1
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Kil Y, Pichkur EB, Sergeev VR, Zabrodskaya Y, Myasnikov A, Konevega AL, Shtam T, Samygina VR, Rychkov GN. The archaeal highly thermostable GH35 family β-galactosidase DaβGal has a unique seven domain protein fold. FEBS J 2024; 291:3686-3705. [PMID: 38825733 DOI: 10.1111/febs.17166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/29/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024]
Abstract
The most extensively studied β-d-galactosidases (EC3.2.1.23) belonging to four glycoside hydrolase (GH) families 1, 2, 35, and 42 are widely distributed among Bacteria, Archaea and Eukaryotes. Here, we report a novel GH35 family β-galactosidase from the hyperthermophilic Thermoprotei archaeon Desulfurococcus amylolyticus (DaβGal). Unlike fungal monomeric six-domain β-galactosidases, the DaβGal enzyme is a dimer; it has an extra jelly roll domain D7 and three composite domains (D4, D5, and D6) that are formed by the distantly located polypeptide chain regions. The enzyme possesses a high specificity for β-d-galactopyranosides, and its distinguishing feature is the ability to cleave pNP-β-d-fucopyranoside. DaβGal efficiently catalyzes the hydrolysis of lactose at high temperatures, remains stable and active at 65 °С, and retains activity at 95 °С with a half-life time value equal to 73 min. These properties make archaeal DaβGal a more attractive candidate for biotechnology than the widely used fungal β-galactosidases.
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Affiliation(s)
- Yury Kil
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Evgeny B Pichkur
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Laboratory of X-ray Analysis and Synchrotron Radiation, Federal Scientific Research Center "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir R Sergeev
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
| | - Yana Zabrodskaya
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
- Department of Molecular Biology of Viruses, Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Alexander Myasnikov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - Andrey L Konevega
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
| | - Tatiana Shtam
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Valeriya R Samygina
- Structural Biology Department, Kurchatov Complex of NBICS Nature-Like Technologies, National Research Center "Kurchatov Institute", Moscow, Russia
- Laboratory of X-ray Analysis and Synchrotron Radiation, Federal Scientific Research Center "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Russia
| | - Georgy N Rychkov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint-Petersburg Polytechnic University, Russia
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2
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Miao M, Yao Y, Yan Q, Jiang Z, He G, Yang S. Biochemical characterization of a novel β-galactosidase from Pedobacter sp. with strong transglycosylation activity at low lactose concentration. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01169-w. [PMID: 38771554 DOI: 10.1007/s12223-024-01169-w] [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: 10/21/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
A novel β-galactosidase gene (PbBgal35A) from Pedobacter sp. CAUYN2 was cloned and expressed in Escherichia coli. The gene had an open reading frame of 1917 bp, encoding 638 amino acids with a predicted molecular mass of 62.3 kDa. The deduced amino acid sequence of the gene shared the highest identity of 41% with a glycoside hydrolase family 35 β-galactosidase from Xanthomonas campestris pv. campestris (AAP86763.1). The recombinant β-galactosidase (PbBgal35A) was purified to homogeneity with a specific activity of 65.9 U/mg. PbBgal35A was optimally active at pH 5.0 and 50 °C, respectively, and it was stable within pH 4.5‒7.0 and up to 45 °C. PbBgal35A efficiently synthesized galacto-oligosaccharides from lactose with a conversion ratio of 32% (w/w) and fructosyl-galacto-oligosaccharides from lactulose with a conversion ratio of 21.9% (w/w). Moreover, the enzyme catalyzed the synthesis of galacto-oligosaccharides from low-content lactose in fresh milk, and the GOS conversion ratios of 17.1% (w/w) and 7.8% (w/w) were obtained when the reactions were performed at 45 and 4 °C, respectively. These properties make PbBgal35A an ideal candidate for commercial use in the manufacturing of GOS-enriched dairy products.
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Affiliation(s)
- Miao Miao
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Yuchen Yao
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Qiaojuan Yan
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Zhengqiang Jiang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing, 100083, China
| | - Guangming He
- Jiangxi Jinsuifeng Sugar Industry Co., Ltd., Yichun, 336000, China
| | - Shaoqing Yang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing, 100083, China.
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3
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Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [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: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
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Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
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Liu P, Chen Y, Ma C, Ouyang J, Zheng Z. β-Galactosidase: a traditional enzyme given multiple roles through protein engineering. Crit Rev Food Sci Nutr 2023:1-20. [PMID: 38108277 DOI: 10.1080/10408398.2023.2292282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
β-Galactosidases are crucial carbohydrate-active enzymes that naturally catalyze the hydrolysis of galactoside bonds in oligo- and disaccharides. These enzymes are commonly used to degrade lactose and produce low-lactose and lactose-free dairy products that are beneficial for lactose-intolerant people. β-galactosidases exhibit transgalactosylation activity, and they have been employed in the synthesis of galactose-containing compounds such as galactooligosaccharides. However, most β-galactosidases have intrinsic limitations, such as low transglycosylation efficiency, significant product inhibition effects, weak thermal stability, and a narrow substrate spectrum, which greatly hinder their applications. Enzyme engineering offers a solution for optimizing their catalytic performance. The study of the enzyme's structure paves the way toward explaining catalytic mechanisms and increasing the efficiency of enzyme engineering. In this review, the structure features of β-galactosidases from different glycosyl hydrolase families and the catalytic mechanisms are summarized in detail to offer guidance for protein engineering. The properties and applications of β-galactosidases are discussed. Additionally, the latest progress in β-galactosidase engineering and the strategies employed are highlighted. Based on the combined analysis of structure information and catalytic mechanisms, the ultimate goal of this review is to furnish a thorough direction for β-galactosidases engineering and promote their application in the food and dairy industries.
