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Li Y, Tang X, Chen L, Ma A, Zhu W, Huang W, Li J. Improvement of the fibrinolytic activity, acid resistance and thermostability of nattokinase by surface charge engineering. Int J Biol Macromol 2023; 253:127373. [PMID: 37839602 DOI: 10.1016/j.ijbiomac.2023.127373] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Nattokinase is a promising thrombolytic drug due to its powerful fibrinolytic effect and few side effects. However, the low fibrinolytic activity and stability of nattokinase have limited its industrial production and oral application. In this study, the basic and neutral amino acid residues on the surface of recombinant nattokinase AprY from Bacillus mojavensis LY-06 (rAprY) were mutated to acidic amino acid residues by surface charge engineering strategy, and two variants K12D and N109D with 92.6 % and 8.4 % increased fibrinolytic activity were obtained. The R45E variant with enhanced acid stability and thermostability was also screened, its acid stability at pH 4 and t1/2 at 55 °C were 3.7-fold and 1.8-fold higher than that of wild type rAprY, respectively. Bioinformatics analysis showed that the increased activities of K12D and N109D variants were related to the increased flexibility of the region around their active centers. The increased rigidity of 97-103 amino acid residues around the active center of R45E may be the reason for its enhanced stability and reduced catalytic activity. The multipoint mutation K12D-N109D (M2)'s catalytic activity did not increase cumulatively, but its pH stability did. The nattokinase variants generated in this study have potential for industrial production and application.
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Affiliation(s)
- Yuan Li
- Institute of Materia Medica, Xinjiang University, Urumqi 830017, China
| | - Xiyu Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Liangqi Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Aixia Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Wenhui Zhu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | | | - Jinyao Li
- Institute of Materia Medica, Xinjiang University, Urumqi 830017, China; Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China.
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2
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Zhang Z, Zhao Z, Huang K, Liang Z. Acid-resistant enzymes: the acquisition strategies and applications. Appl Microbiol Biotechnol 2023; 107:6163-6178. [PMID: 37615723 DOI: 10.1007/s00253-023-12702-1] [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: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Enzymes have promising applications in chemicals, food, pharmaceuticals, and other variety products because of their high efficiency, specificity, and environmentally friendly properties. However, due to the complexity of raw materials, pH, temperature, solvents, etc., the application range of enzymes is greatly limited in the industry. Protein engineering and enzyme immobilization are classical strategies to overcome the limitations of industrial applications. Although the pH tendency of enzymes has been extensively researched, the mechanism underlying enzyme acid resistance is unclear, and a less practical strategy for altering the pH propensity of enzymes has been suggested. This review proposes that the optimum pH of enzyme is determined by the pKa values of active center ionizable amino acid residues. Three levels of acquiring acid-resistant enzymes are summarized: mining from extreme environments and enzyme databases, modification with protein engineering and enzyme microenvironment engineering, and de novo synthesis. The industrial applications of acid-resistant enzymes in chemicals, food, and pharmaceuticals are also summarized. KEY POINTS: • The mechanism of enzyme acid resistance is fundamentally determined. • The three aspects of the method for acquiring acid-resistant enzymes are summarized. • Computer-aided strategies and artificial intelligence are used to obtain acid-resistant enzymes.
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Affiliation(s)
- Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China.
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China.
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3
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Li Y, Chen L, Tang X, Zhu W, Ma A, Shi C, Li J. Combined Computer-Aided Predictors to Improve the Thermostability of Nattokinase. Foods 2023; 12:3045. [PMID: 37628044 PMCID: PMC10453301 DOI: 10.3390/foods12163045] [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: 07/18/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Food-derived nattokinase has strong thrombolytic activity and few side effects. In the field of medicine, nattokinase has been developed as an adjuvant drug for the treatment of thrombosis, and nattokinase-rich beverages and health foods have also shown great potential in the field of food development. At present, the poor thermostability of nattokinase limits its industrial production and application. In this study, we used several thermostability-prediction algorithms to predict nattokinase from Bacillus mojavensis LY-06 (AprY), and screened two variants S33T and T174V with increased thermostability and fibrinolytic activity. The t1/2 of S33T and T174V were 8.87-fold and 2.51-fold those of the wild type AprY, respectively, and their enzyme activities were also increased (1.17-fold and 1.28-fold, respectively). Although the thermostability of N218L was increased by 2.7 times, the fibrinolytic activity of N218L was only 73.3% of that of wild type AprY. The multiple-point mutation results showed that S33T-N218L and S33T-T174V-N218L variants lost their activity, and the T174V-N218L variant did not show any significant change in catalytic performance, while S33T-T174V increased its thermostability and activity by 21.3% and 24.8%, respectively. Although the S33T-T174V variant did not show the additive effect of thermostability, it combined the excellent transient thermostability of S33T with the better thrombolytic activity of T174V. Bioinformatics analysis showed that the overall structure of S33T and T174V variants tended to be stable, while the structure of S33T-T174V variant was more flexible. Local structure analysis showed that the increased rigidity of the active center region (positions 64-75) and the key loop region (positions 129-130, 155-163, 187-192, 237-241, and 268-270) determined the increased thermostability of all variants. In addition, the enhanced flexibility of S33T-T174V variant in the Ca1 binding region (positions 1-4, 75-82) and the peripheral region of the catalytic pocket (positions 210-216) may account for the inability to superpose its thermostability. We explored the effective strategy to enhance the thermostability of nattokinase, and the resulting variants have potential industrial production and application.
