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Glycoside hydrolase

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https://www.readbyqxmd.com/read/28734034/protein-features-as-determinants-of-wild-type-glycoside-hydrolase-thermostability
#1
Henrik Marcus Geertz-Hansen, Lars Kiemer, Morten Nielsen, Kiril Stanchev, Nikolaj Blom, Søren Brunak, Thomas Nordahl Petersen
Thermostable enzymes for conversion of lignocellulosic biomass into biofuels have significant advantages over enzymes with more moderate themostability due to the challenging application conditions. Experimental discovery of thermostable enzymes is highly cost intensive, and the development of in-silico methods guiding the discovery process would be of high value. To develop such an in-silico method and provide the data foundation of it, we determined the melting temperatures of 602 fungal glycoside hydrolases from the families GH5, 6, 7, 10, 11, 43 and AA9 (formerly GH61)...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28731585/bacterial-invertases-occurrence-production-biochemical-characterization-and-significance-of-transfructosylation
#2
REVIEW
Lynette Lincoln, Sunil S More
Invertase or β-D-fructofuranoside fructohydrolase (EC 3.2.1.26) was one of the foremost enzyme biocatalysts and established the primary concepts of most enzyme-kinetic principles. Invertases are glycoside hydrolases and occur mostly in microorganisms. Among microbial strains, for many decades yeast species have been extensively researched for invertase production, characterization, and applications in industries. Besides, limited literature is available on invertases from bacterial strains. The enzymic and molecular biological reports from bacterial invertases are scarce...
July 21, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28725336/high-quality-draft-genome-sequence-of-a-biofilm-forming-lignocellulolytic-aspergillus-niger-strain-atcc-10864
#3
Sujay Paul, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa
Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capability. Here we report the first draft genome sequence of A. niger ATCC 10864 strain. The genome of A. niger ATCC 10864 is 36,172,237 bp long and comprise of 310 scaffolds with 49.5% average GC content. A total of 10,804 protein-coding genes were predicted among which 10,761 genes were with putative functions...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28723089/a-new-class-of-glycoside-hydrolase-mechanism-based-covalent-inhibitors-glycosylation-transition-state-conformations
#4
Saeideh Shamsi Kazem Abadi, Michael Tran, Anuj Yadav, Pal John Pal Adabala, Saswati Chakladar, Andrew J Bennet
The design of covalent inhibitors in glycoscience research is important for the development of chemical biology probes. Here we report the synthesis of a new carbocyclic mechanism-based covalent inhibitor of an α-glucosidase. The enzyme efficiently catalyzes its alkylation via either an allylic cation or a cationic transition state. We show that this allylic covalent inhibitor has very different catalytic proficiencies for pseudo-glycosylation and deglycosylation. Such inhibitors have the potential to be useful chemical biology tools...
July 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28715279/crystal-structure-of-a-%C3%AE-fructofuranosidase-with-high-transfructosylation-activity-from-aspergillus-kawachii
#5
Mika Nagaya, Miyoko Kimura, Yoshifumi Gozu, Shona Sato, Katsuaki Hirano, Takumi Tochio, Atsushi Nishikawa, Takashi Tonozuka
β-Fructofuranosidases belonging to glycoside hydrolase family (GH) 32 are enzymes that hydrolyze sucrose. Some GH32 enzymes also catalyze transfructosylation to produce fructooligosaccharides. We found that Aspergillus kawachii IFO 4308 β-fructofuranosidase (AkFFase) produces fructooligosaccharides, mainly 1-kestose, from sucrose. We determined the crystal structure of AkFFase. AkFFase is composed of an N-terminal small component, a β-propeller catalytic domain, an α-helical linker, and a C-terminal β-sandwich, similar to other GH32 enzymes...
July 17, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28711732/high-level-expression-and-purification-of-a-mollusca-endoglucanase-from-ampullaria-crossean-in-pichia-pastoris
#6
Xiuping Su, Xinwei Geng, Meixian Fu, Yeqing Wu, Longfei Yin, Fukun Zhao, Wei Chen
EG27I is an endogenous glucanase belonging to glycoside hydrolase family (GHF) 45 from the Mollusca, Ampullaria crossean. In this study, the EG27I mature peptide gene fused to HFBII secretion signal of Trichoderma reesei was expressed under GAP promoter of Pichia pastoris in SMD1163 strain. Bioactive EG27I with a molecular weight of 27 kDa was successfully expressed and secreted into the culture medium. When high cell density fermentation of the recombinant Pichia pastoris was performed by a fed-batch strategy for totally 132 h in a 7...