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Affiliation(s)
- Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, People's Republic of China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Yuehua Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
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5
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Li T, Li J, Yan Q, Yang S, Jiang Z. Biochemical characterization of a novel β-galactosidase from Lacticaseibacillus zeae and its application in synthesis of lacto-N-tetraose. J Dairy Sci 2023; 106:6623-6634. [PMID: 37210349 DOI: 10.3168/jds.2023-23221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/02/2023] [Indexed: 05/22/2023]
Abstract
Lacto-N-tetraose (LNT) is one of the most important components of human milk oligosaccharides, which has various beneficial health effects. β-Galactosidase is an important enzyme used in dairy processing. The transglycosylation activity of β-galactosidases offers an attractive approach for LNT synthesis. In this study, we reported for the first time the biochemical characterization of a novel β-galactosidase (LzBgal35A) from Lacticaseibacillus zeae. LzBgal35A belongs to glycoside hydrolases (GH) family 35 and shared the highest identity of 59.9% with other reported GH 35 members. The enzyme was expressed as soluble protein in Escherichia coli. The purified LzBgal35A displayed optimal activity at pH 4.5 and 55°C. It was stable within the pH range of 3.5 to 7.0 and up to 60°C. Moreover, LzBgal35A could catalyze the synthesis of LNT via transferring the galactose residue from o-nitrophenyl-β-galactopyranoside to lacto-N-triose II. Under optimal conditions, the conversion rate of LNT reached 45.4% (6.4 g/L) within 2 h, which was by far the highest yield of LNT synthesized through a β-galactosidase-mediated transglycosylation reaction. This study demonstrated that LzBgal35A has great potential application in LNT synthesis.
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Affiliation(s)
- Ting Li
- Department of Nutrition and Health, College of Engineering, China Agricultural University, Haidian District, Beijing 100083, PR China
| | - Jing Li
- Key Laboratory of China National Light Industry and Food Bioengineering, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing 100083, PR China
| | - Qiaojuan Yan
- Department of Nutrition and Health, College of Engineering, China Agricultural University, Haidian District, Beijing 100083, PR China; College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210023, PR China
| | - Shaoqing Yang
- Key Laboratory of China National Light Industry and Food Bioengineering, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing 100083, PR China
| | - Zhengqiang Jiang
- Key Laboratory of China National Light Industry and Food Bioengineering, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing 100083, PR China.
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Li D, Wang Z, Yu Y, Li H, Luo W, Chen B, Niu G, Ding H. Biochemical Insights into a Novel Family 2 Glycoside Hydrolase with Both β-1,3-Galactosidase and β-1,4-Galactosidase Activity from the Arctic. Mar Drugs 2023; 21:521. [PMID: 37888456 PMCID: PMC10608614 DOI: 10.3390/md21100521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
A novel GH2 (glycoside hydrolase family 2) β-galactosidase from Marinomonas sp. BSi20584 was successfully expressed in E. coli with a stable soluble form. The recombinant enzyme (rMaBGA) was purified to electrophoretic homogeneity and characterized extensively. The specific activity of purified rMaBGA was determined as 96.827 U mg-1 at 30 °C using ONPG (o-nitrophenyl-β-D-galactopyranoside) as a substrate. The optimum pH and temperature of rMaBGA was measured as 7.0 and 50 °C, respectively. The activity of rMaBGA was significantly enhanced by some divalent cations including Zn2+, Mg2+ and Ni2+, but inhibited by EDTA, suggesting that some divalent cations might play important roles in the catalytic process of rMaBGA. Although the enzyme was derived from a cold-adapted strain, it still showed considerable stability against various physical and chemical elements. Moreover, rMaBGA exhibited activity both toward Galβ-(1,3)-GlcNAc and Galβ-(1,4)-GlcNAc, which is a relatively rare occurrence in GH2 β-galactosidase. The results showed that two domains in the C-terminal region might be contributed to the β-1,3-galactosidase activity of rMaBGA. On account of its fine features, this enzyme is a promising candidate for the industrial application of β-galactosidase.
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Affiliation(s)
- Dianyi Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China;
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Zheng Wang
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yong Yu
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Huirong Li
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wei Luo
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Bo Chen
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Guoqing Niu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China;
| | - Haitao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Z.W.); (Y.Y.); (H.L.); (W.L.); (B.C.)