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Affiliation(s)
- Yuan Li
- Institute of Materia Medica, Xinjiang University, Urumqi 830017, China;
| | - Liangqi Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
| | - Xiyu Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
| | - Wenhui Zhu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
| | - Aixia Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
| | - Changyu Shi
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
| | - Jinyao Li
- Institute of Materia Medica, Xinjiang University, Urumqi 830017, China;
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (L.C.); (X.T.); (W.Z.); (A.M.); (C.S.)
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4
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Li SF, Cheng F, Wang YJ, Zheng YG. Strategies for tailoring pH performances of glycoside hydrolases. Crit Rev Biotechnol 2023; 43:121-141. [PMID: 34865578 DOI: 10.1080/07388551.2021.2004084] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycoside hydrolases (GHs) exhibit high activity and stability under harsh conditions, such as high temperatures and extreme pHs, given their wide use in industrial biotechnology. However, strategies for improving the acidophilic and alkalophilic adaptations of GHs are poorly summarized due to the complexity of the mechanisms of these adaptations. This review not only highlights the adaptation mechanisms of acidophilic and alkalophilic GHs under extreme pH conditions, but also summarizes the recent advances in engineering the pH performances of GHs with a focus on four strategies of protein engineering, enzyme immobilization, chemical modification, and medium engineering (additives). The examples described here summarize the methods used in modulating the pH performances of GHs and indicate that methods integrated in different protein engineering techniques or methods are efficient to generate industrial biocatalysts with the desired pH performance and other adapted enzyme properties.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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5
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Yuan L, Liangqi C, Xiyu T, Jinyao L. Biotechnology, Bioengineering and Applications of Bacillus Nattokinase. Biomolecules 2022; 12:biom12070980. [PMID: 35883536 PMCID: PMC9312984 DOI: 10.3390/biom12070980] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Thrombosis has threatened human health in past decades. Bacillus nattokinase is a potential low-cost thrombolytic drug without side-effects and has been introduced into the consumer market as a functional food or dietary supplement. This review firstly summarizes the biodiversity of sources and the fermentation process of nattokinase, and systematically elucidates the structure, catalytic mechanism and enzymatic properties of nattokinase. In view of the problems of low fermentation yield, insufficient activity and stability of nattokinase, this review discusses the heterologous expression of nattokinase in different microbial hosts and summarizes the protein and genetic engineering progress of nattokinase-producing strains. Finally, this review summarizes the clinical applications of nattokinase.
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Affiliation(s)
- Li Yuan
- Department of Materia Medica, Xinjiang University, Urumqi 830017, China;
| | - Chen Liangqi
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (C.L.); (T.X.)
| | - Tang Xiyu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (C.L.); (T.X.)
| | - Li Jinyao
- Department of Materia Medica, Xinjiang University, Urumqi 830017, China;
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (C.L.); (T.X.)
