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Glycoside hydrolase

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https://www.readbyqxmd.com/read/29139580/novel-carbohydrate-binding-modules-in-the-surface-anchored-%C3%AE-amylase-of-eubacterium-rectale-provide-a-molecular-rationale-for-the-range-of-starches-used-by-this-organism-in-the-human-gut
#1
Darrell W Cockburn, Carolyn Suh, Krizia Perez Medina, Rebecca M Duvall, Zdzislaw Wawrzak, Bernard Henrissat, Nicole M Koropatkin
Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell-surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria...
November 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29133092/cloning-and-biochemical-characterization-of-a-novel-%C3%AE%C2%BA-carrageenase-from-newly-isolated-marine-bacterium-pedobacter-hainanensis-nj-02
#2
Benwei Zhu, Fang Ni, Limin Ning, Zhong Yao, Yuguang Du
Enzymatic preparation of carrageenan oligosaccharides has drawn increasing attention due to its advantages of mild reaction conditions and excellent product-specificity. A novel gene (CgkA) encoding a new κ-carrageenase was cloned, heterogeneously expressed and characterized from a newly isolated marine bacterium Pedobacter hainanensis NJ-02. It consisted of 1539bp and encoded 512 amino acid residues with a molecular weight of 57.12kDa. Multiple alignment analysis indicated that CgkA belongs to glycoside hydrolase (GH) family 16 and was most homologous to κ-carrageenase of Zobellia sp...
November 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29133008/biotechnological-potential-of-novel-glycoside-hydrolase-family-70-enzymes-synthesizing-%C3%AE-glucans-from-starch-and-sucrose
#3
REVIEW
Joana Gangoiti, Tjaard Pijning, Lubbert Dijkhuizen
Transglucosidases belonging to the glycoside hydrolase (GH) family 70 are promising enzymatic tools for the synthesis of α-glucans with defined structures from renewable sucrose and starch substrates. Depending on the GH70 enzyme specificity, α-glucans with different structures and physicochemical properties are produced, which have found diverse (potential) commercial applications, e.g. in food, health and as biomaterials. Originally, the GH70 family was established only for glucansucrase enzymes of lactic acid bacteria that catalyze the synthesis of α-glucan polymers from sucrose...
November 10, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/29131232/homogenous-graphene-oxide-peptide-nanofiber-hybrid-hydrogel-as-biomimetic-polysaccharide-hydrolase
#4
Xingxing He, Fuyuan Zhang, Jifeng Liu, Guozhen Fang, Shuo Wang
Cellulose, an impressive potential sustainable fuel, is difficult to hydrolyze because of the protection of β-1,4-glycosidic bonds through the tight hydrogen bonding network. In this study, homogenous graphene oxide (GO)-peptide nanofiber hybrid hydrogels (GO-PNFs) were designed as a β-glycosyl hydrolase mimetic to achieve efficient degradation of cellobiose and cellopentaose. For comparison, free peptides, graphene oxide mixed with free peptides (GO-peptdies) and self-assembled peptide nanofibers (PNFs) were also studied for their activity as a hydrolase mimetics for degradation of cellobiose...
November 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/29128403/cln5-is-secreted-and-functions-as-a-glycoside-hydrolase-in-dictyostelium
#5
Robert J Huber, Sabateeshan Mathavarajah
Ceroid lipofuscinosis neuronal 5 (CLN5) is a member of a family of proteins that are linked to neuronal ceroid lipofuscinosis (NCL). This devastating neurological disorder, known commonly as Batten disease, affects all ages and ethnicities and is currently incurable. The precise function of CLN5, like many of the NCL proteins, remains to be elucidated. In this study, we report the localization, molecular function, and interactome of Cln5, the CLN5 homolog in the social amoeba Dictyostelium discoideum. Residues that are glycosylated in human CLN5 are conserved in the Dictyostelium homolog as are residues that are mutated in patients with CLN5 disease...
November 8, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29122174/differential-gene-expression-profiling-analysis-in-pleurotus-ostreatus-during-interspecific-antagonistic-interactions-with-dichomitus-squalens-and-trametes-versicolor
#6
Zixuan Zhong, Liu Li, Peng Chang, Haiying Xie, Huiting Zhang, Yasuo Igarashi, Nannan Li, Feng Luo
This study provided analysis of differentially expressed genes (DEGs) in Pleurotus ostreatus under the interaction with Dichomitus squalens and Trametes versicolor, which is valuable for exploration on the fungal defence system against stressful condition caused by interspecific antagonistic interaction. Our result showed significant upregulation of abundant defence-related genes encoding laccase, manganese peroxidase, aldo-keto reductase, and glutathione S-transferase, which all play important roles in oxidative stress-resistant response...