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
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Saburi W, Ota T, Kato K, Tagami T, Yamashita K, Yao M, Mori H. Function and Structure of Lacticaseibacillus casei GH35 β-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N-biose I and Galacto- N-biose. J Appl Glycosci (1999) 2023; 70:43-52. [PMID: 37599861 PMCID: PMC10432377 DOI: 10.5458/jag.jag.jag-2022_0014] [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: 12/02/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
β-Galactosidase (EC 3.2.1.23) hydrolyzes β-D-galactosidic linkages at the non-reducing end of substrates to produce β-D-galactose. Lacticaseibacillus casei is one of the most widely utilized probiotic species of lactobacilli. It possesses a putative β-galactosidase belonging to glycoside hydrolase family 35 (GH35). This enzyme is encoded by the gene included in the gene cluster for utilization of lacto-N-biose I (LNB; Galβ1-3GlcNAc) and galacto-N-biose (GNB; Galβ1-3GalNAc) via the phosphoenolpyruvate: sugar phosphotransferase system. The GH35 protein (GnbG) from L. casei BL23 is predicted to be 6-phospho-β-galactosidase (EC 3.2.1.85). However, its 6-phospho-β-galactosidase activity has not yet been examined, whereas its hydrolytic activity against LNB and GNB has been demonstrated. In this study, L. casei JCM1134 LBCZ_0230, homologous to GnbG, was characterized enzymatically and structurally. A recombinant LBCZ_0230, produced in Escherichia coli, exhibited high hydrolytic activity toward o-nitrophenyl β-D-galactopyranoside, p-nitrophenyl β-D-galactopyranoside, LNB, and GNB, but not toward o-nitrophenyl 6-phospho-β-D-galactopyranoside. Crystal structure analysis indicates that the structure of subsite -1 of LBCZ_0230 is very similar to that of Streptococcus pneumoniae β-galactosidase BgaC and not suitable for binding to 6-phospho-β-D-galactopyranoside. These biochemical and structural analyses indicate that LBCZ_0230 is a β-galactosidase. According to the prediction of LNB's binding mode, aromatic residues, Trp190, Trp240, Trp243, Phe244, and Tyr458, form hydrophobic interactions with N-acetyl-D-glucosamine residue of LNB at subsite +1.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University
| | - Tomoya Ota
- Research Faculty of Agriculture, Hokkaido University
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University
| | | | | | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University
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Nakajima M. β-1,2-Glucans and associated enzymes. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01205-5] [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]
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9
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Kobayashi K, Shimizu H, Tanaka N, Kuramochi K, Nakai H, Nakajima M, Taguchi H. Characterization and structural analyses of a novel glycosyltransferase acting on the β-1,2-glucosidic linkages. J Biol Chem 2022; 298:101606. [PMID: 35065074 PMCID: PMC8861115 DOI: 10.1016/j.jbc.2022.101606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 10/26/2022] Open
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10
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Mangiagalli M, Lotti M. Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation. Mar Drugs 2021; 19:md19010043. [PMID: 33477853 PMCID: PMC7832830 DOI: 10.3390/md19010043] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.
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11
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Matsuyama K, Kondo T, Igarashi K, Sakamoto T, Ishimaru M. Substrate-recognition mechanism of tomato β-galactosidase 4 using X-ray crystallography and docking simulation. PLANTA 2020; 252:72. [PMID: 33011862 DOI: 10.1007/s00425-020-03481-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
TBG4 recognize multiple linkage types substrates due to having a spatially wide subsite + 1. This feature allows the degradation of AGI, AGII, and AGP leading to the fruit ripening. β-galactosidase (EC 3. 2. 1. 23) catalyzes the hydrolysis of β-galactan and release of D-galactose. Tomato has at least 17 β-galactosidases (TBGs), of which, TBG 4 is responsible for fruit ripening. TBG4 hydrolyzes not only β-1,4-bound galactans, but also β-1,3- and β-1,6-galactans. In this study, we compared each enzyme-substrate complex using X-ray crystallography, ensemble refinement, and docking simulation to understand the broad substrate-specificity of TBG4. In subsite - 1, most interactions were conserved across each linkage type of galactobioses; however, some differences were seen in subsite + 1, owing to the huge volume of catalytic pocket. In addition to this, docking simulation indicated TBG4 to possibly have more positive subsites to recognize and hydrolyze longer galactans. Taken together, our results indicated that during tomato fruit ripening, TBG4 plays an important role by degrading arabinogalactan I (AGI), arabinogalactan II (AGII), and the carbohydrate moiety of arabinogalactan protein (AGP).
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo, 113-8657, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan
| | - Tatsuya Kondo
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Megumi Ishimaru
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan.
