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Glycoside hydrolase

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https://www.readbyqxmd.com/read/28097217/amylose-recognition-and-ring-size-determination-of-amylomaltase
#1
Christian Roth, Nicole Weizenmann, Nicola Bexten, Wolfram Saenger, Wolfgang Zimmermann, Timm Maier, Norbert Sträter
Starch is a major carbon and energy source throughout all kingdoms of life. It consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. Hence, the enzymatic breakdown by glycoside hydrolases (GHs) is of great biological and societal importance. Amylomaltases (AMs) are GHs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units...
January 2017: Science Advances
https://www.readbyqxmd.com/read/28091525/a-fibrolytic-potential-in-the-human-ileum-mucosal-microbiota-revealed-by-functional-metagenomic
#2
Orlane Patrascu, Fabienne Béguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, Anne-Laure Abraham, Marion Leclerc, Christophe Klopp, Nicolas Terrapon, Bernard Henrissat, Hervé M Blottière, Joël Doré, Christel Béra-Maillet
The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28075353/biochemical-and-structural-insights-into-a-novel-thermostable-%C3%AE-1-3-galactosidase-from-marinomonas-sp-bsi20414
#3
Haitao Ding, Qian Zeng, Lili Zhou, Yong Yu, Bo Chen
A novel β-1,3-galactosidase, designated as MaBGA (β-galactosidase from Marinomonas sp. BSi20414), was successfully purified to homogeneity from Marinomonas sp. BSi20414 isolated from Arctic sea ice by ammonium sulfate precipitation and anion exchange chromatography, resulting in an 8.12-fold increase in specific activity and 9.9% recovery in total activity. MaBGA displayed its maximum activity at pH 6.0 and 60 °C, and maintained at least 90% of its initial activity over the pH range of 5.0-8.0 after incubating for 1 h...
January 8, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28070679/diversity-of-microbial-carbohydrate-active-enzymes-cazymes-associated-with-freshwater-and-soil-samples-from-caatinga-biome
#4
Ana Camila Andrade, Adriana Fróes, Fabyano Álvares Cardoso Lopes, Fabiano L Thompson, Ricardo Henrique Krüger, Elizabeth Dinsdale, Thiago Bruce
Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga...
January 9, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28065507/crystal-structure-of-4-6-%C3%AE-glucanotransferase-supports-diet-driven-evolution-of-gh70-enzymes-from-%C3%AE-amylases-in-oral-bacteria
#5
Yuxiang Bai, Joana Gangoiti, Bauke W Dijkstra, Lubbert Dijkhuizen, Tjaard Pijning
Food processing and refining has dramatically changed the human diet, but little is known about whether this affected the evolution of enzymes in human microbiota. We present evidence that glycoside hydrolase family 70 (GH70) glucansucrases from lactobacilli, synthesizing α-glucan-type extracellular polysaccharides from sucrose, likely evolved from GH13 starch-acting α-amylases, via GH70 4,6-α-glucanotransferases. The crystal structure of a 4,6-α-glucanotransferase explains the mode of action and unique product specificity of these enzymes...
December 21, 2016: Structure
https://www.readbyqxmd.com/read/28059108/4-3-%C3%AE-glucanotransferase-a-novel-reaction-specificity-in-glycoside-hydrolase-family-70-and-clan-gh-h
#6
Joana Gangoiti, Sander S van Leeuwen, Gerrit J Gerwig, Stéphane Duboux, Christina Vafiadi, Tjaard Pijning, Lubbert Dijkhuizen
Lactic acid bacteria possess a diversity of glucansucrase (GS) enzymes that belong to glycoside hydrolase family 70 (GH70) and convert sucrose into α-glucan polysaccharides with (α1 → 2)-, (α1 → 3)-, (α1 → 4)- and/or (α1 → 6)-glycosidic bonds. In recent years 3 novel subfamilies of GH70 enzymes, inactive on sucrose but using maltodextrins/starch as substrates, have been established (e.g. GtfB of Lactobacillus reuteri 121). Compared to the broad linkage specificity found in GSs, all GH70 starch-acting enzymes characterized so far possess 4,6-α-glucanotransferase activity, cleaving (α1 → 4)-linkages and synthesizing new (α1 → 6)-linkages...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28058278/a-%C3%AE-mannanase-with-a-lysozyme-like-fold-and-a-novel-molecular-catalytic-mechanism
#7
Yi Jin, Marija Petricevic, Alan John, Lluís Raich, Huw Jenkins, Leticia Portela De Souza, Fiona Cuskin, Harry J Gilbert, Carme Rovira, Ethan D Goddard-Borger, Spencer J Williams, Gideon J Davies
The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure...
