101
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Ghollasi M, Ghanbari-Safari M, Khajeh K. Improvement of thermal stability of a mutagenised α-amylase by manipulation of the calcium-binding site. Enzyme Microb Technol 2013; 53:406-13. [DOI: 10.1016/j.enzmictec.2013.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
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102
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Housaindokht MR, Bozorgmehr MR, Hosseini HE, Jalal R, Asoodeh A, Saberi M, Haratipour Z, Monhemi H. Structural properties of the truncated and wild types of Taka-amylase: A molecular dynamics simulation and docking study. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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103
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Seung D, Thalmann M, Sparla F, Abou Hachem M, Lee SK, Issakidis-Bourguet E, Svensson B, Zeeman SC, Santelia D. Arabidopsis thaliana AMY3 is a unique redox-regulated chloroplastic α-amylase. J Biol Chem 2013; 288:33620-33633. [PMID: 24089528 DOI: 10.1074/jbc.m113.514794] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. In vascular plants, α-amylases can be classified into three subfamilies. Arabidopsis has one member of each subfamily. Among them, only AtAMY3 is localized in the chloroplast. We expressed and purified AtAMY3 from Escherichia coli and carried out a biochemical characterization of the protein to find factors that regulate its activity. Recombinant AtAMY3 was active toward both insoluble starch granules and soluble substrates, with a strong preference for β-limit dextrin over amylopectin. Activity was shown to be dependent on a conserved aspartic acid residue (Asp(666)), identified as the catalytic nucleophile in other plant α-amylases such as the barley AMY1. AtAMY3 released small linear and branched glucans from Arabidopsis starch granules, and the proportion of branched glucans increased after the predigestion of starch with a β-amylase. Optimal rates of starch digestion in vitro was achieved when both AtAMY3 and β-amylase activities were present, suggesting that the two enzymes work synergistically at the granule surface. We also found that AtAMY3 has unique properties among other characterized plant α-amylases, with a pH optimum of 7.5-8, appropriate for activity in the chloroplast stroma. AtAMY3 is also redox-regulated, and the inactive oxidized form of AtAMY3 could be reactivated by reduced thioredoxins. Site-directed mutagenesis combined with mass spectrometry analysis showed that a disulfide bridge between Cys(499) and Cys(587) is central to this regulation. This work provides new insights into how α-amylase activity may be regulated in the chloroplast.
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Affiliation(s)
- David Seung
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Matthias Thalmann
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Francesca Sparla
- Department of Experimental Evolutionary Biology, University of Bologna, I-40126 Bologna, Italy
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sang Kyu Lee
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | | | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Samuel C Zeeman
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Diana Santelia
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland.
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104
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Nasrollahi S, Golalizadeh L, Sajedi RH, Taghdir M, Asghari SM, Rassa M. Substrate preference of a Geobacillus maltogenic amylase: A kinetic and thermodynamic analysis. Int J Biol Macromol 2013; 60:1-9. [DOI: 10.1016/j.ijbiomac.2013.04.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
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105
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El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 2013; 11:497-504. [PMID: 23748339 DOI: 10.1038/nrmicro3050] [Citation(s) in RCA: 1034] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.
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Affiliation(s)
- Abdessamad El Kaoutari
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7257, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
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106
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Caner S, Nguyen N, Aguda A, Zhang R, Pan YT, Withers SG, Brayer GD. The structure of the Mycobacterium smegmatis trehalose synthase reveals an unusual active site configuration and acarbose-binding mode. Glycobiology 2013; 23:1075-83. [PMID: 23735230 DOI: 10.1093/glycob/cwt044] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trehalose synthase (TreS) catalyzes the reversible conversion of maltose into trehalose in mycobacteria as one of three biosynthetic pathways to this nonreducing disaccharide. Given the importance of trehalose to survival of mycobacteria, there has been considerable interest in understanding the enzymes involved in its production; indeed the structures of the key enzymes in the other two pathways have already been determined. Herein, we present the first structure of TreS from Mycobacterium smegmatis, thereby providing insights into the catalytic machinery involved in this intriguing intramolecular reaction. This structure, which is of interest both mechanistically and as a potential pharmaceutical target, reveals a narrow and enclosed active site pocket within which intramolecular substrate rearrangements can occur. We also present the structure of a complex of TreS with acarbose, revealing a hitherto unsuspected oligosaccharide-binding site within the C-terminal domain. This may well provide an anchor point for the association of TreS with glycogen, thereby enhancing its role in glycogen biosynthesis and degradation.