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12
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Kondo T, Nishimura Y, Matsuyama K, Ishimaru M, Nakazawa M, Ueda M, Sakamoto T. Characterization of three GH35 β-galactosidases, enzymes able to shave galactosyl residues linked to rhamnogalacturonan in pectin, from Penicillium chrysogenum 31B. Appl Microbiol Biotechnol 2019; 104:1135-1148. [DOI: 10.1007/s00253-019-10299-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 11/29/2022]
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13
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Structural Insights into the Molecular Evolution of the Archaeal Exo-β-d-Glucosaminidase. Int J Mol Sci 2019; 20:ijms20102460. [PMID: 31109049 PMCID: PMC6566704 DOI: 10.3390/ijms20102460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/16/2022] Open
Abstract
The archaeal exo-β-d-glucosaminidase (GlmA), a thermostable enzyme belonging to the glycosidase hydrolase (GH) 35 family, hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a novel enzyme in terms of its primary structure, as it is homologous to both GH35 and GH42 β-galactosidases. The catalytic mechanism of GlmA is not known. Here, we summarize the recent reports on the crystallographic analysis of GlmA. GlmA is a homodimer, with each subunit comprising three distinct domains: a catalytic TIM-barrel domain, an α/β domain, and a β1 domain. Surprisingly, the structure of GlmA presents features common to GH35 and GH42 β-galactosidases, with the domain organization resembling that of GH42 β-galactosidases and the active-site architecture resembling that of GH35 β-galactosidases. Additionally, the GlmA structure also provides critical information about its catalytic mechanism, in particular, on how the enzyme can recognize glucosamine. Finally, we postulate an evolutionary pathway based on the structure of an ancestor GlmA to extant GH35 and GH42 β-galactosidases.
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14
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Cloning, purification and biochemical characterisation of a GH35 beta-1,3/beta-1,6-galactosidase from the mucin-degrading gut bacterium Akkermansia muciniphila. Glycoconj J 2018; 35:255-263. [DOI: 10.1007/s10719-018-9824-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/11/2023]
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15
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Hobbs JK, Pluvinage B, Boraston AB. Glycan-metabolizing enzymes in microbe-host interactions: the Streptococcus pneumoniae paradigm. FEBS Lett 2018; 592:3865-3897. [PMID: 29608212 DOI: 10.1002/1873-3468.13045] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the upper airways; however, it is also an accomplished pathogen capable of causing life-threatening diseases. To colonize and cause invasive disease, this bacterium relies on a complex array of factors to mediate the host-bacterium interaction. The respiratory tract is rich in functionally important glycoconjugates that display a vast range of glycans, and, thus, a key component of the pneumococcus-host interaction involves an arsenal of bacterial carbohydrate-active enzymes to depolymerize these glycans and carbohydrate transporters to import the products. Through the destruction of host glycans, the glycan-specific metabolic machinery deployed by S. pneumoniae plays a variety of roles in the host-pathogen interaction. Here, we review the processing and metabolism of the major host-derived glycans, including N- and O-linked glycans, Lewis and blood group antigens, proteoglycans, and glycogen, as well as some dietary glycans. We discuss the role of these metabolic pathways in the S. pneumoniae-host interaction, speculate on the potential of key enzymes within these pathways as therapeutic targets, and relate S. pneumoniae as a model system to glycan processing in other microbial pathogens.
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Affiliation(s)
- Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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16
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Rico‐Díaz A, Ramírez‐Escudero M, Vizoso‐Vázquez Á, Cerdán ME, Becerra M, Sanz‐Aparicio J. Structural features of
Aspergillus niger
β‐galactosidase define its activity against glycoside linkages. FEBS J 2017; 284:1815-1829. [DOI: 10.1111/febs.14083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/14/2017] [Accepted: 04/06/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Agustín Rico‐Díaz
- Grupo EXPRELA Centro de Investigacións Científicas Avanzadas (CICA) Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña Spain
- Department of Crystallography and Structural Biology Institute of Physical‐Chemistry Rocasolano CSIC Madrid Spain
| | - Mercedes Ramírez‐Escudero
- Department of Crystallography and Structural Biology Institute of Physical‐Chemistry Rocasolano CSIC Madrid Spain
| | - Ángel Vizoso‐Vázquez
- Grupo EXPRELA Centro de Investigacións Científicas Avanzadas (CICA) Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña Spain
| | - M. Esperanza Cerdán
- Grupo EXPRELA Centro de Investigacións Científicas Avanzadas (CICA) Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña Spain
| | - Manuel Becerra
- Grupo EXPRELA Centro de Investigacións Científicas Avanzadas (CICA) Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña Spain
| | - Julia Sanz‐Aparicio
- Department of Crystallography and Structural Biology Institute of Physical‐Chemistry Rocasolano CSIC Madrid Spain
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17
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Mine S, Watanabe M, Kamachi S, Abe Y, Ueda T. The Structure of an Archaeal β-Glucosaminidase Provides Insight into Glycoside Hydrolase Evolution. J Biol Chem 2017; 292:4996-5006. [PMID: 28130448 DOI: 10.1074/jbc.m116.766535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
The archaeal exo-β-d-glucosaminidase (GlmA) is a dimeric enzyme that hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a member of the glycosidase hydrolase (GH)-A superfamily-subfamily 35 and is a novel enzyme in terms of its primary structure. Here, we present the crystal structure of GlmA in complex with glucosamine at 1.27 Å resolution. The structure reveals that a monomeric form of GlmA shares structural homology with GH42 β-galactosidases, whereas most of the spatial positions of the active site residues are identical to those of GH35 β-galactosidases. We found that upon dimerization, the active site of GlmA changes shape, enhancing its ability to hydrolyze the smaller substrate in a manner similar to that of homotrimeric GH42 β-galactosidase. However, GlmA can differentiate glucosamine from galactose based on one charged residue while using the "evolutionary heritage residue" it shares with GH35 β-galactosidase. Our study suggests that GH35 and GH42 β-galactosidases evolved by exploiting the structural features of GlmA.
