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Muradova M, Proskura A, Canon F, Aleksandrova I, Schwartz M, Heydel JM, Baranenko D, Nadtochii L, Neiers F. Unlocking Flavor Potential Using Microbial β-Glucosidases in Food Processing. Foods 2023; 12:4484. [PMID: 38137288 PMCID: PMC10742834 DOI: 10.3390/foods12244484] [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: 11/20/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Aroma is among of the most important criteria that indicate the quality of food and beverage products. Aroma compounds can be found as free molecules or glycosides. Notably, a significant portion of aroma precursors accumulates in numerous food products as nonvolatile and flavorless glycoconjugates, termed glycosidic aroma precursors. When subjected to enzymatic hydrolysis, these seemingly inert, nonvolatile glycosides undergo transformation into fragrant volatiles or volatiles that can generate odor-active compounds during food processing. In this context, microbial β-glucosidases play a pivotal role in enhancing or compromising the development of flavors during food and beverage processing. β-glucosidases derived from bacteria and yeast can be utilized to modulate the concentration of particular aroma and taste compounds, such as bitterness, which can be decreased through hydrolysis by glycosidases. Furthermore, oral microbiota can influence flavor perception by releasing volatile compounds that can enhance or alter the perception of food products. In this review, considering the glycosidic flavor precursors present in diverse food and beverage products, we underscore the significance of glycosidases with various origins. Subsequently, we delve into emerging insights regarding the release of aroma within the human oral cavity due to the activity of oral microbial glycosidases.
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Affiliation(s)
- Mariam Muradova
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Alena Proskura
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Francis Canon
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Irina Aleksandrova
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Mathieu Schwartz
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Jean-Marie Heydel
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
| | - Denis Baranenko
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Liudmila Nadtochii
- International Research Center “Biotechnologies of the Third Millennium”, Faculty of Biotechnologies (BioTech), ITMO University, 191002 Saint-Petersburg, Russia; (I.A.); (L.N.)
| | - Fabrice Neiers
- Molecular Mechanisms of Flavor Perception, Center for Taste and Feeding Behavior, INRAE, CNRS, University of Burgundy Franche-Comté, 21000 Dijon, France; (A.P.); (F.C.); (M.S.); (J.-M.H.)
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2
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Bitter J, Pfeiffer M, Borg AJE, Kuhlmann K, Pavkov-Keller T, Sánchez-Murcia PA, Nidetzky B. Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation. Nat Commun 2023; 14:7123. [PMID: 37932298 PMCID: PMC10628242 DOI: 10.1038/s41467-023-42750-0] [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: 01/04/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Biological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-D-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn2+ active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in β-elimination of 3-keto C-β-D-glucosides. We show that CGE catalyzes β-elimination of 3-keto O- and C-β-D-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for β-elimination of 3-keto O-β-D-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.
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Affiliation(s)
- Johannes Bitter
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
| | - Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, A-8010, Graz, Austria
| | - Kirill Kuhlmann
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstraße 50/III, A-8010, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstraße 50/III, A-8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, A-8010, Graz, Austria
- BioHealth Field of Excellence, University of Graz, Humboldtstraße 50, A-8010, Graz, Austria
| | - Pedro A Sánchez-Murcia
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingstalstraße 6/III, A-8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, A-8010, Graz, Austria.
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Shin NR, Pauchet Y. First evidence of a horizontally-acquired GH-7 cellobiohydrolase from a longhorned beetle genome. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-14. [PMID: 37533217 DOI: 10.1002/arch.22039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Xylophagous larvae of longhorned beetles (Coleoptera; Cerambycidae) efficiently break down polysaccharides of the plant cell wall, which make the bulk of their food, using a range of carbohydrate-active enzymes (CAZymes). In this study, we investigated the function and evolutionary history of the first identified example of insect-encoded members of glycoside hydrolase family 7 (GH7) derived from the Lamiinae Exocentrus adspersus. The genome of this beetle contained two genes encoding GH7 proteins located in tandem and flanked by transposable elements. Phylogenetic analysis revealed that the GH7 sequences of E. adspersus were closely related to those of Ascomycete fungi, suggesting that they were acquired through horizontal gene transfer (HGT) from fungi. However, they were more distantly related to those encoded by genomes of Crustacea and of protist symbionts of termites and cockroaches, supporting that the same enzyme family was recruited several times independently in Metazoa during the course of their evolution. The recombinant E. adspersus GH7 was found to primarily break down cellulose polysaccharides into cellobiose, indicating that it is a cellobiohydrolase, and could also use smaller cellulose oligomers as substrates. Additionally, the cellobiohydrolase activity was boosted by the presence of calcium chloride. Our findings suggest that the combination of GH7 cellobiohydrolases with other previously characterized endo-β-1,4-glucanases and β-glucosidases allows longhorned beetles like E. adspersus to efficiently break down cellulose into monomeric glucose.
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Affiliation(s)
- Na Ra Shin
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
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4
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He P, Wang S, Li S, Liu S, Zhou S, Wang J, Tao J, Wang D, Wang R, Ma W. Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C-glycoside cleaving enzyme and an O- to C-glycoside isomerase. Acta Pharm Sin B 2023; 13:246-255. [PMID: 36815035 PMCID: PMC9939296 DOI: 10.1016/j.apsb.2022.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
The C-glycosidic bond that connects the sugar moiety with aglycone is difficult to be broken or made due to its inert nature. The knowledge of C-glycoside breakdown and synthesis is very limited. Recently, the enzyme DgpA/B/C cascade from a human intestinal bacterium PUE was identified to specifically cleave the C-glycosidic bond of puerarin (daidzein-8-C-glucoside). Here we investigated how puerarin is recognized and oxidized by DgpA based on crystal structures of DgpA with or without substrate and biochemical characterization. More strikingly, we found that apart from being a C-glycoside cleaving enzyme, DgpA/B/C is capable of efficiently converting O- to C-glycoside showing the activity as a structure isomerase. A possible mechanistic model was proposed dependently of the simulated complex structure of DgpB/C with 3″-oxo-daidzin and structure-based mutagenesis. Our findings not only shed light on understanding the enzyme-mediated C-glycosidic bond breakage and formation, but also may help to facilitate stereospecific C-glycoside synthesis in pharmaceutical industry.
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Affiliation(s)
- Pengfei He
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Sha Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Sen Li
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Siqi Liu
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shuqi Zhou
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jing Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiayue Tao
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | | | - Rufeng Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China,Corresponding authors. Tel./fax: +86 10 53912152.
| | - Wenfu Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China,Corresponding authors. Tel./fax: +86 10 53912152.