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Affiliation(s)
- Sami Caner
- Department of Biochemistry and Molecular Biology, University of British Columbia, British Columbia, Canada
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107
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Nisha M, Satyanarayana T. Recombinant bacterial amylopullulanases: developments and perspectives. Bioengineered 2013; 4:388-400. [PMID: 23645215 DOI: 10.4161/bioe.24629] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pullulanases are endo-acting enzymes capable of hydrolyzing α-1, 6-glycosidic linkages in starch, pullulan, amylopectin, and related oligosaccharides, while amylopullulanases are bifunctional enzymes with an active site capable of cleaving both α-1, 4 and α-1, 6 linkages in starch, amylose and other oligosaccharides, and α-1, 6 linkages in pullulan. The amylopullulanases are classified in GH13 and GH57 family enzymes based on the architecture of catalytic domain and number of conserved sequences. The enzymes with two active sites, one for the hydrolysis of α-1, 4- glycosidic bond and the other for α-1, 6-glycosidic bond, are called α-amylase-pullulanases, while amylopullulanases have only one active site for cleaving both α-1, 4- and α-1, 6-glycosidic bonds. The amylopullulanases produced by bacteria find applications in the starch and baking industries as a catalyst for one step starch liquefaction-saccharification for making various sugar syrups, as antistaling agent in bread and as a detergent additive.
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Affiliation(s)
- M Nisha
- Department of Microbiology; University of Delhi South Campus; New Delhi, India
| | - T Satyanarayana
- Department of Microbiology; University of Delhi South Campus; New Delhi, India
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108
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van der Maarel MJ, Leemhuis H. Starch modification with microbial alpha-glucanotransferase enzymes. Carbohydr Polym 2013; 93:116-21. [DOI: 10.1016/j.carbpol.2012.01.065] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/09/2012] [Accepted: 01/19/2012] [Indexed: 12/25/2022]
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109
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Evolutionary History of Eukaryotic α-Glucosidases from the α-Amylase Family. J Mol Evol 2013; 76:129-45. [DOI: 10.1007/s00239-013-9545-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/25/2013] [Indexed: 11/26/2022]
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110
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Abstract
Microstructural characteristics of starch-based natural foods such as parenchyma or cotyledon cell shape, cell size and composition, and cell wall composition play a key role in influencing the starch digestibility during gastrointestinal digestion. The stability of cell wall components and the arrangement of starch granules in the cells may affect the free access of amylolytic enzymes during digestion. Commonly used food processing techniques such as thermal processing, extrusion cooking, and post-cooking refrigerated storage alter the physical state of starch (gelatinization, retrogradation, etc.) and its digestibility. Rheological characteristics (viscosity) of food affect the water availability during starch hydrolysis and, consequently, the absorption of digested carbohydrates in the gastrointestinal tract. The nonstarch ingredients and other constituents present in food matrix, such as proteins and lipids interact with starch during processing, which leads to an alteration in the overall starch digestibility and physicochemical characteristics of digesta. Starch digestibility can be controlled by critically manipulating the food microstructure, processing techniques, and food composition.
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111
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Kim Y, Kim YL, Trinh KS, Kim YR, Moon TW. Texture properties of rice cakes made of rice flours treated with 4-α-glucanotransferase and their relationship with structural characteristics. Food Sci Biotechnol 2012. [DOI: 10.1007/s10068-012-0227-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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112
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Majzlová K, Pukajová Z, Janeček S. Tracing the evolution of the α-amylase subfamily GH13_36 covering the amylolytic enzymes intermediate between oligo-1,6-glucosidases and neopullulanases. Carbohydr Res 2012; 367:48-57. [PMID: 23313816 DOI: 10.1016/j.carres.2012.11.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 11/22/2012] [Accepted: 11/24/2012] [Indexed: 11/15/2022]
Abstract
Among the glycoside hydrolases (GHs) classified within the Carbohydrate-Active enZymes (CAZy) server, the α-amylase family GH13 belongs to the largest GH families. It has been divided into the official 36 subfamilies by the CAZy curators. Originally the subfamilies of oligo-1,6-glucosidase and neopullulanase were defined using the sequence of the fifth conserved sequence region (CSR) as a selection marker. It is localized outside the catalytic α-amylase (β/α)(8)-barrel in the domain B, that is, in a longer loop connecting the strand β3 with the helix α3 of the barrel. It is sequentially positioned 26-28 residues in front of the invariant aspartic acid residue in the β4-strand acting as the GH13 catalytic nucleophile. The CSR V is characteristic as QpDln and MpKln for the former and latter subfamilies, respectively. A group of intermediate sequences possessing the CSR V as a mix of the two above-mentioned subfamilies, that is, MpDln, was also proposed previously. The present bioinformatics analysis was done in an effort to reveal as many as possible GH13 members of this intermediary group, currently classified as the subfamily GH13_36, and to discuss their evolutionary relationships to known GH13 specificities as well as with regard to their taxonomic origin. Using the BLAST tool with the sequence of the α-amylase from Halothermothrix orenii AmyA exhibiting the intermediary features, 152 GH13 enzymes, and hypothetical proteins were retrieved covering defined specificities (GH13 subfamilies 4, 16, 17, 18, 20, 21, 23, 29, 30, 31, 34, and 35) and intermediary enzymes and proteins (GH13_36). In both evolutionary trees-based on the alignment of CSRs and complete sequences-most of the 'intermediary' proteins (i.e., those with MPDLN signature) were positioned in several closely related clusters forming, however, a single GH13_36 large part of the trees. A few novel GH13 subfamilies were proposed as well as the specificity implications were discussed based on the presented in silico analysis. The results may also be helpful in assigning any GH13-like amino acid sequence the subfamily GH13_36 affiliation without additional biochemical characterization.