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Affiliation(s)
- Shouhei Mine
- From the Biomedical Research Institute (BMD), National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577,
| | - Masahiro Watanabe
- the Research Institute for Sustainable Chemistry (ISC), AIST, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, and
| | - Saori Kamachi
- the Research Institute for Sustainable Chemistry (ISC), AIST, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, and
| | - Yoshito Abe
- the Laboratory of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tadashi Ueda
- the Laboratory of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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18
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Ding H, Zeng Q, Zhou L, Yu Y, Chen B. Biochemical and Structural Insights into a Novel Thermostable β-1,3-Galactosidase from Marinomonas sp. BSi20414. Mar Drugs 2017; 15:md15010013. [PMID: 28075353 PMCID: PMC5295233 DOI: 10.3390/md15010013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/20/2016] [Accepted: 12/24/2016] [Indexed: 12/25/2022] Open
Abstract
A novel β-1,3-galactosidase, designated as MaBGA (β-galactosidase from Marinomonas sp. BSi20414), was successfully purified to homogeneity from Marinomonas sp. BSi20414 isolated from Arctic sea ice by ammonium sulfate precipitation and anion exchange chromatography, resulting in an 8.12-fold increase in specific activity and 9.9% recovery in total activity. MaBGA displayed its maximum activity at pH 6.0 and 60 °C, and maintained at least 90% of its initial activity over the pH range of 5.0-8.0 after incubating for 1 h. It also exhibited considerable thermal stability, which retained 76% of its initial activity after incubating at 50 °C for 6 h. In contrast to other β-galactosidases, MaBGA displayed strict substrate specificity, not only for the glycosyl group, but also for the linkage type. To better understand the structure-function relationship, the encoding gene of MaBGA was obtained and subject to bioinformatics analysis. Multiple alignments and phylogenetic analysis revealed that MaBGA belonged to the glycoside hydrolase family 42 and had closer genetic relationships with thermophilic β-galactosidases of extremophiles. With the aid of homology modeling and molecular docking, we proposed a reasonable explanation for the linkage selectivity of MaBGA from a structural perspective. On account of the robust stability and 1,3-linkage selectivity, MaBGA would be a promising candidate in the biosynthesis of galacto-oligosaccharide with β1-3 linkage.
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Affiliation(s)
- Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Qian Zeng
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Lili Zhou
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
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19
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Soto D, Escobar S, Guzmán F, Cárdenas C, Bernal C, Mesa M. Structure-activity relationships on the study of β-galactosidase folding/unfolding due to interactions with immobilization additives: Triton X-100 and ethanol. Int J Biol Macromol 2016; 96:87-92. [PMID: 27965126 DOI: 10.1016/j.ijbiomac.2016.12.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 12/28/2022]
Abstract
Improving the enzyme stability is a challenge for allowing their practical application. The surfactants are stabilizing agents, however, there are still questions about their influence on enzyme properties. The structure-activity/stability relationship for β-galactosidase from Bacillus circulans is studied here by Circular Dichroism and activity measurements, as a function of temperature and pH. The tendency of preserving the β-sheet and α-helix structures at temperatures below 65°C and different pH is the result of the balance between the large- and short-range effects, respecting to the active site. This information is fundamental for explaining the structural changes of this enzyme in the presence of Triton X-100 surfactant and ethanol. The enzyme thermal stabilization in the presence of this surfactant responds to the rearrangement of the secondary structure for having optimal activity/stability. The effect of ethanol is more related with changes in the dielectric properties of the aqueous solution than with protein structural transformations. These results contribute to understand the effects of surfactant-enzyme interactions on the enzyme behavior, from the structural point of view and to rationalize the surfactant-based stabilizing strategies for β-galactosidades.