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5
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Jiang Z, Qu L, Song G, Liu J, Zhong G. The Potential Binding Interaction and Hydrolytic Mechanism of Carbaryl with the Novel Esterase PchA in Pseudomonas sp. PS21. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2136-2145. [PMID: 35147028 DOI: 10.1021/acs.jafc.1c06465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microbial bioremediation is a very potent and eco-friendly approach to alleviate pesticide pollution in agricultural ecosystems, and hydrolase is an effective element for contaminant degradation. In the present study, a novel Mn2+-dependent esterase, PchA, that efficiently hydrolyzes carbamate pesticides with aromatic structures was identified from Pseudomonas sp. PS21. The hydrolytic activity was confirmed to be related closely to the core catalytic domain, which consists of six residues. The crucial residues indirectly stabilized the position of carbaryl via chelating Mn2+ according to the binding model clarified by molecular simulations, and the additional hydrophobic interactions between carbaryl with several hydrophobic residues also stabilized the binding conformation. The residue Glu398, by serving as the general base, might activate a water molecule and facilitate PchA catalysis. This work offers valuable insights into the binding interaction and hydrolytic mechanism of carbaryl with the hydrolase PchA and will be crucial to designing strategies leading to the protein variants that are capable of degrading related contaminants.
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Affiliation(s)
- Zhiyan Jiang
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Liwen Qu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Gaopeng Song
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Jie Liu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Guohua Zhong
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, P.R. China
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Structural basis of catalysis and substrate recognition by the NAD(H)-dependent α-d-glucuronidase from the glycoside hydrolase family 4. Biochem J 2021; 478:943-959. [PMID: 33565573 DOI: 10.1042/bcj20200824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022]
Abstract
Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure-function relationships within the unique GH4 family.
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Walter A, Friz S, Mayer C. Chitin, Chitin Oligosaccharide, and Chitin Disaccharide Metabolism of Escherichia coli Revisited: Reassignment of the Roles of ChiA, ChbR, ChbF, and ChbG. Microb Physiol 2021; 31:178-194. [PMID: 33794535 DOI: 10.1159/000515178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 11/19/2022]
Abstract
Escherichia coli is unable to grow on polymeric and oligomeric chitin, but grows on chitin disaccharide (GlcNAc-GlcNAc; N,N'-diacetylchitobiose) and chitin trisaccharide (GlcNAc-GlcNAc-GlcNAc; N,N',N''-triacetylchitotriose) via expression of the chb operon (chbBCARFG). The phosphotransferase system (PTS) transporter ChbBCA facilitates transport of both saccharides across the inner membrane and their concomitant phosphorylation at the non-reducing end, intracellularly yielding GlcNAc 6-phosphate-GlcNAc (GlcNAc6P-GlcNAc) and GlcNAc6P-GlcNAc-GlcNAc, respectively. We revisited the intracellular catabolism of the PTS products, thereby correcting the reported functions of the 6-phospho-glycosidase ChbF, the monodeacetylase ChbG, and the transcriptional regulator ChbR. Intracellular accumulation of glucosamine 6P-GlcNAc (GlcN6P-GlcNAc) and GlcN6P-GlcNAc-GlcNAc in a chbF mutant unraveled a role for ChbG as a monodeacetylase that removes the N-acetyl group at the non-reducing end. Consequently, GlcN6P- but not GlcNAc6P-containing saccharides likely function as coactivators of ChbR. Furthermore, ChbF removed the GlcN6P from the non-reducing terminus of the former saccharides, thereby degrading the inducers of the chb operon and facilitating growth on the saccharides. Consequently, ChbF was unable to hydrolyze GlcNAc6P-residues from the non-reducing end, contrary to previous assumptions but in agreement with structural modeling data and with the unusual catalytic mechanism of the family 4 of glycosidases, to which ChbF belongs. We also refuted the assumption that ChiA is a bifunctional endochitinase/lysozyme ChiA, and show that it is unable to degrade peptidoglycans but acts as a bona fide chitinase in vitro and in vivo, enabling growth of E. coli on chitin oligosaccharides when ectopically expressed. Overall, this study revises our understanding of the chitin, chitin oligosaccharide, and chitin disaccharide metabolism of E. coli.
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Affiliation(s)
- Axel Walter
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Simon Friz
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls Universität Tübingen, Tübingen, Germany
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Müller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C. The exo-β-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. J Biol Chem 2021; 296:100519. [PMID: 33684445 PMCID: PMC8054146 DOI: 10.1016/j.jbc.2021.100519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 11/11/2022] Open
Abstract
Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that catalyze an endo-lytic cleavage of peptidoglycan; i.e., they hydrolyze the β-1,4-glycosidic bonds connecting N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). In contrast, little is known about exo-β-N-acetylmuramidases, which catalyze an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We now report that ybbC of B. subtilis, renamed namZ, encodes the reported exo-β-N-acetylmuramidase. A ΔnamZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover and recycling. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-l-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. A structure model of NamZ, built on the basis of two crystal structures of putative orthologs from Bacteroides fragilis, revealed a two-domain structure including a Rossmann-fold-like domain that constitutes a unique glycosidase fold. Thus, NamZ, a member of the DUF1343 protein family of unknown function, is now classified as the founding member of a new family of glycosidases (CAZy GH171; www.cazy.org/GH171.html). NamZ-like peptidoglycan hexosaminidases are mainly present in the phylum Bacteroidetes and less frequently found in individual genomes within Firmicutes (Bacilli, Clostridia), Actinobacteria, and γ-proteobacteria.
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Affiliation(s)
- Maraike Müller
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Matthew Calvert
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Chemistry, Saarland University, Saarbrücken, Germany
| | - Isabel Hottmann
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Robert Maria Kluj
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Tim Teufel
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Katja Balbuchta
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Alicia Engelbrecht
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Khaled A Selim
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany; Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Center, Giza, Egypt
| | - Qingping Xu
- GM/CA @ APS, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Chemistry, Saarland University, Saarbrücken, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
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Mohapatra SB, Manoj N. A conserved π-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140523. [PMID: 32853774 DOI: 10.1016/j.bbapap.2020.140523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Here, we characterize the role of a π-helix in the molecular mechanisms underlying thermoadaptation in the glycoside hydrolase family 4 (GH4). The interspersed π-helix present in a subgroup is evolutionarily related to a conserved α-helix in other orthologs by a single residue insertion/deletion event. The insertional residue, Phe407, in a hyperthermophilic α-glucuronidase, makes specific interactions across the inter-subunit interface. In order to establish the sequence-structure-stability implications of the π-helix, the wild-type and the deletion variant (Δ407) were characterized. The variant showed a significant lowering of melting temperature and optimum temperature for the highest activity. Crystal structures of the proteins show a transformation of the π-helix to a continuous α-helix in the variant, identical to that in orthologs lacking this insertion. Thermodynamic parameters were determined from stability curves representing the temperature dependence of unfolding free energy. Though the proteins display maximum stabilities at similar temperatures, a higher melting temperature in the wild-type is achieved by a combination of higher enthalpy and lower heat capacity of unfolding. Comparisons of the structural changes, and the activity and thermodynamic profiles allow us to infer that specific non-covalent interactions, and the existence of residual structure in the unfolded state, are crucial determinants of its thermostability. These features permit the enzyme to balance the preservation of structure at a higher temperature with the thermodynamic stability required for optimum catalysis.