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Affiliation(s)
- Katarína Majzlová
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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113
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Camacho E, Sepulveda VE, Goldman WE, San-Blas G, Niño-Vega GA. Expression of Paracoccidioides brasiliensis AMY1 in a Histoplasma capsulatum amy1 mutant, relates an α-(1,4)-amylase to cell wall α-(1,3)-glucan synthesis. PLoS One 2012; 7:e50201. [PMID: 23185578 PMCID: PMC3502345 DOI: 10.1371/journal.pone.0050201] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/17/2012] [Indexed: 02/06/2023] Open
Abstract
In the cell walls of the pathogenic yeast phases of Paracoccidioides brasiliensis, Blastomyces dermatitidis and Histoplasma capsulatum, the outer α-(1,3)-glucan layer behaves as a virulence factor. In H. capsulatum, an α-(1,4)-amylase gene (AMY1) is essential for the synthesis of this polysaccharide, hence related to virulence. An orthologous gene to H. capsulatum AMY1 was identified in P. brasiliensis and also labeled AMY1. P. brasiliensis AMY1 transcriptional levels were increased during the yeast phase, which correlates with the presence of α-(1,3)-glucan as the major yeast cell wall polysaccharide. Complementation of a H. capsulatum amy1 mutant strain with P. brasiliensis AMY1, suggests that P. brasiliensis Amy1p may play a role in the synthesis of cell wall α-(1,3)-glucan. To study some biochemical properties of P. brasiliensis Amy1p, the enzyme was overexpressed, purified and studied its activity profile with starch and amylopeptin. It showed a relatively higher hydrolyzing activity on amylopeptin than starch, producing oligosaccharides from 4 to 5 glucose residues. Our findings show that P. brasiliensis Amy1p produces maltooligosaccharides which may act as a primer molecule for the fungal cell wall α-(1,3)-glucan biosynthesis by Ags1p.
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Affiliation(s)
- Emma Camacho
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Victoria E. Sepulveda
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - William E. Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gioconda San-Blas
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Gustavo A. Niño-Vega
- Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
- * E-mail:
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114
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Chen W, Xie T, Shao Y, Chen F. Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi. PLoS One 2012; 7:e49679. [PMID: 23166747 PMCID: PMC3499471 DOI: 10.1371/journal.pone.0049679] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.