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Affiliation(s)
- Dayana Soto
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia - UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Sindy Escobar
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia - UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Fanny Guzmán
- Laboratorio de Síntesis de Péptidos e Inmunología Molecular, Pontificia Universidad Católica de Valparaíso, Núcleo de Biotecnología Curauma, Valparaíso, Chile
| | - Constanza Cárdenas
- Laboratorio de Síntesis de Péptidos e Inmunología Molecular, Pontificia Universidad Católica de Valparaíso, Núcleo de Biotecnología Curauma, Valparaíso, Chile
| | - Claudia Bernal
- Departamento de Ingeniería de Alimentos, Universidad de La Serena, Raul Bitran 1305, La Serena, Chile
| | - Monica Mesa
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia - UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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20
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Talens-Perales D, Górska A, Huson DH, Polaina J, Marín-Navarro J. Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2). PLoS One 2016; 11:e0168035. [PMID: 27930742 PMCID: PMC5145203 DOI: 10.1371/journal.pone.0168035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/23/2016] [Indexed: 11/23/2022] Open
Abstract
In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.
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Affiliation(s)
- David Talens-Perales
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
| | - Anna Górska
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Daniel H. Huson
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Julio Polaina
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
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21
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Fleming E, Camilli A. ManLMN is a glucose transporter and central metabolic regulator in Streptococcus pneumoniae. Mol Microbiol 2016; 102:467-487. [PMID: 27472033 PMCID: PMC5116393 DOI: 10.1111/mmi.13473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 01/24/2023]
Abstract
Streptococcus pneumoniae is a common colonizer of the human nasopharynx and a leading cause of bacterial pneumonia and otitis media, among other invasive diseases. During both colonization and invasive disease S. pneumoniae ferments host-derived carbohydrates as its primary means of generating energy. This pathogen is adept at transporting and metabolizing a wide variety of carbohydrates. We found the highly conserved PTS ManLMN contributes to growth on glucose and is also essential for growth on a variety of nonpreferred carbohydrates, suggesting it is a multisubstrate transporter. Exploration of this phenotype revealed ManLMN is required for inducing expression of downstream metabolic genes in response to carbohydrate stimuli. We further demonstrate that ManLMN's role as a constitutively expressed transporter is likely unique and integral to pneumococcus's strategy of carbon catabolite repression (CCR). Using a selection for suppressors, we explored how ManLMN is integrated into the CCR regulatory framework in S. pneumoniae. We identified two hypothetical small proteins and the virulence regulator SmrC as potential mediators of CCR in connection with ManLMN. Characterization of these two hypothetical proteins revealed they influence transcriptional regulation of carbohydrate transporters. We propose a model unifying these observations in which ManLMN is a versatile surveyor of available carbohydrates in S. pneumoniae.
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Affiliation(s)
- Eleanor Fleming
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Andrew Camilli
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA.
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22
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Structure of a plant β-galactosidase C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1411-8. [PMID: 27451952 DOI: 10.1016/j.bbapap.2016.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/17/2016] [Accepted: 07/19/2016] [Indexed: 02/02/2023]
Abstract
Most plant β-galactosidases, which belong to glycoside hydrolase family 35, have a C-terminal domain homologous to animal galactose and rhamnose-binding lectins. To investigate the structure and function of this domain, the C-terminal domain of the rice (Oryza sativa L.) β-galactosidase 1 (OsBGal1 Cter) was expressed in Escherichia coli and purified to homogeneity. The free OsBGal1 Cter is monomeric with a native molecular weight of 15kDa. NMR spectroscopy indicated that OsBGal1 Cter comprises five β-strands and one α-helix. The structure of this domain is similar to lectin domains from animals, but loops A and C of OsBGal1 Cter are longer than the corresponding loops from related animal lectins with known structures. In addition, loop A of OsBGal1 Cter was not well defined, suggesting it is flexible. Although OsBGal1 Cter was predicted to be a galactose/rhamnose-binding domain, binding with rhamnose, galactose, glucose, β-1,4-d-galactobiose and raffinose could not be observed in NMR experiments.
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23
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Eda M, Matsumoto T, Ishimaru M, Tada T. Structural and functional analysis of tomato β-galactosidase 4: insight into the substrate specificity of the fruit softening-related enzyme. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:300-7. [PMID: 26959282 DOI: 10.1111/tpj.13160] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/25/2016] [Accepted: 02/29/2016] [Indexed: 05/23/2023]
Abstract
Plant β-galactosidases hydrolyze cell wall β-(1,4)-galactans to play important roles in cell wall expansion and degradation, and turnover of signaling molecules, during ripening. Tomato β-galactosidase 4 (TBG4) is an enzyme responsible for fruit softening through the degradation of β-(1,4)-galactan in the pericarp cell wall. TBG4 is the only enzyme among TBGs 1-7 that belongs to the β-galactosidase/exo-β-(1,4)-galactanase subfamily. The enzyme can hydrolyze a wide range of plant-derived (1,4)- or 4-linked polysaccharides, and shows a strong ability to attack β-(1,4)-galactan. To gain structural insight into its substrate specificity, we determined crystal structures of TBG4 and its complex with β-d-galactose. TBG4 comprises a catalytic TIM barrel domain followed by three β-sandwich domains. Three aromatic residues in the catalytic site that are thought to be important for substrate specificity are conserved in GH35 β-galactosidases derived from bacteria, fungi and animals; however, the crystal structures of TBG4 revealed that the enzyme has a valine residue (V548) replacing one of the conserved aromatic residues. The V548W mutant of TBG4 showed a roughly sixfold increase in activity towards β-(1,6)-galactobiose, and ~0.6-fold activity towards β-(1,4)-galactobiose, compared with wild-type TBG4. Amino acid residues corresponding to V548 of TBG4 thus appear to determine the substrate specificities of plant β-galactosidases towards β-1,4 and β-1,6 linkages.