December 28, 2016: ACS Central Science
https://www.readbyqxmd.com/read/28050853/metagenomic-insights-into-the-rumen-microbial-fibrolytic-enzymes-in-indian-crossbred-cattle-fed-finger-millet-straw
#8
V Lyju Jose, Thulasi Appoothy, Ravi P More, A Sha Arun
The rumen is a unique natural habitat, exhibiting an unparalleled genetic resource of fibrolytic enzymes of microbial origin that degrade plant polysaccharides. The objectives of this study were to identify the principal plant cell wall-degrading enzymes and the taxonomic profile of rumen microbial communities that are associated with it. The cattle rumen microflora and the carbohydrate-active enzymes were functionally classified through a whole metagenomic sequencing approach. Analysis of the assembled sequences by the Carbohydrate-active enzyme analysis Toolkit identified the candidate genes encoding fibrolytic enzymes belonging to different classes of glycoside hydrolases(11,010 contigs), glycosyltransferases (6366 contigs), carbohydrate esterases (4945 contigs), carbohydrate-binding modules (1975 contigs), polysaccharide lyases (480 contigs), and auxiliary activities (115 contigs)...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28045386/learning-from-oligosaccharide-soaks-of-crystals-of-an-aa13-lytic-polysaccharide-monooxygenase-crystal-packing-ligand-binding-and-active-site-disorder
#9
Kristian E H Frandsen, Jens Christian Navarro Poulsen, Morten Tovborg, Katja S Johansen, Leila Lo Leggio
Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28042032/characterization-of-divergent-pseudo-sucrose-isomerase-from-azotobacter-vinelandii-deciphering-the-absence-of-sucrose-isomerase-activity
#10
Jong-Hyun Jung, Min-Ji Kim, Woo-Soo Jeong, Dong-Ho Seo, Suk-Jin Ha, Young Wan Kim, Cheon-Seok Park
Among members of the glycoside hydrolase (GH) family, sucrose isomerase (SIase) and oligo-1,6-glucosidase (O16G) are evolutionarily closely related even though their activities show different specificities. A gene (Avin_08330) encoding a putative SIase (AZOG: Azotobacterglucocosidase) from the nitrogen-fixing bacterium Azotobacter vinelandii is a type of pseudo-SIase harboring the "RLDRD" motif, a SIase-specific region in 329-333. However, neither sucrose isomerization nor hydrolysis activities were observed in recombinant AZOG (rAZOG)...
December 30, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28039140/the-loop-3-of-fungal-endoglucanases-of-glycoside-hydrolase-family-12-modulates-the-catalytic-efficiency
#11
Hong Yang, Pengjun Shi, Yun Liu, Wei Xia, Xiaoyu Wang, Huifang Cao, Rui Ma, Huiying Luo, Yingguo Bai, Bin Yao
: The GH family 12 comprises enzymes with a wide range of activities critical for the degradation of lignocellulose. However, the important roles of loop regions of GH12 enzymes in substrate specificity and catalytic efficiency remain poorly understood. This study examined how the loop 3 region affects the enzymatic properties of GH12 glucanases using NfEG12A from Neosartorya fischeri P1 and EG (PDB: 1KS4) from Aspergillus niger Acidophilic and thermophilic NfEG12A had the highest catalytic efficiency (kcat/Km, 3001 and 263 mL/mg/s towards lichenin and CMC-Na, respectively) known so far...
December 30, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28019666/engineering-the-n-terminal-end-of-cela-results-in-improved-performance-and-growth-of-caldicellulosiruptor-bescii-on-crystalline-cellulose
#12
Sun-Ki Kim, Daehwan Chung, Michael E Himmel, Yannick J Bomble, Janet Westpheling
CelA is the most abundant enzyme secreted by Caldicellulosiruptor bescii and has been shown to outperform mixtures of commercially available exo- and endoglucanases in vitro. CelA contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. Here, repeated aspartate residues were introduced into the N-terminal ends of CelA GH9 and GH48 domains to improve secretion efficiency and/or catalytic efficiency of CelA...