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Affiliation(s)
- Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Ting Xie
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yanchun Shao
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei Province, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Fusheng Chen
- National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei Province, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- * E-mail:
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115
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Characterization of recombinant amylopullulanase (gt-apu) and truncated amylopullulanase (gt-apuT) of the extreme thermophile Geobacillus thermoleovorans NP33 and their action in starch saccharification. Appl Microbiol Biotechnol 2012; 97:6279-92. [DOI: 10.1007/s00253-012-4538-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
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116
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Sato T, Hasegawa N, Saito J, Umezawa S, Honda Y, Kino K, Kirimura K. Purification, characterization, and gene identification of an α-glucosyl transfer enzyme, a novel type α-glucosidase from Xanthomonas campestris WU-9701. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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117
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Tintu I, Dileep KV, Augustine A, Sadasivan C. An Isoquinoline Alkaloid, Berberine, Can Inhibit Fungal Alpha Amylase: Enzyme Kinetic and Molecular Modeling Studies. Chem Biol Drug Des 2012; 80:554-60. [DOI: 10.1111/j.1747-0285.2012.01426.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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118
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Goh PH, Illias RM, Goh KM. Rational mutagenesis of cyclodextrin glucanotransferase at the calcium binding regions for enhancement of thermostability. Int J Mol Sci 2012; 13:5307-5323. [PMID: 22754298 PMCID: PMC3382795 DOI: 10.3390/ijms13055307] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/08/2012] [Accepted: 04/13/2012] [Indexed: 11/16/2022] Open
Abstract
Studies related to the engineering of calcium binding sites of CGTase are limited. The calcium binding regions that are known for thermostability function were subjected to site-directed mutagenesis in this study. The starting gene-protein is a variant of CGTase Bacillus sp. G1, reported earlier and denoted as “parent CGTase” herein. Four CGTase variants (S182G, S182E, N132R and N28R) were constructed. The two variants with a mutation at residue 182, located adjacent to the Ca-I site and the active site cleft, possessed an enhanced thermostability characteristic. The activity half-life of variant S182G at 60 °C was increased to 94 min, while the parent CGTase was only 22 min. This improvement may be attributed to the formation of a shorter α-helix and the alleviation of unfavorable steric strains by glycine at the corresponding region. For the variant S182E, an extra ionic interaction at the A/B domain interface increased the half-life to 31 min, yet it reduced CGTase activity. The introduction of an ionic interaction at the Ca-I site via the mutation N132R disrupted CGTase catalytic activity. Conversely, the variant N28R, which has an additional ionic interaction at the Ca-II site, displayed increased cyclization activity. However, thermostability was not affected.
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Affiliation(s)
| | | | - Kian Mau Goh
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +607-5534346; Fax: +607-5531112
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119
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Tintu I, Dileep KV, Remya C, Augustine A, Sadasivan C. 6-Gingerol inhibits fungal alpha amylase: Enzyme kinetic and molecular modeling studies. STARCH-STARKE 2012. [DOI: 10.1002/star.201200004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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120
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Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57. Extremophiles 2012; 16:497-506. [PMID: 22527043 DOI: 10.1007/s00792-012-0449-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
Abstract
The glycoside hydrolase family 57 (GH57) contains five well-established enzyme specificities: α-amylase, amylopullulanase, branching enzyme, 4-α-glucanotransferase and α-galactosidase. Around 700 GH57 members originate from Bacteria and Archaea, a substantial number being produced by thermophiles. An intriguing feature of family GH57 is that only slightly more than 2 % of its members (i.e., less than 20 enzymes) have already been biochemically characterized. The main goal of the present bioinformatics study was to retrieve from databases, and analyze in detail, sequences having clear features of the five GH57 enzyme specificities mentioned above. Of the 367 GH57 sequences, 56 were evaluated as α-amylases, 99 as amylopullulanases, 158 as branching enzymes, 46 as 4-α-glucanotransferases and 8 as α-galactosidases. Based on the analysis of collected sequences, sequence logos were created for each specificity and unique sequence features were identified within the logos. These features were proposed to define the so-called sequence fingerprints of GH57 enzyme specificities. Domain arrangements characteristic of the individual enzyme specificities as well as evolutionary relationships within the family GH57 are also discussed. The results of this study could find use in rational protein design of family GH57 amylolytic enzymes and also in the possibility of assigning a GH57 specificity to a hypothetical GH57 member prior to its biochemical characterization.
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121
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Molecular characterization of a novel trehalose-6-phosphate hydrolase, TreA, from Bacillus licheniformis. Int J Biol Macromol 2012; 50:459-70. [DOI: 10.1016/j.ijbiomac.2012.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 11/20/2022]
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122
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Leemhuis H, Pijning T, Dobruchowska JM, Dijkstra BW, Dijkhuizen L. Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676301] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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123
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Matsuoka K, Arai H, Oka H, Koyama T, Hatano K. Synthetic Assembly of Bifluorescence-Labeled Glycopolymers as Substrates for Assaying α-Amylase by Resonance Energy Transfer. ACS Macro Lett 2012; 1:266-269. [PMID: 35578520 DOI: 10.1021/mz200135y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To meet the need for a convenient substrate for sensitive and continuous assay for α-amylase, we developed a fluorescence resonance energy transfer (FRET)-based polymer substrate. Radical copolymerization of FRET-component monomers in different ratios of fluorogenic donor and acceptor was utilized to prepare such polymers. A glycomonomer as a fluorogenic donor was derived from naphthylmethylated maltotetraose, and a dansyl derivative monomer was used as an acceptor. Their mixture and acryl amide were copolymerized in a typical radical polymerization to yield a bifluorescence-labeled polymer in good yield. All of the polymers showed effective FRET and were used for the continuous assay of human salivary α-amylase. The time course of α-amylase reactions led to the apparent kinetic parameters of Km = 4 μM and Vmax = 0.29 nmol/min. The results strongly suggested that FRET-sensitive polymers are conveniently accessible and applicable for the sensitive determination of biochemical events.