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Affiliation(s)
- Samar Bhallabha Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Vetter ND, Jagdhane RC, Richter BJ, Palmer DRJ. Carbocyclic Substrate Analogues Reveal Kanosamine Biosynthesis Begins with the α-Anomer of Glucose 6-Phosphate. ACS Chem Biol 2020; 15:2205-2211. [PMID: 32786294 DOI: 10.1021/acschembio.0c00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NtdC is an NAD-dependent dehydrogenase that catalyzes the conversion of glucose 6-phosphate (G6P) to 3-oxo-glucose 6-phosphate (3oG6P), the first step in kanosamine biosynthesis in Bacillus subtilis and other closely-related bacteria. The NtdC-catalyzed reaction is unusual because 3oG6P undergoes rapid ring opening, resulting in a 1,3-dicarbonyl compound that is inherently unstable due to enolate formation. We have reported the steady-state kinetic behavior of NtdC, but many questions remain about the nature of this reaction, including whether it is the α-anomer, β-anomer, or open-chain form that is the substrate for the enzyme. Here, we report the synthesis of carbocyclic G6P analogues by two routes, one based upon the Ferrier II rearrangement to generate the carbocycle and one based upon a Claisen rearrangement. We were able to synthesize both pseudo-anomers of carbaglucose 6-phosphate (C6P) using the Ferrier approach, and activity assays revealed that the pseudo-α-anomer is a good substrate for NtdC, while the pseudo-β-anomer and the open-chain analogue, sorbitol 6-phosphate (S6P), are not substrates. A more efficient synthesis of α-C6P was achieved using the Claisen rearrangement approach, which allowed for a thorough evaluation of the NtdC-catalyzed oxidation of α-C6P. The requirement for the α-anomer indicates that NtdC and NtdA, the subsequent enzyme in the pathway, have co-evolved to recognize the α-anomer in order to avoid mutarotation between enzymatic steps.
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Affiliation(s)
- Natasha D. Vetter
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Rajendra C. Jagdhane
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Brett J. Richter
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - David R. J. Palmer
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
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11
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Bhatia S, Singh A, Batra N, Singh J. Microbial production and biotechnological applications of α-galactosidase. Int J Biol Macromol 2019; 150:1294-1313. [PMID: 31747573 DOI: 10.1016/j.ijbiomac.2019.10.140] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
α-Galactosidase, (E.C. 3.2.1.22) is an exoglycosidase that target galactooligosaccharides such as raffinose, melibiose, stachyose and branched polysaccharides like galactomannans and galacto-glucomannans by catalysing the hydrolysis of α-1,6 linked terminal galactose residues. The enzyme has been isolated and characterized from microbial, plant and animal sources. This ubiquitous enzyme possesses physiological significance and immense industrial potential. Optimization of the growth conditions and efficient purification strategies can lead to a significant increase in the enzyme production. To boost commercial productivity, cloning of novel α-galactosidase genes and their heterologous expression in suitable host has gained popularity. Enzyme immobilization leads to its greater reutilization, superior thermostability, pH tolerance and increased activity. The enzyme is well explored in food industry in the removal of raffinose family oligosaccharides (RFOs) in soymilk and sugar crystallization process. It also improves animal feed quality and biomass processing. Applications of the enzyme is in the area of biomedicine includes therapeutic advances in treatment of Fabry disease, blood group conversion and removal of α-gal type immunogenic epitopes in xenotransplantation. With considerable biotechnological applications, this enzyme has been vastly commercialized and holds greater future prospects.
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Affiliation(s)
- Sonu Bhatia
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Abhinashi Singh
- Department of Biotechnology, G.G.D.S.D. College, Sector-32-C, Chandigarh, India
| | - Navneet Batra
- Department of Biotechnology, G.G.D.S.D. College, Sector-32-C, Chandigarh, India
| | - Jagtar Singh
- Department of Biotechnology, Panjab University, Chandigarh, India.
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12
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Colombo C, Bennet AJ. The physical organic chemistry of glycopyranosyl transfer reactions in solution and enzyme-catalyzed. Curr Opin Chem Biol 2019; 53:145-157. [PMID: 31689605 DOI: 10.1016/j.cbpa.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Our understanding of the mechanisms of glycopyranosyl transfer that occur in solution, both for the chemical synthesis of complex structures and that for the cleavage of glycosidic bonds has allowed us to design biologically active molecules. Recent efforts on the reactivity of glycopyranosides, which are critical entities in all biological systems, coupled with the advent of modern spectroscopic instrumentation have allowed physical organic chemists to broaden our knowledge of glycosyl transfer reaction transition states, both in solution and for enzyme-catalyzed processes, and of critical high energy intermediates. This review details recent physical organic, kinetic and structural studies that have led to elucidation of several different mechanism for the transfer of glycopyranosyl moieties from various substrates to acceptors, such as water or a sugar hydroxyl group.
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13
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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14
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Structure of an α-glucuronidase in complex with Co2+ and citrate provides insights into the mechanism and substrate recognition in the family 4 glycosyl hydrolases. Biochem Biophys Res Commun 2019; 518:197-203. [DOI: 10.1016/j.bbrc.2019.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 11/23/2022]
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15
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Swietnicki W, Brzozowska E. In silico analysis of bacteriophage tail tubular proteins suggests a putative sugar binding site and a catalytic mechanism. J Mol Graph Model 2019; 92:8-16. [PMID: 31302501 DOI: 10.1016/j.jmgm.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
Bacteriophage base tailplate proteins were recently discovered to have hydrolytic activity towards disaccharides. The putative assignment of sugar binding sites was based on known lectin structures and identified residues a.a. 40-120 as the potential binding region for disaccharides [1]. To help verify the prediction, an in silico analysis was performed on the structure of a base tailplate protein gp31 from Klebsiella pneumoniae bacteriophage KP32 (PDB: 5MU4) which shows activity towards maltose but not trehalose [1]. Based on the information, a full surface docking was performed for both sugars which identified 2 regions different than originally predicted. The first region clearly favored maltose during the docking phase while the second one allowed for the energetically-equivalent binding of trehalose. To verify the assignment, a molecular dynamics simulation was performed to assess the stability of the docked substrates. MD simulations suggested that the first site included residues D131, D133, and E134, and was also superior for maltose binding while clearly disfavoring trehalose. Analysis of the putative catalytic mechanism suggested residues D131, D133 and E134 as critical for substrate binding. The residue D133 did participate in a stable substrate binding and was positioned near the scissile bond, potentially making it a catalytic residue. Catalytic residues were most likely D131 and D133, one of the two options proposed by Pyra et al. [1]. A comparison with known hydrolase mechanisms suggested that the enzyme most likely retains configuration during hydrolysis of maltose. The findings are discussed for other bacteriophage proteins regarding their potential specificities and catalytic mechanisms.