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Affiliation(s)
- Masahiro Eda
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Takashi Matsumoto
- Application Laboratories, Rigaku Corporation, Akishima, Tokyo, 196-8666, Japan
| | - Megumi Ishimaru
- Faculty of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Wakayama, 649-6493, Japan
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
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24
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Eda M, Ishimaru M, Tada T. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of tomato β-galactosidase 4. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:153-6. [PMID: 25664788 DOI: 10.1107/s2053230x14027800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/20/2014] [Indexed: 11/10/2022]
Abstract
Plant β-galactosidases play important roles in carbohydrate-reserve mobilization, cell-wall expansion and degradation, and turnover of signalling molecules during ripening. Tomato β-galactosidase 4 (TBG4) not only has β-galactosidase activity but also has exo-β-(1,4)-galactanase activity, and prefers β-(1,4)-galactans longer than pentamers as its substrates; most other β-galactosidases only have the former activity. Recombinant TBG4 protein expressed in the yeast Pichia pastoris was crystallized by the sitting-drop vapour-diffusion method using PEG 10,000 as a precipitant. The crystals belonged to the orthorhombic space group P212121, with unit-parameters a = 92.82, b = 96.30, c = 159.26 Å, and diffracted to 1.65 Å resolution. Calculation of the Matthews coefficient suggested the presence of two monomers per asymmetric unit (VM = 2.2 Å(3) Da(-1)), with a solvent content of 45%.
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Affiliation(s)
- Masahiro Eda
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Megumi Ishimaru
- Faculty of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Wakayama 631-8505, Japan
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
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25
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Fan QH, Claunch KA, Striegler S. Structure–Activity Relationship of Highly Potent Galactonoamidine Inhibitors toward β-Galactosidase (Aspergillus oryzae). J Med Chem 2014; 57:8999-9009. [PMID: 25295392 DOI: 10.1021/jm501111y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qiu-Hua Fan
- Department of Chemistry and
Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Kailey A. Claunch
- Department of Chemistry and
Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Susanne Striegler
- Department of Chemistry and
Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
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26
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Eda M, Ishimaru M, Tada T, Sakamoto T, Kotake T, Tsumuraya Y, Mort AJ, Gross KC. Enzymatic activity and substrate specificity of the recombinant tomato β-galactosidase 1. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1454-60. [PMID: 25105231 DOI: 10.1016/j.jplph.2014.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 05/20/2023]
Abstract
The open reading frame of tomato β-galactosidase 1 was expressed in yeast, and the enzymatic properties and substrate specificity were investigated. The enzyme had peak activity at pH 5.0 and 40-50°C. TBG1 was active on β-(1,3)- and β-(1,6)-galactobiose and lactose. TBG1 released galactose from lupin galactan, tomato fruit alkali soluble pectin, arabinogalactan, gum arabic and methyl β-(1,6)-galactohexaoside, but not from labeled β-(1,4)-galactoheptaose. TBG1 was assessed for its ability to degrade three galactosyl-containing cell wall fractions purified from different development and ripening stages of tomato fruit. TBG1 released galactose from all of the fractions from all of the stages tested. TBG1 activity was highest on the hemicellulose fraction at the 10 and 20d after pollination stage. This result is not correlated the with TBG1 expression pattern. TBG1 might act on a small but specific set of polysaccharide containing galactose.
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Affiliation(s)
- Masahiro Eda
- Graduate School of Science, Osaka Prefecture University, Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Megumi Ishimaru
- Faculty of Biology-Oriented Science and Technology, Kinki University, Nishimitani, Kinokawa, Wakayama 649-6493, Japan.