July 12, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28710263/enzymatic-mechanism-for-arabinan-degradation-and-transport-in-the-thermophilic-bacterium-caldanaerobius-polysaccharolyticus
#7
Daniel Wefers, Jia Dong, Ahmed M Abdel-Hamid, Hans Müller Paul, Gabriel V Pereira, Yejun Han, Dylan Dodd, Ramiya Baskaran, Beth Mayer, Roderick I Mackie, Isaac Cann
The plant cell wall polysaccharide arabinan is an important supply of arabinose, and unraveling arabinan degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-L-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endo-arabinanase (CpAbn43A), a GH27 β-L-arabinopyranosidase (CpAbp27A), and two GH127 β-L-arabinofuranosidases (CpAbf127A, CpAbf127B)...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28707339/neutron-structure-of-the-t26h-mutant-of-t4-phage-lysozyme-provides-insight-into-the-catalytic-activity-of-the-mutant-enzyme-and-how-it-differs-from-that-of-wild-type
#8
Takeshi Hiromoto, Flora Meilleur, Rumi Shimizu, Chie Shibazaki, Motoyasu Adachi, Taro Tamada, Ryota Kuroki
T4 phage lysozyme is an inverting glycoside hydrolase that degrades the murein of bacterial cell walls by cleaving the β-1,4-glycosidic bond. The substitution of the catalytic Thr26 residue to a histidine converts the wild type from an inverting to a retaining enzyme, which implies that the original general acid Glu11 can also act as an acid/base catalyst in the hydrolysis. Here, we have determined the neutron structure of the perdeuterated T26H mutant to clarify the protonation states of Glu11 and the substituted His26, which are key in the retaining reaction...
July 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28706242/draft-whole-genome-sequence-of-groundnut-stem-rot-fungus-athelia-rolfsii-revealing-genetic-architect-of-its-pathogenicity-and-virulence
#9
M A Iquebal, Rukam S Tomar, M V Parakhia, Deepak Singla, Sarika Jaiswal, V M Rathod, S M Padhiyar, Neeraj Kumar, Anil Rai, Dinesh Kumar
Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28703279/lactulose-production-by-a-thermostable-glycoside-hydrolase-from-the-hyperthermophilic-archaeon-caldivirga-maquilingensis-ic-167
#10
Rebaone Letsididi, Hinawi A M Hassanin, Marwa Y F Koko, Tao Zhang, Bo Jiang, Wanmeng Mu
BACKGROUND: Lactulose has various uses in the food and pharmaceutical fields. Thermostable enzymes have many advantages for industrial exploitation, including high substrate solubilities as well as reduced risk of process contamination. RESULTS: Enzymatic synthesis of lactulose employing a transgalactosylation reaction by a recombinant thermostable GH1 from the hyperthermophilic archaeon Caldivirga maquilingensis IC-167 was investigated and its optimum pH for lactulose production was found to be 4...
July 12, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28698247/carbohydrate-binding-architecture-of-the-multi-modular-%C3%AE-1-6-glucosyltransferase-from%C3%A2-paenibacillus-sp-598k-which-produces-%C3%AE-1-6-glucosyl-%C3%AE-glucosaccharides-from-starch
#11
Zui Fujimoto, Nobuhiro Suzuki, Naomi Kishine, Hitomi Ichinose, Mitsuru Momma, Atsuo Kimura, Kazumi Funane
Paenibacillus sp. 598K α-1,6-glucosyltransferase (Ps6TG31A), a member of glycoside hydrolase family 31, catalyzes exo-α-glucohydrolysis and transglucosylation and produces α-1,6-glucosyl-α-glucosaccharides from α-glucan via its disproportionation activity. The crystal structure of Ps6TG31A was determined by an anomalous dispersion method using a terbium derivative. The monomeric Ps6TG31A consisted of one catalytic (β/α)8-barrel domain and six small domains, one on the N-terminal, and five on the C-terminal side...
July 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28695848/crystal-structure-of-a-family-6-cellobiohydrolase-from-the-basidiomycete-phanerochaete-chrysosporium
#12
Mikako Tachioka, Akihiko Nakamura, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima
Cellobiohydrolases belonging to glycoside hydrolase family 6 (CBH II, Cel6A) play key roles in the hydrolysis of crystalline cellulose. CBH II from the white-rot fungus Phanerochaete chrysosporium (PcCel6A) consists of a catalytic domain (CD) and a carbohydrate-binding module connected by a linker peptide, like other known fungal cellobiohydrolases. In the present study, the CD of PcCel6A was crystallized without ligands, and p-nitrophenyl β-D-cellotrioside (pNPG3) was soaked into the crystals. The determined structures of the ligand-free and pNPG3-soaked crystals revealed that binding of cellobiose at substrate subsites +1 and +2 induces a conformational change of the N-terminal and C-terminal loops, switching the tunnel-shaped active site from the open to the closed form...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28688044/effects-of-mutation-of-asn694-in-aspergillus-niger-%C3%AE-glucosidase-on-hydrolysis-and-transglucosylation
#13
Min Ma, Masayuki Okuyama, Megumi Sato, Takayoshi Tagami, Patcharapa Klahan, Yuya Kumagai, Haruhide Mori, Atsuo Kimura
Aspergillus niger α-glucosidase (ANG), a member of glycoside hydrolase family 31, catalyzes hydrolysis of α-glucosidic linkages at the non-reducing end. In the presence of high concentrations of maltose, the enzyme also catalyzes the formation of α-(1→6)-glucosyl products by transglucosylation and it is used for production of the industrially useful panose and isomaltooligosaccharides. The initial transglucosylation by wild-type ANG in the presence of 100 mM maltose [Glc(α1-4)Glc] yields both α-(1→6)- and α-(1→4)-glucosidic linkages, the latter constituting ~25% of the total transfer reaction product...