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Affiliation(s)
- Wieslaw Swietnicki
- L. Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Science, Department of Immunology and Infectious Diseases, ul. R. Weigla 12, 53-114, Wroclaw, PL, Poland.
| | - Ewa Brzozowska
- L. Hirszfeld Institute of Immunology and Experimental Therapy of the Polish Academy of Science, Department of Immunology and Infectious Diseases, ul. R. Weigla 12, 53-114, Wroclaw, PL, Poland
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16
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Srivastava N, Rathour R, Jha S, Pandey K, Srivastava M, Thakur VK, Sengar RS, Gupta VK, Mazumder PB, Khan AF, Mishra PK. Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application. Biomolecules 2019; 9:E220. [PMID: 31174354 PMCID: PMC6627771 DOI: 10.3390/biom9060220] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 01/10/2023] Open
Abstract
The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. The production of biofuels from biomass is an enzyme mediated process, wherein β-glucosidase (BGL) enzymes play a key role in biomass hydrolysis by producing monomeric sugars from cellulose-based oligosaccharides. However, the production and availability of these enzymes realize their major role to increase the overall production cost of biomass to biofuels production technology. Therefore, the present review is focused on evaluating the production and efficiency of β-glucosidase enzymes in the bioconversion of cellulosic biomass for biofuel production at an industrial scale, providing its mechanism and classification. The application of BGL enzymes in the biomass conversion process has been discussed along with the recent developments and existing issues. Moreover, the production and development of microbial BGL enzymes have been explained in detail, along with the recent advancements made in the field. Finally, current hurdles and future suggestions have been provided for the future developments. This review is likely to set a benchmark in the area of cost effective BGL enzyme production, specifically in the biorefinery area.
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Affiliation(s)
- Neha Srivastava
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
| | - Rishabh Rathour
- Department of Bioengineering, Integral University, Lucknow 226026, India.
| | - Sonam Jha
- Department of Botany, Banaras Hindu University, Varanasi 221005, India.
| | - Karan Pandey
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
| | - Manish Srivastava
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India.
| | - Vijay Kumar Thakur
- Enhanced Composites and Structures Center, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, UK.
| | - Rakesh Singh Sengar
- Department of Agriculture Biotechnology, College of Agriculture, Sardar Vallabhbhai Patel, University of Agriculture and Technology, Meerut 250110, U.P., India.
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | | | - Ahamad Faiz Khan
- Department of Bioengineering, Integral University, Lucknow 226026, India.
| | - Pradeep Kumar Mishra
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
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17
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Enzymatic Conversion of RBCs by α-N-Acetylgalactosaminidase from Spirosoma linguale. Enzyme Res 2019; 2019:6972835. [PMID: 31186954 PMCID: PMC6521355 DOI: 10.1155/2019/6972835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/06/2019] [Indexed: 11/25/2022] Open
Abstract
Spirosoma linguale is a free-living nonpathogenic organism. Like many other bacteria, S. linguale produces a cell-associated α-N-acetylgalactosaminidase. This work was undertaken to elucidate the nature of this activity. The recombinant enzyme was produced, purified, and examined for biochemical attributes. The purified enzyme was ~50 kDa active as a homodimer in solution. It catalyzed hydrolysis of α-N-acetylgalactosamine at pH 7. Calculated KM was 1.1 mM with kcat of 173 s−1. The described enzyme belongs to the GH109 family.
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18
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Lansky S, Zehavi A, Belrhali H, Shoham Y, Shoham G. Structural basis for enzyme bifunctionality – the case of Gan1D fromGeobacillus stearothermophilus. FEBS J 2017; 284:3931-3953. [DOI: 10.1111/febs.14283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | | | - Yuval Shoham
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Gil Shoham
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
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19
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Ati J, Lafite P, Daniellou R. Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides. Beilstein J Org Chem 2017; 13:1857-1865. [PMID: 29062404 PMCID: PMC5629408 DOI: 10.3762/bjoc.13.180] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/17/2017] [Indexed: 01/02/2023] Open
Abstract
Carbohydrate related enzymes, like glycosyltransferases and glycoside hydrolases, are nowadays more easily accessible and are thought to represent powerful and greener alternatives to conventional chemical glycosylation procedures. The knowledge of their corresponding mechanisms has already allowed the development of efficient biocatalysed syntheses of complex O-glycosides. These enzymes can also now be applied to the formation of rare or unnatural glycosidic linkages.
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Affiliation(s)
- Jihen Ati
- ICOA UMR CNRS 7311, University of Orléans, rue de Chartres, BP 6759, 45067 Orléans cedex 2, France
| | - Pierre Lafite
- ICOA UMR CNRS 7311, University of Orléans, rue de Chartres, BP 6759, 45067 Orléans cedex 2, France
| | - Richard Daniellou
- ICOA UMR CNRS 7311, University of Orléans, rue de Chartres, BP 6759, 45067 Orléans cedex 2, France
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20
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Jose VL, More RP, Appoothy T, Arun AS. In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle. Syst Appl Microbiol 2017; 40:160-170. [DOI: 10.1016/j.syapm.2017.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
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21
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Singh G, Verma AK, Kumar V. Catalytic properties, functional attributes and industrial applications of β-glucosidases. 3 Biotech 2016; 6:3. [PMID: 28330074 PMCID: PMC4697909 DOI: 10.1007/s13205-015-0328-z] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/19/2015] [Indexed: 12/18/2022] Open
Abstract
β-Glucosidases are diverse group of enzymes with great functional importance to biological systems. These are grouped in multiple glycoside hydrolase families based on their catalytic and sequence characteristics. Most studies carried out on β-glucosidases are focused on their industrial applications rather than their endogenous function in the target organisms. β-Glucosidases performed many functions in bacteria as they are components of large complexes called cellulosomes and are responsible for the hydrolysis of short chain oligosaccharides and cellobiose. In plants, β-glucosidases are involved in processes like formation of required intermediates for cell wall lignification, degradation of endosperm’s cell wall during germination and in plant defense against biotic stresses. Mammalian β-glucosidases are thought to play roles in metabolism of glycolipids and dietary glucosides, and signaling functions. These enzymes have diverse biotechnological applications in food, surfactant, biofuel, and agricultural industries. The search for novel and improved β-glucosidase is still continued to fulfills demand of an industrially suitable enzyme. In this review, a comprehensive overview on detailed functional roles of β-glucosidases in different organisms, their industrial applications, and recent cloning and expression studies with biochemical characterization of such enzymes is presented for the better understanding and efficient use of diverse β-glucosidases.