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Affiliation(s)
- Koji Matsuoka
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Hirokatsu Arai
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Hiroyuki Oka
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Tetsuo Koyama
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Ken Hatano
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
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124
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PARK H, HAN S, HAN G. Application of Retrogradation-retardation Technology to Korean Rice Cake, Garaedduk Made from Non-waxy Rice. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2012. [DOI: 10.3136/fstr.18.371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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125
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Yamamoto K, Miyake H, Kusunoki M, Osaki S. Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae. J Biosci Bioeng 2011; 112:545-50. [DOI: 10.1016/j.jbiosc.2011.08.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022]
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126
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Alves MJ, Costa FT, Duarte VCM, Fortes AG, Martins JA, Micaelo NM. Advances in the Synthesis of Homochiral (−)-1-Azafagomine and (+)-5-epi-1-Azafagomine. 1-N-Phenyl Carboxamide Derivatives of both Enantiomers of 1-Azafagomine: Leads for the Synthesis of Active α-Glycosidase Inhibitors. J Org Chem 2011; 76:9584-92. [DOI: 10.1021/jo201486q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. José Alves
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057
Braga, Portugal
| | - Flora T. Costa
- Faculdade
de Ciências
da Saúde, Universidade Fernando Pessoa, R. Carlos da Maia, 296, 4100-150 Porto, Portugal
| | - Vera C. M. Duarte
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057
Braga, Portugal
| | - Antonio Gil Fortes
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057
Braga, Portugal
| | - José A. Martins
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057
Braga, Portugal
| | - Nuno M. Micaelo
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057
Braga, Portugal
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127
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Li F, Zhu X, Li Y, Cao H, Zhang Y. Functional characterization of a special thermophilic multifunctional amylase OPMA-N and its N-terminal domain. Acta Biochim Biophys Sin (Shanghai) 2011; 43:324-34. [PMID: 21355000 DOI: 10.1093/abbs/gmr013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A gene encoding a special thermophilic multifunctional amylase OPMA-N was cloned from Bacillus sp. ZW2531-1. OPMA-N has an additional 124-residue N-terminal domain compared with typical amylases and forms a relatively independent domain with a β-pleated sheet and random coil structure. Here we reported an unusual substrate and product specificities of OPMA-N and the impact of the additional N-terminal domain (1-124 aa) on the function and properties of OPMA-N. Both OPMA-N (12.82 U/mg) and its N-terminal domain-truncated ΔOPMA-N (12.55 U/mg) only degraded starch to produce oligosaccharides including maltose, maltotriose, isomaltotriose, and isomaltotetraose, but not to produce glucose. Therefore, the N-terminal domain did not determine its substrate and product specificities that were probably regulated by its C-terminal β-pleated sheet structure. However, the N-terminal domain of OPMA-N seemed to modulate its catalytic feature, leading to the production of more isomaltotriose and less maltose, and it seemed to contribute to OPMA-N's thermostability since OPMA-N showed higher activity than ΔOPMA-N in a temperature range from 40 to 80°C and the half-life (t(1/2)) was 5 h for OPMA-N and 2 h for ΔOPMA-N at 60°C. Both OPMA-N and ΔOPMA-N were Ca(2+)-independent, but their activities could be influenced by Cu(2+), Ni(2+), Zn(2+), EDTA, SDS (1 mM), or Triton-X100 (1%). Kinetic analysis and starch-adsorption assay indicated that the N-terminal domain of OPMA-N could increase the OPMA-N-starch binding and subsequently increase the catalytic efficiency of OPMA-N for starch. In particular, the N-terminal domain of OPMA-N did not determine its oligomerization, because both OPMA-N and ΔOPMA-N could exist in the forms of monomer, homodimer, and homooligomer at the same time.