July 7, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28683920/computational-glycobiology-mechanistic-studies-of-carbohydrate-active-enzymes-and-implication-for-inhibitor-design
#14
Andrew P Montgomery, Kela Xiao, Xingyong Wang, Danielle Skropeta, Haibo Yu
Carbohydrate-active enzymes (CAZymes) are families of essential and structurally related enzymes, which catalyze the creation, modification, and degradation of glycosidic bonds in carbohydrates to maintain essentially all kingdoms of life. CAZymes play a key role in many biological processes underpinning human health and diseases (e.g., cancer, diabetes, Alzheimer's diseases, AIDS) and have thus emerged as important drug targets in the fight against pathogenesis. The realization of the full potential of CAZymes remains a significant challenge, relying on a deeper understanding of the molecular mechanisms of catalysis...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28674832/heterologous-expression-and-characterization-of-an-acidic-gh11-family-xylanase-from-hypocrea-orientalis
#15
Hailong Li, Hongli Wu, Fengjiao Jiang, Jinlian Wu, Yong Xue, Lihui Gan, Jian Liu, Minnan Long
A gene encoding glycoside hydrolase family 11 xylanase (HoXyn11B) from Hypocrea orientalis EU7-22 was expressed in Pichia pastoris with a high activity (413 IU/ml). HoXyn11B was partly N-glycosylated and appeared two protein bands (19-29 kDa) on SDS-PAGE. The recombinant enzyme exhibited optimal activity at pH 4.5 and 55 °C, and retained more than 90% of the original activity after incubation at 50 °C for 60 min. The determined apparent K m and V max values using beechwood xylan were 10.43 mg/ml and 3246...
July 3, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28669588/gh62-arabinofuranosidases-structure-function-and-applications
#16
REVIEW
Casper Wilkens, Susan Andersen, Claire Dumon, Jean-Guy Berrin, Birte Svensson
Motivated by industrial demands and ongoing scientific discoveries continuous efforts are made to identify and create improved biocatalysts dedicated to plant biomass conversion. α-1,2 and α-1,3 arabinofuranosyl specific α-l-arabinofuranosidases (EC 3.2.1.55) are debranching enzymes catalyzing hydrolytic release of α-l-arabinofuranosyl residues, which decorate xylan or arabinan backbones in lignocellulosic and pectin constituents of plant cell walls. The CAZy database classifies α-l-arabinofuranosidases in Glycoside Hydrolase (GH) families GH2, GH3, GH43, GH51, GH54 and GH62...
June 29, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28667610/measure-of-peptidoglycan-hydrolase-activity
#17
Yoann G Santin, Eric Cascales
Most gene clusters encoding multiprotein complexes of the bacterial cell envelope, such as conjugation and secretion systems, Type IV pili, and flagella, bear a gene encoding an enzyme with peptidoglycan hydrolase activity. These enzymes are usually glycoside hydrolases that cleave the glycan chains of the peptidoglycan. Their activities are spatially controlled to avoid cell lysis and to create localized rearrangement of the cell wall. This is assured by interaction with the structural subunits of the apparatus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28666924/role-of-carbon-source-in-the-shift-from-oxidative-to-hydrolytic-wood-decomposition-by-postia-placenta
#18
Jiwei Zhang, Jonathan S Schilling
Brown rot fungi initiate wood decay using oxidative pretreatments to improve access for cellulolytic enzymes. These pretreatments are incompatible with enzymes, and we recently showed that Postia placenta overcomes this issue by delaying glycoside hydrolase (GH) gene upregulation briefly (<48h) until expression of oxidoreductases (ORs) is repressed. This implies an inducible cellulase system rather than a constitutive system, as often reported, and it remains unclear what cues this transition. To address this, we grew P...
June 27, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28663545/towards-an-understanding-of-enhanced-biomass-digestibility-by-in-planta-expression-of-a-family-5-glycoside-hydrolase
#19
Bryon S Donohoe, Hui Wei, Ashutosh Mittal, Todd Shollenberger, Vladimir V Lunin, Michael E Himmel, Roman Brunecky
In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Our results suggest that cellulose β-1-4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development...
June 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28660507/raw-sugarcane-bagasse-as-carbon-source-for-xylanase-production-by-paenibacillus-species-a-potential-degrader-of-agricultural-wastes
#20
Enzo Di Marco, Pablo M Soraire, Cintia M Romero, Liliana B Villegas, María Alejandra Martínez
Paenibacillus species isolated from a variety of natural sources have shown to be important glycoside hydrolases producers. These enzymes play a key role in bio-refining applications, as they are central biocatalysts for the processing of different types of polymers from vegetal biomass. Xylanase production by three native isolates belonging to the genus Paenibacillus was approached by utilizing mineral-based medium and agricultural by-products as a convenient source to produce biocatalysts suitable for their degradation...
June 28, 2017: Environmental Science and Pollution Research International
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