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Affiliation(s)
- Gopal Singh
- Institute of Himalayan Bioresource Technology, Palampur, 176062, India
| | - A K Verma
- Department of Biochemistry, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Vinod Kumar
- Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, India.
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22
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23
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Bakunina IY, Balabanova LA, Pennacchio A, Trincone A. Hooked on α-d-galactosidases: from biomedicine to enzymatic synthesis. Crit Rev Biotechnol 2015; 36:233-45. [PMID: 25394540 DOI: 10.3109/07388551.2014.949618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-d-Galactosidases (EC 3.2.1.22) are enzymes employed in a number of useful bio-based applications. We have depicted a comprehensive general survey of α-d-galactosidases from different origin with special emphasis on marine example(s). The structures of natural α-galactosyl containing compounds are described. In addition to 3D structures and mechanisms of action of α-d-galactosidases, different sources, natural function and genetic regulation are also covered. Finally, hydrolytic and synthetic exploitations as free or immobilized biocatalysts are reviewed. Interest in the synthetic aspects during the next years is anticipated for access to important small molecules by green technology with an emphasis on alternative selectivity of this class of enzymes from different sources.
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Affiliation(s)
- Irina Yu Bakunina
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Larissa A Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Angela Pennacchio
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
| | - Antonio Trincone
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
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24
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Jordan DB, Braker JD, Wagschal K, Lee CC, Chan VJ, Dubrovska I, Anderson S, Wawrzak Z. X-ray Crystal Structure of Divalent Metal-Activated β-xylosidase, RS223BX. Appl Biochem Biotechnol 2015. [DOI: 10.1007/s12010-015-1767-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Characterization of two-step deglycosylation via oxidation by glycoside oxidoreductase and defining their subfamily. Sci Rep 2015; 5:10877. [PMID: 26057169 PMCID: PMC4650693 DOI: 10.1038/srep10877] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/06/2015] [Indexed: 12/02/2022] Open
Abstract
Herein, we report a two-step deglycosylation mediated by the oxidation of glycoside which is different from traditional glycoside hydrolase (GH) mechanism. Previously, we reported a novel flavin adenine dinucleotide (FAD)-dependent glycoside oxidoreductase (FAD-GO) having deglycosylation activity. Various features of the reaction of FAD-GO such as including mechanism and catalytic residue and substrate specificity were studied. In addition, classification of novel FAD-GO subfamily was attempted. Deglycosylation of glycoside was performed spontaneously via oxidation of 3-OH of glycone moiety by FAD-GO mediated oxidation reaction. His493 residue was identified as a catalytic residue for the oxidation step. Interestingly, this enzyme has broad glycone and aglycon specificities. For the classification of FAD-GO enzyme subfamily, putative FAD-GOs were screened based on the FAD-GO from Rhizobium sp. GIN611 (gi 365822256) using BLAST search. The homologs of R. sp. GIN611 included the putative FAD-GOs from Stenotrophomonas strains, Sphingobacterium strains, Agrobacterium tumefaciens str. C58, and etc. All the cloned FAD-GOs from the three strains catalyzed the deglycosylation via enzymatic oxidation. Based on their substrate specificities, deglycosylation and oxidation activities to various ginsenosides, the FAD-GO subfamily members can be utilized as novel biocatalysts for the production of various aglycones.
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26
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Liu DM, Chen J, Shi YP. An online immobilized α-glucosidase microreactor for enzyme kinetics and inhibition assays. RSC Adv 2015. [DOI: 10.1039/c5ra07982a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A novel online α-glucosidase-immobilized microreactor was developed by immobilizing α-glucosidase on capillary inner wall. The microreactor combination with capillary electrophoresis was applied in studying enzyme kinetics and inhibition kinetics.
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Affiliation(s)
- Dong-Mei Liu
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Juan Chen
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Yan-Ping Shi
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
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27
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Okuyama M, Yoshida T, Hondoh H, Mori H, Yao M, Kimura A. Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase. FEBS Lett 2014; 588:3213-7. [PMID: 25017438 DOI: 10.1016/j.febslet.2014.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022]
Abstract
The role of calcium ion in the active site of the inverting glycoside hydrolase family 97 enzyme, BtGH97a, was investigated through structural and kinetic studies. The calcium ion was likely directly involved in the catalytic reaction. The pH dependence of kcat/Km values in the presence or absence of calcium ion indicated that the calcium ion lowered the pKa of the base catalyst. The significant decreases in kcat/Km for hydrolysis of substrates with basic leaving groups in the absence of calcium ion confirmed that the calcium ion facilitated the leaving group departure.
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Affiliation(s)
- Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan.
| | - Takuya Yoshida
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hironori Hondoh
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan; Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Hiroshima 739-8528, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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28
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Function and Structure Studies of GH Family 31 and 97 α-Glycosidases. Biosci Biotechnol Biochem 2014; 75:2269-77. [DOI: 10.1271/bbb.110610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Chakladar S, Shamsi Kazem Abadi S, Bennet AJ. A mechanistic study on the α-N-acetylgalactosaminidase from E. meningosepticum: a family 109 glycoside hydrolase. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00104d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies on the mechanism of action used by a GH109 enzyme.
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30
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Jordan DB, Lee CC, Wagschal K, Braker JD. Activation of a GH43 β-xylosidase by divalent metal cations: slow binding of divalent metal and high substrate specificity. Arch Biochem Biophys 2013; 533:79-87. [PMID: 23500142 DOI: 10.1016/j.abb.2013.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/19/2022]
Abstract
RS223-BX of glycoside hydrolase family 43 is a β-d-xylosidase that is strongly activated (k(cat)/K(m) as much as 116-fold) by the addition of divalent metal cations, Ca(2+), Co(2+), Fe(2+), Mg(2+), Mn(2+) and Ni(2+). Slow activation by Mg(2+) was demonstrated (k(on) 0.013 s(-1) mM(-1), k(off) 0.008 s(-1)) at pH 7.0 and 25 °C. k(off) and k(on) values are independent of Mg(2+) concentration, but k(off) and k(on) are slower in the presence of increasing levels of substrate 4-nitrophenyl-β-D-xylopyranoside. The kinetics strongly suggest that M(2+) binds to the enzyme rapidly, forming E M(2+), followed by slow isomerization to the activated enzyme, E* M(2+). Moderately high values of kcat (7-30 s(-1)) were found for M(2+)-activated RS223-BX acting on xylobiose (natural substrate) at pH 7.0 and 25 °C. Certain M(2+)-activated RS223-BX exhibit the highest reported values of k(cat)/K(m) of any β-xylosidase acting on natural substrates: for example, at pH 7.0 and 25°C, xylobiose (Mn(2+), 190 s(-1) mM(-1)), xylotriose (Ca(2+), 150 s(-1) mM(-1)) and xylotetraose (Ca(2+), 260 s(-1) mM(-1)). There is potential for the enzyme to add value to industrial saccharification operations at low substrate and high d-glucose and high d-xylose concentrations.