December 26, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28013403/xyloglucan-breakdown-by-endo-xyloglucanase-family-74-from-aspergillus-fumigatus
#13
André Ricardo de Lima Damasio, Marcelo Ventura Rubio, Thiago Augusto Gonçalves, Gabriela Felix Persinoti, Fernando Segato, Rolf Alexander Prade, Fabiano Jares Contesini, Amanda Pereira de Souza, Marcos Silveira Buckeridge, Fabio Marcio Squina
Xyloglucan is the most abundant hemicellulose in primary walls of spermatophytes except for grasses. Xyloglucan-degrading enzymes are important in lignocellulosic biomass hydrolysis because they remove xyloglucan, which is abundant in monocot-derived biomass. Fungal genomes encode numerous xyloglucanase genes, belonging to at least six glycoside hydrolase (GH) families. GH74 endo-xyloglucanases cleave xyloglucan backbones with unsubstituted glucose at the -1 subsite or prefer xylosyl-substituted residues in the -1 subsite...
December 24, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28012227/widespread-selective-sweeps-throughout-the-genome-of-model-plant-pathogenic-fungi-and-identification-of-effector-candidates
#14
H Badouin, P Gladieux, J Gouzy, S Siguenza, G Aguileta, A Snirc, S Le Prieur, C Jeziorski, A Branca, T Giraud
Identifying the genes underlying adaptation, their distribution in genomes, and the evolutionary forces shaping genomic diversity, are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside of a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther-smut fungi and mapping them against a high-quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome...
December 24, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28010772/characterization-of-clostridium-thermocellum-b8-secretome-and-purified-cellulosomes-for-lignocellulosic-biomass-degradation
#15
Karen O Osiro, Brenda R de Camargo, Rachel Satomi, Pedro Ricardo V Hamann, Jéssica Pinheiro Silva, Marcelo Valle de Sousa, Betania F Quirino, Elaine N Aquino, Carlos R Felix, André Melro Murad, Eliane F Noronha
The main goal of the present study was a complete proteomic characterization of total proteins eluted from residual substrate-bound proteins (RSBP), and cellulosomes secreted by Clostridium thermocellum B8 during growth in the presence of microcrystalline cellulose as a carbon source. The second goal was to evaluate their potential use as enzymatic blends for hydrolyzing agro-industrial residues to produce fermentable sugars. Protein identification through LC-MS/MS mass spectrometry showed that the RSBP sample, in addition to cellulosomal proteins, contains a wide variety of proteins, including those without a well-characterized role in plant cell wall degradation...
February 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28003194/laci-transcriptional-regulatory-networks-in-clostridium-thermocellum-dsm1313
#16
Charlotte M Wilson, Dawn M Klingeman, Caleb Schlachter, Mustafa H Syed, Chia-Wei Wu, Adam M Guss, Steven D Brown
: Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. One LacI regulator termed GlyR3 in C. thermocellum ATCC27405 was previously identified as a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain...
December 21, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27995311/comparison-of-lipases-and-glycoside-hydrolases-as-catalysts-in-synthesis-reactions
#17
REVIEW
Patrick Adlercreutz
Lipases and glycoside hydrolases have large similarities concerning reaction mechanisms. Acyl-enzyme intermediates are formed during lipase-catalyzed reactions and in an analogous way, retaining glycoside hydrolases form glycosyl-enzyme intermediates during catalysis. In both cases, the covalent enzyme intermediates can react with water or other nucleophiles containing hydroxyl groups. Simple alcohols are accepted as nucleophiles by both types of enzymes. Lipases are used very successfully in synthesis applications due to their efficiency in catalyzing reversed hydrolysis and transesterification reactions...
January 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27992426/glycoside-hydrolases-across-environmental-microbial-communities
#18
Renaud Berlemont, Adam C Martiny
Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27992199/contribution-of-shape-and-charge-to-the-inhibition-of-a-family-gh99-endo-%C3%AE-1-2-mannanase
#19
Marija Petricevic, Lukasz F Sobala, Pearl Z Fernandes, Lluís Raich, Andrew J Thompson, Ganeko Bernardo-Seisdedos, Oscar Millet, Sha Zhu, Matthieu Sollogoub, Jesús Jiménez-Barbero, Carme Rovira, Gideon J Davies, Spencer J Williams
Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27986827/potential-of-semiarid-soil-from-caatinga-biome-as-a-novel-source-for-mining-lignocellulose-degrading-enzymes
#20
Gileno Lacerda Júnior, Melline Noronha, Sanderson Tarciso de Sousa, Lucélia Cabral, Daniela Domingos, Mírian Sáber, Itamar de Melo, Valéria Oliveira
The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material...
December 15, 2016: FEMS Microbiology Ecology
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