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Affiliation(s)
- Fan Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, China
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128
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Kumar V. Identification of the sequence motif of glycoside hydrolase 13 family members. Bioinformation 2011; 6:61-3. [PMID: 21544166 PMCID: PMC3082856 DOI: 10.6026/97320630006061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/07/2011] [Indexed: 11/23/2022] Open
Abstract
A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the -1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 family members.
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Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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129
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Tonozuka T, Miyazaki T, Nishikawa A. Structural Similarity between a Starch-hydrolyzing Enzyme and an N-Glycan-Hydrolyzing Enzyme: Exohydrolases Cleaving α-1,X-Glucosidic Linkages to Produce β-Glucose. TRENDS GLYCOSCI GLYC 2011. [DOI: 10.4052/tigg.23.93] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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130
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Gabriško M, Janeček Š. Characterization of Maltase Clusters in the Genus Drosophila. J Mol Evol 2010; 72:104-18. [DOI: 10.1007/s00239-010-9406-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 10/27/2010] [Indexed: 11/28/2022]
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131
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Biophysical Characterization of a Recombinant α-Amylase from Thermophilic Bacillus sp. strain TS-23. Protein J 2010; 29:572-82. [DOI: 10.1007/s10930-010-9287-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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132
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Tyler L, Bragg JN, Wu J, Yang X, Tuskan GA, Vogel JP. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics 2010; 11:600. [PMID: 20973991 PMCID: PMC3091745 DOI: 10.1186/1471-2164-11-600] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 10/25/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families. RESULTS We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. CONCLUSIONS This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a grass model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.
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Affiliation(s)
- Ludmila Tyler
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer N Bragg
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Jiajie Wu
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Xiaohan Yang
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John P Vogel
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
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133
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Ferrando ML, Fuentes S, de Greeff A, Smith H, Wells JM. ApuA, a multifunctional α-glucan-degrading enzyme of Streptococcus suis, mediates adhesion to porcine epithelium and mucus. Microbiology (Reading) 2010; 156:2818-2828. [DOI: 10.1099/mic.0.037960-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We have identified apuA in Streptococcus suis, which encodes a bifunctional amylopullulanase with conserved α-amylase and pullulanase substrate-binding domains and catalytic motifs. ApuA exhibited properties typical of a Gram-positive surface protein, with a putative signal sequence and LPKTGE cell-wall-anchoring motif. A recombinant protein containing the predicted N-terminal α-amylase domain of ApuA was shown to have α-(1,4) glycosidic activity. Additionally, an apuA mutant of S. suis lacked the pullulanase α-(1,6) glycosidic activity detected in a cell-surface protein extract of wild-type S. suis. ApuA was required for normal growth in complex medium containing pullulan as the major carbon source, suggesting that this enzyme plays a role in nutrient acquisition in vivo via the degradation of glycogen and food-derived starch in the nasopharyngeal and oral cavities. ApuA was shown to promote adhesion to porcine epithelium and mucus in vitro, highlighting a link between carbohydrate utilization and the ability of S. suis to colonize and infect the host.
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Affiliation(s)
- Maria Laura Ferrando
- Host-Microbe Interactomics, Wageningen University and Research Centre, Marijkeweg 40, 6709 PG Wageningen, The Netherlands
| | - Susana Fuentes
- Host-Microbe Interactomics, Wageningen University and Research Centre, Marijkeweg 40, 6709 PG Wageningen, The Netherlands
| | - Astrid de Greeff
- Central Veterinary Institute of Wageningen UR, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
| | - Hilde Smith
- Central Veterinary Institute of Wageningen UR, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
| | - Jerry M. Wells
- Host-Microbe Interactomics, Wageningen University and Research Centre, Marijkeweg 40, 6709 PG Wageningen, The Netherlands
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134
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Yamamoto K, Miyake H, Kusunoki M, Osaki S. Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose. FEBS J 2010; 277:4205-14. [PMID: 20812985 DOI: 10.1111/j.1742-4658.2010.07810.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures of isomaltase from Saccharomyces cerevisiae and in complex with maltose were determined at resolutions of 1.30 and 1.60 Å, respectively. Isomaltase contains three domains, namely, A, B, and C. Domain A consists of the (β/α)(8) -barrel common to glycoside hydrolase family 13. However, the folding of domain C is rarely seen in other glycoside hydrolase family 13 enzymes. An electron density corresponding to a nonreducing end glucose residue was observed in the active site of isomaltase in complex with maltose; however, only incomplete density was observed for the reducing end. The active site pocket contains two water chains. One water chain is a water path from the bottom of the pocket to the surface of the protein, and may act as a water drain during substrate binding. The other water chain, which consists of six water molecules, is located near the catalytic residues Glu277 and Asp352. These water molecules may act as a reservoir that provides water for subsequent hydrolytic events. The best substrate for oligo-1,6-glucosidase is isomaltotriose; other, longer-chain, oligosaccharides are also good substrates. However, isomaltase shows the highest activity towards isomaltose and very little activity towards longer oligosaccharides. This is because the entrance to the active site pocket of isomaltose is severely narrowed by Tyr158, His280, and loop 310-315, and because the isomaltase pocket is shallower than that of other oligo-1,6-glucosidases. These features of the isomaltase active site pocket prevent isomalto-oligosaccharides from binding to the active site effectively.