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Tatsuji Sakamoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yoichi Tsumuraya
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078-3035, USA
| | - Kenneth C Gross
- Produce Quality and Safety Laboratory, USDA-ARS, Building 002, Henry A. Wallace Beltsville Area Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
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Larsbrink J, Thompson AJ, Lundqvist M, Gardner JG, Davies GJ, Brumer H. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus. Mol Microbiol 2014; 94:418-33. [PMID: 25171165 PMCID: PMC4285296 DOI: 10.1111/mmi.12776] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities – and notable differences – to the complex polysaccharide utilization loci of the Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
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Rational design of a glycosynthase by the crystal structure of β-galactosidase from Bacillus circulans (BgaC) and its use for the synthesis of N-acetyllactosamine type 1 glycan structures. J Biotechnol 2014; 191:78-85. [PMID: 25034434 DOI: 10.1016/j.jbiotec.2014.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/01/2014] [Accepted: 07/04/2014] [Indexed: 11/20/2022]
Abstract
The crystal structure of β-galactosidase from Bacillus circulans (BgaC) was determined at 1.8Å resolution. The overall structure of BgaC consists of three distinct domains, which are the catalytic domain with a TIM-barrel structure and two all-β domains (ABDs). The main-chain fold and steric configurations of the acidic and aromatic residues at the active site were very similar to those of Streptococcus pneumoniae β(1,3)-galactosidase BgaC in complex with galactose. The structure of BgaC was used for the rational design of a glycosynthase. BgaC belongs to the glycoside hydrolase family 35. The essential nucleophilic amino acid residue has been identified as glutamic acid at position 233 by site-directed mutagenesis. Construction of the active site mutant BgaC-Glu233Gly gave rise to a galactosynthase transferring the sugar moiety from α-d-galactopyranosyl fluoride (αGalF) to different β-linked N-acetylglucosamine acceptor substrates in good yield (40-90%) with a remarkably stable product formation. Enzymatic syntheses with BgaC-Glu233Gly afforded the stereo- and regioselective synthesis of β1-3-linked key galactosides like galacto-N-biose or lacto-N-biose.
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Díez-Municio M, Herrero M, Olano A, Moreno FJ. Synthesis of novel bioactive lactose-derived oligosaccharides by microbial glycoside hydrolases. Microb Biotechnol 2014; 7:315-31. [PMID: 24690139 PMCID: PMC4241725 DOI: 10.1111/1751-7915.12124] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 12/17/2022] Open
Abstract
Prebiotic oligosaccharides are increasingly demanded within the Food Science domain because of the interesting healthy properties that these compounds may induce to the organism, thanks to their beneficial intestinal microbiota growth promotion ability. In this regard, the development of new efficient, convenient and affordable methods to obtain this class of compounds might expand even further their use as functional ingredients. This review presents an overview on the most recent interesting approaches to synthesize lactose-derived oligosaccharides with potential prebiotic activity paying special focus on the microbial glycoside hydrolases that can be effectively employed to obtain these prebiotic compounds. The most notable advantages of using lactose-derived carbohydrates such as lactosucrose, galactooligosaccharides from lactulose, lactulosucrose and 2-α-glucosyl-lactose are also described and commented.
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Affiliation(s)
- Marina Díez-Municio
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - Miguel Herrero
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - Agustín Olano
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
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The β-galactosidase (BgaC) of the zoonotic pathogen Streptococcus suis is a surface protein without the involvement of bacterial virulence. Sci Rep 2014; 4:4140. [PMID: 24556915 PMCID: PMC3931136 DOI: 10.1038/srep04140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/30/2014] [Indexed: 12/27/2022] Open
Abstract
Streptococcal pathogens have evolved to express exoglycosidases, one of which is BgaC β-galactosidase, to deglycosidate host surface glycolconjucates with exposure of the polysaccharide receptor for bacterial adherence. The paradigm BgaC protein is the bgaC product of Streptococcus, a bacterial surface-exposed β-galactosidase. Here we report the functional definition of the BgaC homologue from an epidemic Chinese strain 05ZYH33 of the zoonotic pathogen Streptococcus suis. Bioinformatics analyses revealed that S. suis BgaC shared the conserved active sites (W240, W243 and Y454). The recombinant BgaC protein of S. suis was purified to homogeneity. Enzymatic assays confirmed its activity of β-galactosidase. Also, the hydrolysis activity was found to be region-specific and sugar-specific for the Gal β-1,3-GlcNAc moiety of oligosaccharides. Flow cytometry analyses combined with immune electron microscopy demonstrated that S. suis BgaC is an atypical surface-anchored protein in that it lacks the “LPXTG” motif for typical surface proteins. Integrative evidence from cell lines and mice-based experiments showed that an inactivation of bgaC does not significantly impair the ability of neither adherence nor anti-phagocytosis, and consequently failed to attenuate bacterial virulence, which is somewhat similar to the scenario seen with S. pneumoniae. Therefore we concluded that S. suis BgaC is an atypical surface-exposed protein without the involvement of bacterial virulence.
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Li C, Kim YW. Characterization of a Galactosynthase Derived fromBacillus circulansβ-Galactosidase: Facile Synthesis ofD-Lacto- andD-Galacto-N-bioside. Chembiochem 2014; 15:522-6. [DOI: 10.1002/cbic.201300699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Indexed: 11/10/2022]
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Li C, Ahn HJ, Kim JH, Kim YW. Transglycosylation of engineered cyclodextrin glucanotransferases as O-glycoligases. Carbohydr Polym 2014; 99:39-46. [DOI: 10.1016/j.carbpol.2013.08.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 11/28/2022]
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Maksimainen MM, Lampio A, Mertanen M, Turunen O, Rouvinen J. The crystal structure of acidic β-galactosidase from Aspergillus oryzae. Int J Biol Macromol 2013; 60:109-15. [DOI: 10.1016/j.ijbiomac.2013.05.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 12/27/2022]
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