- Correspondence: ; Tel.: +86-130-0968-6488
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6
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Wang CH, Xiong WP, Huang C, Li XM, Wang QY, Huang RB. Engineering better catalytic activity and acidic adaptation into Kluyveromyces marxianus exoinulinase using site-directed mutagenesis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:2472-2482. [PMID: 33034040 DOI: 10.1002/jsfa.10873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 10/03/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Exoinulinase catalyzes the successive removal of individual fructose moiety from the non-reducing end of the inulin molecule, which is useful for biotechnological applications like producing fructan-based non-grain biomass energy and high-fructose syrup. In this study, an exoinulinase (KmINU) from Kluyveromyces marxianus DSM 5418 was tailored for increased catalytic activity and acidic adaptation for inulin hydrolysis processes by rational site-directed mutagenesis. RESULTS Three mutations, S124Y, N158S and Q215V distal to the catalytic residues of KmINU were designed and heterologously expressed in Pichia pastoris GS115. Compared to the wild-type, S124Y shifted the pH-activity profile towards acidic pH values and increased the catalytic activity and catalytic efficiency by 59% and 99% to 688.4 ± 17.03 s-1 and 568.93 L mmol-1 s-1 , respectively. N158S improved the catalytic activity under acidic pH conditions, giving a maximum value of 464.06 ± 14.06 s-1 on inulin at pH 4.5. Q215V markedly improved the substrate preference for inulin over sucrose by 5.56-fold, and showed catalytic efficiencies of 208.82 and 6.88 L mmol-1 s-1 towards inulin and sucrose, respectively. Molecular modeling and computational docking indicated that structural reorientation may underlie the increased catalytic activity, acidic adaptation and substrate preference. CONCLUSIONS The KmINU mutants may serve as industrially promising candidates for inulin hydrolysis. Protein engineering of exoinulinase here provides a successful example of the extent to which mutating non-conserved substrate recognition and binding residues distal to the active site can be used for industrial enzyme improvements. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Wu-Ping Xiong
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Cheng Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Xiao-Ming Li
- Nanning Sinozyme Biotechnology Co., Ltd, Nanning, China
| | - Qing-Yan Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Ri-Bo Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China
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7
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Røjel N, Kari J, Sørensen TH, Borch K, Westh P. pH profiles of cellulases depend on the substrate and architecture of the binding region. Biotechnol Bioeng 2019; 117:382-391. [PMID: 31631319 DOI: 10.1002/bit.27206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/09/2019] [Accepted: 10/13/2019] [Indexed: 01/06/2023]
Abstract
Understanding the pH effect of cellulolytic enzymes is of great technological importance. In this study, we have examined the influence of pH on activity and stability for central cellulases (Cel7A, Cel7B, Cel6A from Trichoderma reesei, and Cel7A from Rasamsonia emersonii). We systematically changed pH from 2 to 7, temperature from 20°C to 70°C, and used both soluble (4-nitrophenyl β- d-lactopyranoside [pNPL]) and insoluble (Avicel) substrates at different concentrations. Collective interpretation of these data provided new insights. An unusual tolerance to acidic conditions was observed for both investigated Cel7As, but only on real insoluble cellulose. In contrast, pH profiles on pNPL were bell-shaped with a strong loss of activity both above and below the optimal pH for all four enzymes. On a practical level, these observations call for the caution of the common practice of using soluble substrates for the general characterization of pH effects on cellulase activity. Kinetic modeling of the experimental data suggested that the nucleophile of Cel7A experiences a strong downward shift in pKa upon complexation with an insoluble substrate. This shift was less pronounced for Cel7B, Cel6A, and for Cel7A acting on the soluble substrate, and we hypothesize that these differences are related to the accessibility of water to the binding region of the Michaelis complex.
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Affiliation(s)
- Nanna Røjel
- Department of Science and Environment (INM), Roskilde University, Roskilde, Denmark.,Present address: Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department of Science and Environment (INM), Roskilde University, Roskilde, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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8
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Saxena H, Hsu B, de Asis M, Zierke M, Sim L, Withers SG, Wakarchuk W. Characterization of a thermostable endoglucanase from Cellulomonas fimi ATCC484. Biochem Cell Biol 2017; 96:68-76. [PMID: 28982013 DOI: 10.1139/bcb-2017-0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacteria in the genus Cellulomonas are well known as secretors of a variety of mesophilic carbohydrate degrading enzymes (e.g., cellulases and hemicellulases), active against plant cell wall polysaccharides. Recent proteomic analysis of the mesophilic bacterium Cellulomonas fimi ATCC484 revealed uncharacterized enzymes for the hydrolysis of plant cell wall biomass. Celf_1230 (CfCel6C), a secreted protein of Cellulomonas fimi ATCC484, is a novel member of the GH6 family of cellulases that could be successfully expressed in Escherichia coli. This enzyme displayed very little enzymatic/hydrolytic activity at 30 °C, but showed an optimal activity around 65 °C, and exhibited a thermal denaturation temperature of 74 °C. In addition, it also strongly bound to filter paper despite having no recognizable carbohydrate binding module. Our experiments show that CfCel6C is a thermostable endoglucanase with activity on a variety of β-glucans produced by an organism that struggles to grow above 30 °C.