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Affiliation(s)
- Douglas B Jordan
- USDA-ARS-National Center for Agricultural Utilization Research, Peoria, IL 61604, USA.
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Mokhtari A, Blancato VS, Repizo GD, Henry C, Pikis A, Bourand A, de Fátima Álvarez M, Immel S, Mechakra-Maza A, Hartke A, Thompson J, Magni C, Deutscher J. Enterococcus faecalis utilizes maltose by connecting two incompatible metabolic routes via a novel maltose 6'-phosphate phosphatase (MapP). Mol Microbiol 2013; 88:234-53. [PMID: 23490043 DOI: 10.1111/mmi.12183] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
Similar to Bacillus subtilis, Enterococcus faecalis transports and phosphorylates maltose via a phosphoenolpyruvate (PEP):maltose phosphotransferase system (PTS). The maltose-specific PTS permease is encoded by the malT gene. However, E. faecalis lacks a malA gene encoding a 6-phospho-α-glucosidase, which in B. subtilis hydrolyses maltose 6'-P into glucose and glucose 6-P. Instead, an operon encoding a maltose phosphorylase (MalP), a phosphoglucomutase and a mutarotase starts upstream from malT. MalP was suggested to split maltose 6-P into glucose 1-P and glucose 6-P. However, purified MalP phosphorolyses maltose but not maltose 6'-P. We discovered that the gene downstream from malT encodes a novel enzyme (MapP) that dephosphorylates maltose 6'-P formed by the PTS. The resulting intracellular maltose is cleaved by MalP into glucose and glucose 1-P. Slow uptake of maltose probably via a maltodextrin ABC transporter allows poor growth for the mapP but not the malP mutant. Synthesis of MapP in a B. subtilis mutant accumulating maltose 6'-P restored growth on maltose. MapP catalyses the dephosphorylation of intracellular maltose 6'-P, and the resulting maltose is converted by the B. subtilis maltose phosphorylase into glucose and glucose 1-P. MapP therefore connects PTS-mediated maltose uptake to maltose phosphorylase-catalysed metabolism. Dephosphorylation assays with a wide variety of phospho-substrates revealed that MapP preferably dephosphorylates disaccharides containing an O-α-glycosyl linkage.
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Affiliation(s)
- Abdelhamid Mokhtari
- INRA, Microbiologie de l'alimentation au service de la santé humaine (MICALIS), UMR1319, F-78350, Jouy en Josas, France
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α-Galacturonidase(s): a new class of Family 4 glycoside hydrolases with strict specificity and a unique CHEV active site motif. FEBS Lett 2013; 587:799-803. [PMID: 23416295 DOI: 10.1016/j.febslet.2013.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/18/2013] [Accepted: 02/01/2013] [Indexed: 11/20/2022]
Abstract
The catalytic activity of the Family 4 glycosidase LplD protein, whose active site motif is CHEV, is unknown despite its crystal structure having been determined in 2008. Here we identify that activity as being an α-galacturonidase whose natural substrate is probably α-1,4-di-galacturonate (GalUA2). Phylogenetic analysis shows that LplD belongs to a monophyletic clade of CHEV Family 4 enzymes, of which four other members are also shown to be galacturonidases. Family GH 4 enzymes catalyze the cleavage of the glycosidic bond, via a non-canonical redox-assisted mechanism that contrasts with Koshland's double-displacement mechanism.
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Characterization of a novel metagenome-derived 6-phospho-β-glucosidase from black liquor sediment. Appl Environ Microbiol 2013; 79:2121-7. [PMID: 23335769 DOI: 10.1128/aem.03528-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzyme 6-phospho-β-glucosidase is an important member of the glycoside hydrolase family 1 (GH1). However, its catalytic mechanisms, especially the key residues determining substrate specificity and affinity, are poorly understood. A metagenome-derived gene sequence, encoding a novel 6-phospho-β-glucosidase designated Pbgl25-217, was isolated and characterized. The optimal conditions for enzymatic activity were 37°C and pH 7; Ca(2+), Mg(2+), and Mn(2+) stabilized the activity of Pbgl25-217, whereas Ni(2+), Fe(2+), Zn(2+), Cu(2+), and Fe(3+) inhibited its activity. The Km and Vmax of Pbgl25-217 were 4.8 mM and 1,987.0 U mg(-1), respectively. Seven conserved residues were recognized by multiple alignments and were tested by site-directed mutagenesis for their functions in substrate recognition and catalytic reaction. The results suggest that residues S427, Lys435, and Tyr437 act as "gatekeepers" in a phosphate-binding loop and play important roles in phosphate recognition. This functional identification may provide insights into the specificity of 6-phospho-β-glycosidases in GH1 and be useful for designing further directed evolution.
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Abstract
From a generated PES, one can determine the relative energies of species involved, the sequence in which they occur, and the activation barrier(s) associated with individual steps or the overall mechanism. Furthermore, they can provide more insights than a simple indication of a path of sequential mechanistic structures and their energetic relationships. The investigation into the activation of O2 by alpha-ketoglutarate-dependent dioxygenase (AlkB) clearly shows the opportunity for spin inversion, where one can see that the lowest energy product may be formed via several possible routes. In the investigation of uroporphyrinogen decarboxylase III (UROD), the use of QM/MM methods allowed for the inclusion of the anisotropic protein environment providing greater insight into the rate-limiting barrier. Lastly, the mechanism of 6-phospho-α-glucosidase (GlvA) was discussed using different active site models. In particular, a continuum model PES was compared to the gas-phase PES.