December 2017: Fungal Biology
https://www.readbyqxmd.com/read/29121496/properties-of-two-fungal-endo-%C3%AE-1-3-galactanases-and-their-synergistic-action-with-an-exo-%C3%AE-1-3-galactanase-in-degrading-arabinogalactan-proteins
#7
Yoshihisa Yoshimi, Kaori Yaguchi, Satoshi Kaneko, Yoichi Tsumuraya, Toshihisa Kotake
Arabinogalactan-proteins (AGPs) are plant proteoglycans, which are widely encountered in the plant kingdom, usually localized on the cell surface. The carbohydrate moieties of AGPs consist of β-1,3-galactan main chains and β-1,6-galactan side chains, to which other auxiliary sugars are attached. To date, FvEn3GAL isolated from Flammulina velutipes is the sole β-1,3-galactanase acting on β-1,3-galactan in an endo-manner. Here we cloned two homologous genes, designated Af3G and NcEn3GAL, possibly encoding endo-β-1,3-galactanase from Aspergillus flavus and Neurospora crassa, respectively...
October 25, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/29118851/targeted-metatranscriptomics-of-compost-derived-consortia-reveals-a-gh11-exerting-an-unusual-exo-1-4-%C3%AE-xylanase-activity
#8
Bruno L Mello, Anna M Alessi, Diego M Riaño-Pachón, Eduardo R deAzevedo, Francisco E G Guimarães, Melissa C Espirito Santo, Simon McQueen-Mason, Neil C Bruce, Igor Polikarpov
Background: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29109478/a-bacterial-pioneer-produces-cellulase-complexes-that-persist-through-community-succession
#9
Sebastian Kolinko, Yu-Wei Wu, Firehiwot Tachea, Evelyn Denzel, Jennifer Hiras, Raphael Gabriel, Nora Bäcker, Leanne Jade G Chan, Stephanie A Eichorst, Dario Frey, Qiushi Chen, Parastoo Azadi, Paul D Adams, Todd R Pray, Deepti Tanjore, Christopher J Petzold, John M Gladden, Blake A Simmons, Steven W Singer
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs)...
November 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29108954/a-flexible-loop-for-mannan-recognition-and-activity-enhancement-in-a-bifunctional-glycoside-hydrolase-family-5
#10
Po-Huang Liang, Wen-Ling Lin, Han-Yu Hsieh, Tsung-Yi Lin, Chun-Hsu Chen, Sunil K Tewary, Hsiao-Lin Lee, Shuo-Fu Yuan, Barbara Yang, Jyun-Yu Yao, Meng-Chiao Ho
BACKGROUND: An array of glycoside hydrolases with multiple substrate specificities are required to digest plant cell wall polysaccharides. Cel5E from Clostridium thermocellum and Cel5A from Thermotoga maritima are two glycoside hydrolase family 5 (GH5) enzymes with high sequence and structural similarity, but notably possess different substrate specificities; the former is a bifunctional cellulase/xylanase and the latter is a cellulase/mannanase. A specific loop in TmCel5A, Tmloop, is one of the most structurally divergent regions compared to CtCel5E and interacts with substrates, suggesting the importance for mannan recognition...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29108625/a-first-glycoside-hydrolase-family-50-endo-%C3%AE-1-3-d-glucanase-from-pseudomonas-aeruginosa
#11
Ping Yi, Qiaojuan Yan, Zhengqiang Jiang, Ling Wang
A novel β-1,3-glucanase gene (PaBglu50A) from Pseudomonas aeruginosa CAU 342A was cloned and expressed in Escherichia coli. The deduced amino acid sequence of PaBglu50A showed the highest identity of 34% with the β-agarase belonging to glycoside hydrolase (GH) family 50. The purified PaBglu50A had maximal activity at pH 5.5 and 45°C, respectively. It was stable in the range of pH 4.0-8.0 and at temperatures below 40°C. The Km and Vmax of PaBglu50A for curdlan and laminarin were 94.4mgml(-1) and 23.4μmolmin(-1)mg(-1), 3...
January 2018: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/29103167/enhancement-in-catalytic-activity-of-aspergillus-niger-xynb-by-selective-site-directed-mutagenesis-of-active-site-amino-acids
#12
Xiuyun Wu, Zhennan Tian, Xukai Jiang, Qun Zhang, Lushan Wang
XynB from Aspergillus niger ATCC1015 (AnXynB) is a mesophilic glycoside hydrolase (GH) family 11 xylanase which holds great potentials in a wide variety of industrial applications. In the present study, the catalytic activity and stability of AnXynB were improved by a combination of computational and experimental approaches. Virtual mutation and molecular dynamics simulations indicated that the introduction of Glu and Asn altered the interaction network at the - 3 subsite. Interestingly, the double mutant S41N/T43E displayed 72% increase in catalytic activity when compared to the wild type (WT)...
