1), from oral and intestinal bacteria, which is implicated in the degradation of oligosaccharides in caramel. The structural basis of αFFase1 and its ligands provided many insights. This discovery opened the door to several research fields, including the structural and phylogenetic relationship between the GH172 family enzymes and viral capsid proteins and the degradation of cell membrane glycans of acid-fast bacteria by some αFFase1 homologs. This review article is an extended version of the Japanese article, Identification and Structural Basis of an Enzyme Degrading Oligosaccharides in Caramel, published in SEIBUTSU BUTSURI Vol. 62, p. 184-186 (2022).
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Affiliation(s)
- Toma Kashima
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ishiwata
- Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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8
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Xu H, Li Q, Zhao W, Yu S. Improving the catalytic activity of difructose anhydride III hydrolase from Arthrobacter chlorophenolicus A6 by modification of two residues. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.021] [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: 10/31/2022]
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9
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Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
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Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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10
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Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. J Biol Chem 2021; 297:101324. [PMID: 34688653 PMCID: PMC8605356 DOI: 10.1016/j.jbc.2021.101324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
Fructooligosaccharides and their anhydrides are widely used as health-promoting foods and prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been used to produce functional compounds. However, enzymes that hydrolyze and form α-D-fructofuranosyl linkages have been less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase from Bifidobacterium dentium [αFFase1]) as an enzyme with α-D-fructofuranosidase and α-D-arabinofuranosidase activities and an anomer-retaining manner. αFFase1 is not homologous with any known enzymes, suggesting that it is a member of a novel glycoside hydrolase family. When caramelized fructose sugar was incubated with αFFase1, conversions of β-D-Frup-(2→1)-α-D-Fruf to α-D-Fruf-1,2′:2,1′-β-D-Frup (diheterolevulosan II) and β-D-Fruf-(2→1)-α-D-Fruf (inulobiose) to α-D-Fruf-1,2′:2,1′-β-D-Fruf (difructose dianhydride I [DFA I]) were observed. The reaction equilibrium between inulobiose and DFA I was biased toward the latter (1:9) to promote the intramolecular dehydrating condensation reaction. Thus, we named this enzyme DFA I synthase/hydrolase. The crystal structures of αFFase1 in complex with β-D-Fruf and β-D-Araf were determined at the resolutions of up to 1.76 Å. Modeling of a DFA I molecule in the active site and mutational analysis also identified critical residues for catalysis and substrate binding. The hexameric structure of αFFase1 revealed the connection of the catalytic pocket to a large internal cavity via a channel. Molecular dynamics analysis implied stable binding of DFA I and inulobiose to the active site with surrounding water molecules. Taken together, these results establish DFA I synthase/hydrolase as a member of a new glycoside hydrolase family (GH172).
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11
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Wang Z, Shen H, He B, Teng M, Guo Q, Li X. The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus. FEBS J 2021; 288:6019-6034. [PMID: 33955674 DOI: 10.1111/febs.15911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/27/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
Staphylococcus aureus is a well-known clinical pathogenic bacterium. In recent years, due to the emergence of multiple drug-resistant strains of S. aureus in clinical practice, S. aureus infections have become an increasingly severe clinical problem. Ntdp (nucleoside tri- and diphosphatase, also known as Sa1684) is a nucleotide phosphatase that has a significant effect on the proliferation of S. aureus colonies and the killing ability of the host. Here, we identified the nucleoside tri- and diphosphate hydrolysis activity of Ntdp and obtained the three-dimensional structures of apo-Ntdp and three substrate analog (ATPγ S, GDPβ S, and GTPγ S) complexes of Ntdp. Through structural analysis and biochemical verification, we illustrated the structural basis for the divalent cation selectivity, substrate recognition model, and catalytic mechanism of Ntdp. We also revealed a possible basal functional pattern of the DUF402 domain and hypothesized the potential pathways by which the protein regulates the expression of the two-component regulatory factor agr and the downstream virulence factors. Overall, the above findings provide crucial insights into our understanding of the Ntdp functional mechanism in the infection process.
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Affiliation(s)
- Zhenhua Wang
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hui Shen
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Binbin He
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Maikun Teng
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qiong Guo
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xu Li
- National Synchrotron Radiation Laboratory, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
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Insight into the significant roles of the Trp372 and flexible loop in directing the catalytic direction and substrate specificity in AGE superfamily enzymes. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Xie X, Ban X, Gu Z, Li C, Hong Y, Cheng L, Li Z. Structure-Based Engineering of a Maltooligosaccharide-Forming Amylase To Enhance Product Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:838-844. [PMID: 31896254 DOI: 10.1021/acs.jafc.9b07234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Maltooligosaccharide-forming amylases (MFAses) are promising tools for a variety of food industry applications because they convert starch into functional maltooligosaccharides. The MFAse from Bacillus stearothermophilus STB04 (BstMFAse) is a thermostable enzyme that preferentially produces maltopentaose and maltohexaose. An X-ray crystal structure of the BstMFAse-acarbose complex suggested that mutation of glycine 109 would increase its maltohexaose specificity. Using site-directed mutagenesis, glycine 109 was replaced with several different amino acids. Mutant-containing asparagine (G109N), aspartic acid (G109D), and phenylalanine (G109F) produced 36.1, 42.4, and 39.0% maltohexaose from starch, respectively, which was greater than that produced by the wild-type (32.9%). These mutants also exhibited substantially altered oligosaccharide hydrolysis patterns in favor of maltohexaose production. Homology models suggested that the mutants form extra interactions with the substrate at subsite -6, which were responsible for the enhanced maltohexaose specificity of BstMFAse. The results of this study support the proposition that binding of the substrate's nonreducing end in the nonreducing end-subsite of the MFAse active center plays a crucial role in its product specificity.
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Affiliation(s)
- Xiaofang Xie
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Xiaofeng Ban
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
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