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Yip VLY, Withers SG. Identification of Tyr241 as a key catalytic base in the family 4 glycoside hydrolase BglT from Thermotoga maritima. Biochemistry 2012; 51:8464-74. [PMID: 23025815 DOI: 10.1021/bi301021u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While the vast majority of glycosidases catalyze glycoside hydrolysis via oxocarbenium ion-like transition states and typically employ carboxylic acid residues as acid/base or nucleophile catalysts, two subfamilies of these enzymes (GH4 and GH109 in the CAZY classification) conduct hydrolysis via a redox-assisted mechanism involving anionic transition states. While good evidence of this mechanism has been obtained, the identities of the catalytic residues involved have not yet been confirmed. Mechanistic analyses of mutants of the 6-phospho-β-glucosidase from Thermotoga maritima (BglT), in which the active site tyrosine residue (Tyr 241) has been replaced with Phe and Ala, provide support for its role as a catalytic base. The pH dependence of k(cat) and k(cat)/K(m), particularly of the acidic limb corresponding to the base, is shifted relative to that of the wild-type enzyme. Kinetic isotope effects for hydrolysis of substrates deuterated at C1, C2, and C3 by the Tyr 241 mutants are strongly pH-dependent, with essentially full primary kinetic isotope effects being observed for the 2-deutero substrate at low pH with the Tyr241Ala mutant. This is consistent with a slowing of the deprotonation step upon removal of the base.
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Affiliation(s)
- Vivian L Y Yip
- 2036 Main Mall, Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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Yun BY, Jun SY, Kim NA, Yoon BY, Piao S, Park SH, Jeong SH, Lee H, Ha NC. Crystal structure and thermostability of a putative α-glucosidase from Thermotoga neapolitana. Biochem Biophys Res Commun 2011; 416:92-8. [DOI: 10.1016/j.bbrc.2011.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/01/2011] [Indexed: 11/15/2022]
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Thompson J, Pikis A. Metabolism of sugars by genetically diverse species of oral Leptotrichia. Mol Oral Microbiol 2011; 27:34-44. [PMID: 22230464 DOI: 10.1111/j.2041-1014.2011.00627.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leptotrichia buccalis ATCC 14201 is a gram-negative, anaerobic rod-shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525, Lebu_1526 and Lebu_1527. The translation products of these genes exhibit significant homology with phospho-α-glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate-dependent sugar transport protein (EIICB), respectively. In non-oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50-kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP10 cells. In the presence of two cofactors, NAD(+) and Mn(2+) ions, the enzyme readily hydrolyzed p-nitrophenyl-α-glucopyranoside 6-phosphate (pNPαG6P), a chromogenic analogue of the phosphorylated isomers of sucrose. By comparative sequence alignment, immunoreactivity and signature motifs, the enzyme can be assigned to the phospho-α-glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and Lebu_1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA-related, species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined.
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Affiliation(s)
- J Thompson
- Microbial Biochemistry and Genetics Unit, Oral Infection and Immunity Branch, NIDCR, National Institutes of Health, Bethesda, MD 20892, USA.
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Oxidoreductive cellulose depolymerization by the enzymes cellobiose dehydrogenase and glycoside hydrolase 61. Appl Environ Microbiol 2011; 77:7007-15. [PMID: 21821740 DOI: 10.1128/aem.05815-11] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several members of the glycoside hydrolase 61 (GH61) family of proteins have recently been shown to dramatically increase the breakdown of lignocellulosic biomass by microbial hydrolytic cellulases. However, purified GH61 proteins have neither demonstrable direct hydrolase activity on various polysaccharide or lignacious components of biomass nor an apparent hydrolase active site. Cellobiose dehydrogenase (CDH) is a secreted flavocytochrome produced by many cellulose-degrading fungi with no well-understood biological function. Here we demonstrate that the binary combination of Thermoascus aurantiacus GH61A (TaGH61A) and Humicola insolens CDH (HiCDH) cleaves cellulose into soluble, oxidized oligosaccharides. TaGH61A-HiCDH activity on cellulose is shown to be nonredundant with the activities of canonical endocellulase and exocellulase enzymes in microcrystalline cellulose cleavage, and while the combination of TaGH61A and HiCDH cleaves highly crystalline bacterial cellulose, it does not cleave soluble cellodextrins. GH61 and CDH proteins are coexpressed and secreted by the thermophilic ascomycete Thielavia terrestris in response to environmental cellulose, and the combined activities of T. terrestris GH61 and T. terrestris CDH are shown to synergize with T. terrestris cellulose hydrolases in the breakdown of cellulose. The action of GH61 and CDH on cellulose may constitute an important, but overlooked, biological oxidoreductive system that functions in microbial lignocellulose degradation and has applications in industrial biomass utilization.
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Vorontsov II, Minasov G, Kiryukhina O, Brunzelle JS, Shuvalova L, Anderson WF. Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. J Biol Chem 2011; 286:33158-66. [PMID: 21757692 PMCID: PMC3190883 DOI: 10.1074/jbc.m111.250456] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.
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Affiliation(s)
- Ivan I Vorontsov
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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40
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Tsai LC, Hsiao CH, Liu WY, Yin LM, Shyur LF. Structural basis for the inhibition of 1,3-1,4-β-d-glucanase by noncompetitive calcium ion and competitive Tris inhibitors. Biochem Biophys Res Commun 2011; 407:593-8. [DOI: 10.1016/j.bbrc.2011.03.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
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Gandy MN, Debowski AW, Stubbs KA. A general method for affinity-based proteomic profiling of exo-α-glycosidases. Chem Commun (Camb) 2011; 47:5037-9. [PMID: 21431156 DOI: 10.1039/c1cc10308c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of iminosugar-based affinity-based proteomics probes for use in probing exo-α-glycosidase activity.
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Affiliation(s)
- Michael N Gandy
- Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA Australia6009
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42
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Huang W, Llano J, Gauld JW. Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-alpha-glucosidase: a DFT study. J Phys Chem B 2010; 114:11196-206. [PMID: 20698522 DOI: 10.1021/jp102399h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosidic bonds are remarkably resistant to cleavage by chemical hydrolysis. Glycoside hydrolases catalyze their selective hydrolysis in oligosaccharides, polysaccharides, and glycoconjugates by following nonredox catalytic pathways or a net redox-neutral catalytic pathway using NAD(+) and divalent metal ions as cofactors. GlvA (6-phospho-alpha-glucosidase) is a glycosidase belonging to family GH4 and follows a regioselective redox-neutral mechanism of glycosidic-bond hydrolysis that favors alpha- over beta-glycosides. Its proposed catalytic mechanism can be divided into two half-reactions: the first one activates the glucopyranose ring by successively forming intermediates that are oxidized at the 3-, 2-, and 1-positions of the ring, which ultimately facilitate the heterolytic deglycosylation. The second half-reaction is essentially the reverse of the first half-reaction, beginning with the pyranose ring hydroxylation at the anomeric carbon, and it is followed by 3-reduction and regeneration of the active forms of the catalytic site and its cofactors. We investigated the NAD(+)-dependent redox mechanism of glycosidic bond hydrolysis as catalyzed by GlvA through the combined application of density functional theory and a self-consistent reaction field to a large active-site model obtained from the crystallographic structure of the enzyme, then we applied natural bond orbital and second-order perturbation analyses to monitor the electron flow and change in oxidation state on each atomic center along the reaction coordinate to rationalize the energetics and regioselectivity of this catalytic mechanism. We find that in GlvA, the redox catalytic mechanism of hydrolysis is driven by the gradual strengthening of the axial endo-anomeric component within the hexose ring along the reaction coordinate to facilitate the heterolytic dissociation of the axial C1-O bond. In addition, the combined influence of specific components of the generalized anomeric effect fully explains the regioselectivity observed in the catalytic activity of GlvA.