November 4, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29100023/lignocellulose-deconstruction-in-the-biosphere
#13
REVIEW
Yannick J Bomble, Chien-Yuan Lin, Antonella Amore, Hui Wei, Evert K Holwerda, Peter N Ciesielski, Bryon S Donohoe, Stephen R Decker, Lee R Lynd, Michael E Himmel
Microorganisms have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction...
October 31, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29098725/the-structure-of-the-large-regulatory-%C3%AE-subunit-of-phosphorylase-kinase-examined-by-modeling-and-hydrogen-deuterium-exchange
#14
Mary Ashley Rimmer, Owen W Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M Carlson
Phosphorylase kinase (PhK), a 1.3 MDa regulatory enzyme complex in the glycogenolysis cascade, has four copies each of four subunits, (αβγδ)4 , and 325 kDa of unique sequence (the mass of an αβγδ protomer). The α, β and δ subunits are regulatory, and contain allosteric activation sites that stimulate the activity of the catalytic γ subunit in response to diverse signaling molecules. Due to its size and complexity, no high resolution structures have been solved for the intact complex or its regulatory α and β subunits...
November 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29095151/the-n253f-mutant-structure-of-trehalose-synthase-from-deinococcus-radiodurans-reveals-an-open-active-site-topology
#15
Sih Yao Chow, Yung Lin Wang, Yu Chiao Hsieh, Guan Chiun Lee, Shwu Huey Liaw
Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29093477/identification-and-characterization-of-a-novel-%C3%AE-glucosidase-via-metagenomic-analysis-of-bursaphelenchus-xylophilus-and-its-microbial-flora
#16
Lin Zhang, Qiang Fu, Wenpeng Li, Bowen Wang, Xiaoyan Yin, Suyao Liu, Zhaonan Xu, Qiuhong Niu
β-glucosidases catalyze the final step of cellulose hydrolysis and are essential in cellulose degradation. A β-glucosidase gene, cen502, was identified and isolated from a metagenomic library from Bursaphelenchus xylophilus via functional screening. Analyses indicated that cen502 encodes a 465 amino acid polypeptide that contains a catalytic domain belonging to the glycoside hydrolase family 1 (GH1). Cen502 was heterologously expressed, purified, and biochemically characterized. Recombinant Cen502 displayed optimum enzymatic activity at pH 8...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29083543/the-molecular-structure-of-the-glycoside-hydrolase-domain-of-cwp19-from-clostridium-difficile
#17
William J Bradshaw, Jonathan M Kirby, April K Roberts, Clifford C Shone, K Ravi Acharya
Clostridium difficile is a burden to health care systems around the world, causing tens of thousands of deaths annually. The S-layer of the bacterium, a layer of protein found of the surface of cells, has received a significant amount of attention over the past two decades as a potential target to combat the growing threat presented by C. difficile infections. The S-layer contains a wide range of proteins, each of which possess three cell wall binding domains, while many also possess a "functional" region. Here, we present the high resolution structure of the functional region of one such protein, Cwp19 along with preliminary functional characterisation of the predicted glycoside hydrolase...
October 30, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29067645/secretome-profiling-reveals-temperature-dependent-growth-of-aspergillus-fumigatus
#18
Dongyu Wang, Lili Zhang, Haiyue Zou, Lushan Wang
Aspergillus fumigatus is a ubiquitous opportunistic fungus. In this study, systematic analyses were carried out to study the temperature adaptability of A. fumigatus. A total of 241 glycoside hydrolases and 69 proteases in the secretome revealed the strong capability of A. fumigatus to degrade plant biomass and protein substrates. In total, 129 pathogenesis-related proteins detected in the secretome were strongly correlated with glycoside hydrolases and proteases. The variety and abundance of proteins remained at temperatures of 34°C-45°C...
October 23, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29062404/enzymatic-synthesis-of-glycosides-from-natural-o-and-n-glycosides-to-rare-c-and-s-glycosides
#19
REVIEW
Jihen Ati, Pierre Lafite, Richard Daniellou
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.
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29061847/discovery-of-%C3%AE-l-arabinopyranosidases-from-human-gut-microbiome-expands-the-diversity-within-glycoside-hydrolase-family-42
#20
Alexander Holm Viborg, Takane Katayama, Takatoshi Arakawa, Maher Abou Hachem, Leila Lo Leggio, Motomitsu Kitaoka, Birte Svensson, Shinya Fushinobu
Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-L-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides...
October 23, 2017: Journal of Biological Chemistry
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