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135
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Molecular cloning and expression of an extracellular α-amylase gene from an Antarctic deep sea psychrotolerant Pseudomonas stutzeri strain 7193. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0526-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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136
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Leemhuis H, Dijkhuizen L. Engineering of Hydrolysis Reaction Specificity in the Transglycosylase Cyclodextrin Glycosyltransferase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001614333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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137
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Veith B, Zverlov V, Lunina N, Berezina O, Raasch C, Velikodvorskaya G, Liebl W. Comparative Analysis of the Recombinant α-Glucosidases from theThermotoga neapolitanaandThermotoga maritimaMaltodextrin Utilization Gene Clusters. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001614324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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138
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Kumar V. Identification of the conserved spatial position of key active-site atoms in glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:1564-9. [PMID: 20557875 DOI: 10.1016/j.carres.2010.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 11/30/2022]
Abstract
A computational study on the glycoside hydrolase 13 (GH13) family of the CAZy database has been carried out at the atomic level in order to identify the conserved positions that may be responsible for recognition of the substrate. Analysis with substrate analog-, inhibitor-, or product-bound 3D structures was carried out to find the atomic spatial arrangement of the amino acids that make -2, -1, +1, and +2 subsites and water oxygen atoms around the ligand. The identified conserved positions of subsites were independent from the nature of the amino acid. The -1 and +1 subsites have more conserved positions than the -2 and +2 subsites. Some of the clusters of the -1 and +1 subsites have atoms of the same chemical nature. A spatially conserved position for water, which is stabilized by a hydrogen bond with the carboxyl group of a proton donor (Glu) and Asp of the catalytic triad, was found in the -1 subsite of 75% of the enzymes subjected to analysis. This position could be the region of hydrolytic water.
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Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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139
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Analysis of the key active subsites of glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:893-8. [DOI: 10.1016/j.carres.2010.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 02/07/2010] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
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140
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141
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Dumbrepatil AB, Choi JH, Park JT, Kim MJ, Kim TJ, Woo EJ, Park KH. Structural features of theNostoc punctiformedebranching enzyme reveal the basis of its mechanism and substrate specificity. Proteins 2010; 78:348-56. [DOI: 10.1002/prot.22548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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142
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Chi MC, Chen YH, Wu TJ, Lo HF, Lin LL. Engineering of a truncated alpha-amylase of Bacillus sp. strain TS-23 for the simultaneous improvement of thermal and oxidative stabilities. J Biosci Bioeng 2009; 109:531-8. [PMID: 20471589 DOI: 10.1016/j.jbiosc.2009.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/28/2009] [Accepted: 11/13/2009] [Indexed: 11/30/2022]
Abstract
BACDeltaNC/Delta RS is a thermostable variant derived from the truncated alpha-amylase (BAC Delta NC) of alkaliphilic Bacillus sp. strain TS-23. With the aim of enhancing its resistance towards chemical oxidation, Met231 of BAC Delta NC/Delta RS was replaced by leucine to create BAC Delta NC/Delta RS/M231L. The functional significance of the 31 C-terminal residues of BAC Delta NC/Delta RS/M231L was also explored by site-directed mutagenesis of the 483 th codon in the gene to stop codon (TAA), thereon the engineered enzyme was named BAC Delta NC/Delta RS/M231L/Delta C31. BAC Delta NC/Delta RS/M231L and BAC Delta NC/Delta RS/M231L/Delta C31 were very similar to BAC Delta NC in terms of specific activity, kinetic parameters, pH-activity profile, and the hydrolysis of raw starch; however, the engineered enzymes showed an increased half-life at 70 degrees C. The intrinsic fluorescence and circular dichroism spectra were nearly identical for wild-type and engineered enzymes, but they exhibited a different sensitivity towards GdnHCl-induced denaturation. This implicates that the rigidity of the enzyme has been changed as the consequence of mutations. Performance of the engineered enzymes was evaluated in the presence of commonly used detergent compounds and some detergents from the local markets. A high compatibility and performance of both BAC Delta NC/Delta RS/M231L and BAC Delta NC/Delta RS/M231L/Delta C31 may be desirable for their practical uses in the detergent industry.