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Affiliation(s)
- Wenjuan Huang
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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43
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Sulzenbacher G, Liu QP, Bennett EP, Levery SB, Bourne Y, Ponchel G, Clausen H, Henrissat B. A novel α-N-acetylgalactosaminidase family with an NAD+-dependent catalytic mechanism suitable for enzymatic removal of blood group A antigens. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.3109/10242420903424259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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44
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Zhang Q, Peng H, Gao F, Liu Y, Cheng H, Thompson J, Gao GF. Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes. Protein Sci 2009; 18:294-303. [PMID: 19177572 DOI: 10.1002/pro.32] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gluconate 5-dehydrogenase (Ga5DH) is an NADP(H)-dependent enzyme that catalyzes a reversible oxidoreduction reaction between D-gluconate and 5-keto-D-gluconate, thereby regulating the flux of this important carbon and energy source in bacteria. Despite the considerable amount of physiological and biochemical knowledge of Ga5DH, there is little physical or structural information available for this enzyme. To this end, we herein report the crystal structures of Ga5DH from pathogenic Streptococcus suis serotype 2 in both substrate-free and liganded (NADP(+)/D-gluconate/metal ion) quaternary complex forms at 2.0 A resolution. Structural analysis reveals that Ga5DH adopts a protein fold similar to that found in members of the short chain dehydrogenase/reductase (SDR) family, while the enzyme itself represents a previously uncharacterized member of this family. In solution, Ga5DH exists as a tetramer that comprised four identical approximately 29 kDa subunits. The catalytic site of Ga5DH shows considerable architectural similarity to that found in other enzymes of the SDR family, but the S. suis protein contains an additional residue (Arg104) that plays an important role in the binding and orientation of substrate. The quaternary complex structure provides the first clear crystallographic evidence for the role of a catalytically important serine residue and also reveals an amino acid tetrad RSYK that differs from the SYK triad found in the majority of SDR enzymes. Detailed analysis of the crystal structures reveals important contributions of Ca(2+) ions to active site formation and of specific residues at the C-termini of subunits to tetramer assembly. Because Ga5DH is a potential target for therapy, our findings provide insight not only of catalytic mechanism, but also suggest a target of structure-based drug design.
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Affiliation(s)
- Qiangmin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic Of China
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45
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Hall BG, Pikis A, Thompson J. Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations. Mol Biol Evol 2009; 26:2487-97. [PMID: 19625389 DOI: 10.1093/molbev/msp162] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Glycosyl hydrolase Family 4 (GH4) is exceptional among the 114 families in this enzyme superfamily. Members of GH4 exhibit unusual cofactor requirements for activity, and an essential cysteine residue is present at the active site. Of greatest significance is the fact that members of GH4 employ a unique catalytic mechanism for cleavage of the glycosidic bond. By phylogenetic analysis, and from available substrate specificities, we have assigned a majority of the enzymes of GH4 to five subgroups. Our classification revealed an unexpected relationship between substrate specificity and the presence, in each subgroup, of a motif of four amino acids that includes the active-site Cys residue: alpha-glucosidase, CHE(I/V); alpha-galactosidase, CHSV; alpha-glucuronidase, CHGx; 6-phospho-alpha-glucosidase, CDMP; and 6-phospho-beta-glucosidase, CN(V/I)P. The question arises: Does the presence of a particular motif sufficiently predict the catalytic function of an unassigned GH4 protein? To test this hypothesis, we have purified and characterized the alpha-glucoside-specific GH4 enzyme (PalH) from the phytopathogen, Erwinia rhapontici. The CHEI motif in this protein has been changed by site-directed mutagenesis, and the effects upon substrate specificity have been determined. The change to CHSV caused the loss of all alpha-glucosidase activity, but the mutant protein exhibited none of the anticipated alpha-galactosidase activity. The Cys-containing motif may be suggestive of enzyme specificity, but phylogenetic placement is required for confidence in that specificity. The Acholeplasma laidlawii GH4 protein is phylogenetically a phospho-beta-glucosidase but has a unique SSSP motif. Lacking the initial Cys in that motif it cannot hydrolyze glycosides by the normal GH4 mechanism because the Cys is required to position the metal ion for hydrolysis, nor can it use the more common single or double-displacement mechanism of Koshland. Several considerations suggest that the protein has acquired a new function as the consequence of positive selection. This study emphasizes the importance of automatic annotation systems that by integrating phylogenetic analysis, functional motifs, and bioinformatics data, may lead to innovative experiments that further our understanding of biological systems.
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Affiliation(s)
- Barry G Hall
- Bellingham Research Institute, Bellingham, WA, USA.
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46
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Yip VLY, Withers SG. Family 4 glycoside hydrolases are special: The first β-elimination mechanism amongst glycoside hydrolases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500515926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
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Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
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48
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Rakić B, Withers SG. Recent Developments in Glycoside Synthesis with Glycosynthases and Thioglycoligases. Aust J Chem 2009. [DOI: 10.1071/ch09059] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Glycosynthases are hydrolytically incompetent engineered glycosidases that catalyze the high-yielding synthesis of glycoconjugates from glycosyl fluoride donor substrates and appropriate acceptors. Glycosynthases from more than 10 glycoside hydrolase families have now been generated, allowing the synthesis of a wide range of oligosaccharides. Recent examples include glycosynthase-mediated syntheses of xylo-oligosaccharides, xyloglucans, glycolipids, and aryl glycosides. Glycosynthases have also now been generated from inverting glycosidases, increasing the range of enzyme scaffolds. Improvement of glycosynthase activity and broadening of specificity has been achieved through directed evolution approaches, and several novel high-throughput screens have been developed to allow this. Finally, metabolically stable glycoside analogues have been generated using another class of mutant glycosidases: thioglycoligases. Recent developments in all these aspects are discussed.
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49
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Kluger R, Rathgeber S. Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation. FEBS J 2008; 275:6089-100. [DOI: 10.1111/j.1742-4658.2008.06739.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. ACTA ACUST UNITED AC 2008; 15:1058-67. [PMID: 18848471 PMCID: PMC2670981 DOI: 10.1016/j.chembiol.2008.09.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/01/2008] [Accepted: 09/11/2008] [Indexed: 11/26/2022]
Abstract
Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining α-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron α-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining α-galactosidase.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK.
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