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Affiliation(s)
- Hirak Saxena
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Bryan Hsu
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Marc de Asis
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Mirko Zierke
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lyann Sim
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Stephen G Withers
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Warren Wakarchuk
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
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9
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Zhang F, Huang N, Zhou L, Cui W, Liu Z, Zhu L, Liu Y, Zhou Z. Modulating the pH Activity Profiles of Phenylalanine Ammonia Lyase from Anabaena variabilis by Modification of Center-Near Surface Residues. Appl Biochem Biotechnol 2017; 183:699-711. [DOI: 10.1007/s12010-017-2458-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/12/2017] [Indexed: 10/19/2022]
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10
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Okuyama M, Saburi W, Mori H, Kimura A. α-Glucosidases and α-1,4-glucan lyases: structures, functions, and physiological actions. Cell Mol Life Sci 2016; 73:2727-51. [PMID: 27137181 PMCID: PMC11108350 DOI: 10.1007/s00018-016-2247-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022]
Abstract
α-Glucosidases (AGases) and α-1,4-glucan lyases (GLases) catalyze the degradation of α-glucosidic linkages at the non-reducing ends of substrates to release α-glucose and anhydrofructose, respectively. The AGases belong to glycoside hydrolase (GH) families 13 and 31, and the GLases belong to GH31 and share the same structural fold with GH31 AGases. GH13 and GH31 AGases show diverse functions upon the hydrolysis of substrates, having linkage specificities and size preferences, as well as upon transglucosylation, forming specific α-glucosidic linkages. The crystal structures of both enzymes were determined using free and ligand-bound forms, which enabled us to understand the important structural elements responsible for the diverse functions. A series of mutational approaches revealed features of the structural elements. In particular, amino-acid residues in plus subsites are of significance, because they regulate transglucosylation, which is used in the production of industrially valuable oligosaccharides. The recently solved three-dimensional structure of GLase from red seaweed revealed the amino-acid residues essential for lyase activity and the strict recognition of the α-(1 → 4)-glucosidic substrate linkage. The former was introduced to the GH31 AGase, and the resultant mutant displayed GLase activity. GH13 and GH31 AGases hydrate anhydrofructose to produce glucose, suggesting that AGases are involved in the catabolic pathway used to salvage unutilized anhydrofructose.
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Affiliation(s)
- Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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11
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Saburi W, Kobayashi M, Mori H, Okuyama M, Kimura A. Replacement of the catalytic nucleophile aspartyl residue of dextran glucosidase by cysteine sulfinate enhances transglycosylation activity. J Biol Chem 2013; 288:31670-7. [PMID: 24052257 DOI: 10.1074/jbc.m113.491449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dextran glucosidase from Streptococcus mutans (SmDG) catalyzes the hydrolysis of an α-1,6-glucosidic linkage at the nonreducing end of isomaltooligosaccharides and dextran. This enzyme has an Asp-194 catalytic nucleophile and two catalytically unrelated Cys residues, Cys-129 and Cys-532. Cys-free SmDG was constructed by replacement with Ser (C129S/C532S (2CS), the activity of which was the same as that of the wild type, SmDG). The nucleophile mutant of 2CS was generated by substitution of Asp-194 with Cys (D194C-2CS). The hydrolytic activity of D194C-2CS was 8.1 × 10(-4) % of 2CS. KI-associated oxidation of D194C-2CS increased the activity up to 0.27% of 2CS, which was 330 times higher than D194C-2CS. Peptide-mapping mass analysis of the oxidized D194C-2CS (Ox-D194C-2CS) revealed that Cys-194 was converted into cysteine sulfinate. Ox-D194C-2CS and 2CS shared the same properties (optimum pH, pI, and substrate specificity), whereas Ox-D194C-2CS had much higher transglucosylation activity than 2CS. This is the first study indicating that a more acidic nucleophile (-SOO(-)) enhances transglycosylation. The introduction of cysteine sulfinate as a catalytic nucleophile could be a novel approach to enhance transglycosylation.
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Affiliation(s)
- Wataru Saburi
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8689, Japan
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12
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Bu L, Crowley MF, Himmel ME, Beckham GT. Computational investigation of the pH dependence of loop flexibility and catalytic function in glycoside hydrolases. J Biol Chem 2013; 288:12175-86. [PMID: 23504310 DOI: 10.1074/jbc.m113.462465] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ~5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pK(a) values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pK(a) values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pK(a) values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, Colorado School of Mines, Golden, Colorado 80401, USA.