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Affiliation(s)
- Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 University Road, Chiayi, Taiwan
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143
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Cho KH, Auh JH, Ryu JH, Kim JH, Park K, Park CS, Yoo SH. Structural modification and characterization of rice starch treated by Thermus aquaticus 4-α-glucanotransferase. Food Hydrocoll 2009. [DOI: 10.1016/j.foodhyd.2009.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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144
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Gabriško M, Janeček Š. Looking for the ancestry of the heavy-chain subunits of heteromeric amino acid transporters rBAT and 4F2hc within the GH13 α-amylase family. FEBS J 2009; 276:7265-78. [DOI: 10.1111/j.1742-4658.2009.07434.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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145
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Liu Y, Shen W, Shi GY, Wang ZX. Role of the calcium-binding residues Asp231, Asp233, and Asp438 in alpha-amylase of Bacillus amyloliquefaciens as revealed by mutational analysis. Curr Microbiol 2009; 60:162-6. [PMID: 19841977 DOI: 10.1007/s00284-009-9517-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 09/24/2009] [Indexed: 11/26/2022]
Abstract
Role of the calcium-binding residues Asp231, Asp233, and Asp438 of Bacillus amyloliquefaciens alpha-amylase (BAA) on the enzyme properties was investigated by site-directed mutagenesis. The calcium-binding residues Asp231, Asp233, and Asp438 were replaced with Asn, Asn, and Gly to produce the mutants D231N, D233N, and D438G, respectively. The mutant amylases were purified to homogeneity and the purified enzymes was estimated to be approximately 58 kDa. The specific activity for the mutant enzyme D233N was decreased by 84.8%, while D231N and D438G showed a decrease of 6.3% and 3.5% to that of the wild-type enzyme, respectively. No significant changes in the K (m) value, thermo-stability, optimum temperature, and optimum pH were observed in the mutations of D231N and D438G, while substitution of Asp233 with Asn resulted in a dramatic reduction in the value of catalytic efficiency (K (cat)/K (m)) and thermo-stability at 60 degrees C. The ranges of optimum temperature and optimum pH for D233N were also reduced to about 10 degrees C and 3-4 units, respectively.
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Affiliation(s)
- Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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146
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Alpha-Glucosidase Folding During Urea Denaturation: Enzyme Kinetics and Computational Prediction. Appl Biochem Biotechnol 2009; 160:1341-55. [DOI: 10.1007/s12010-009-8636-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
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147
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Hondoh H, Otsuka-Rachi H, Saburi W, Mori H, Okuyama M, Kimura A. Structural Comparison of <i>Streptococcus mutans</i> Dextran Glucosidase with Glucoside Hydrolases in GH13. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Hironori Hondoh
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
| | - Hiroaki Otsuka-Rachi
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
| | - Wataru Saburi
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
| | - Haruhide Mori
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
| | - Masayuki Okuyama
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
| | - Atsuo Kimura
- Division of Applied Bioscience Research, Faculty of Agriculture, Hokkaido University
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148
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Kamasaka H, To-o K, Nishimura T, Kimura T, Matsuzawa N, Sakamoto R. Studies on Mass Production and Application of Phosphoryl Oligosaccharides from Potato Starch. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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149
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Noguchi A, Inohara-Ochiai M, Ishibashi N, Fukami H, Nakayama T, Nakao M. A Novel Glucosylation Enzyme: Molecular Cloning, Expression, and Characterization of Trichoderma viride JCM22452 α-Amylase and Enzymatic Synthesis of Some Flavonoid Monoglucosides and Oligoglucosides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:12016-24. [PMID: 0 DOI: 10.1021/jf801712g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Akio Noguchi
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
| | - Misa Inohara-Ochiai
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
| | - Noriko Ishibashi
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
| | - Harukazu Fukami
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
| | - Toru Nakayama
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
| | - Masahiro Nakao
- Institute for Advanced Core Technology, Suntory Ltd., 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan; Department of Bioenvironmental Science, Kyoto Gakuen University, Najo-ohtani 1-1, Sokabe-cho, Kameoka, Kyoto 621-8555, Japan; and Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579, Japan
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