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Tamura M, Miyazaki T, Tanaka Y, Yoshida M, Nishikawa A, Tonozuka T. Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea--a tweezer-like motion in the structure of CcCel6C. FEBS J 2012; 279:1871-82. [PMID: 22429290 DOI: 10.1111/j.1742-4658.2012.08568.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The basidiomycete Coprinopsis cinerea produces five cellobiohydrolases belonging to glycoside hydrolase family 6 (GH6). Among these enzymes, C. cinerea cellulase 6C (CcCel6C), but not C. cinerea cellulase 6A (CcCel6A), can efficiently hydrolyze carboxymethyl cellulose and is constitutively expressed in C. cinerea. In contrast, CcCel6A possesses a cellulose-binding domain, and is strongly induced by cellobiose. Here, we determined the crystal structures of the CcCel6A catalytic domain complexed with a Hepes buffer molecule, with cellobiose, and with p-nitrophenyl β-D-cellotrioside (pNPG3). A notable feature of the GH6 cellobiohydrolases is that the active site is enclosed by two loops to form a tunnel, and the loops have been demonstrated to open and close in response to ligand binding. The enclosed tunnel of CcCel6A-Hepes is seen as the open form, whereas the tunnels of CcCel6A-cellobiose and CcCel6A-pNPG3 adopt the closed form. pNPG3 was not hydrolyzed by CcCel6A, and bound in subsites +1 to +4. On the basis of this observation, we constructed two mutants, CcCel6A D164A and CcCel6C D102A. Neither CcCel6A D164A nor CcCel6C D102A hydrolyze phosphoric acid-swollen cellulose. We have previously determined the crystal structures of CcCel6C unbound and in complex with ligand, both of which adopt the open form. In the present study, both CcCel6A and CcCel6C mutants were identified as the closed form. However, the motion angle of CcCel6C was more than 10-fold greater than that of CcCel6A. The width of the active site cleft of CcCel6C was narrowed, owing to a tweezer-like motion.
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Affiliation(s)
- Mizuki Tamura
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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Pfeffer JM, Clarke AJ. Identification of the first known inhibitors of O-acetylpeptidoglycan esterase: a potential new antibacterial target. Chembiochem 2012; 13:722-31. [PMID: 22351512 DOI: 10.1002/cbic.201100744] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Indexed: 11/08/2022]
Abstract
The O-acetylation of peptidoglycan (PG) is now known to occur in 53 species, including numerous human pathogens such as, Staphylococcus aureus, Bacillus anthracis, species of Enterococcus, Campylobacter jejuni, Helicobacter pylori, Neisseria gonorrhoeae and N. meningitidis. This modification, which occurs at the C-6 hydroxyl of N-acetylmuramoyl residues within PG, serves to regulate autolytic activity during PG metabolism and contributes to pathogenesis and persistence within a host. O-Acetylpeptidoglycan esterase (Ape) was recently discovered as an enzyme responsible for the removal of O-acetyl groups from PG, thus permitting the continued maintenance and metabolism of the sacculus. Recombinant Ape1 from N. gonorrhoeae was purified to apparent homogeneity and optimal storage conditions for the enzyme were determined. Using 4-methylumbelliferyl acetate as substrate, a fluorogenic assay amenable for the high-throughput screening for potential inhibitors was developed and Ape1 was screened against a subset of compounds of the Canadian Compound Collection. The overall Z' score for the screen was 0.62, indicative of a well-suited assay with a sufficient signal window, and the threshold was set at 65 %. After eliminating a number of false-positives, seven compounds were identified as true inhibitors of Ape1, the first to be identified for this class of enzyme. Dose-response curves were generated leading to the identification of five of these compounds with IC(50) values ranging between 0.3 and 23 μM. Of these, purpurin was selected for further analysis and it was found to inhibit the growth of both Gram-positive and Gram-negative bacteria that produce both O-acetylated PG and Ape.
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Affiliation(s)
- John M Pfeffer
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Cockburn DW, Clarke AJ. Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues. Protein Eng Des Sel 2011; 24:429-37. [DOI: 10.1093/protein/gzr004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vuong TV, Wilson DB. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng 2010; 107:195-205. [PMID: 20552664 DOI: 10.1002/bit.22838] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.
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Affiliation(s)
- Thu V Vuong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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