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Glycoside hydrolase

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https://www.readbyqxmd.com/read/27907169/crystal-structure-of-chitinase-chiw-from-paenibacillus-sp-str-fpu-7-reveals-a-novel-type-of-bacterial-cell-surface-expressed-multi-modular-enzyme-machinery
#1
Takafumi Itoh, Takao Hibi, Fumiko Suzuki, Ikumi Sugimoto, Akihiro Fujiwara, Koji Inaka, Hiroaki Tanaka, Kazunori Ohta, Yutaka Fujii, Akira Taketo, Hisashi Kimoto
The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18)...
2016: PloS One
https://www.readbyqxmd.com/read/27905050/transcriptional-analysis-of-genes-encoding-%C3%AE-glucosidase-of-schizophyllum-commune-kuc9397-under-optimal-conditions
#2
Young Min Lee, Hanbyul Lee, Young Mok Heo, Hwanhwi Lee, Joo-Hyun Hong, Jae-Jin Kim
The present study was conducted to determine the gene responsible for beta-glucosidase (BGL) production and to generate a full-length complementary DNA (cDNA) of one of the putative BGL genes, which showed a significant expression level when Schizophyllum commune KUC9397 was grown in optimized medium. The relative expression levels of seven genes encoding BGL of S. commune KUC9397 were determined with real-time quantitative reverse transcription PCR in cellulose-containing optimized medium (OM) compared to glucose-containing basal medium (BM)...
November 30, 2016: Folia Microbiologica
https://www.readbyqxmd.com/read/27902421/domain-evolution-in-enzymes-of-the-neopullulanase-subfamily
#3
Andrea Kuchtova, Stefan Janecek
Among the glycoside hydrolases (GHs) classified within the CAZy database, the α-amylase family GH13 containing ~30 different enzyme specificities and more than 37,000 sequences, represents one of the largest GH families. Earlier, based on a characteristic sequence motif in their 5th conserved sequence region (CSR), the two closely related subfamilies, the so-called oligo-1,6-glucosidase and neopullulanase subfamilies were described. Currently the two subfamilies cover several CAZy-defined GH13 subfamilies because the α-amylase family GH13 has officially been divided into 41 subfamilies...
November 1, 2016: Microbiology
https://www.readbyqxmd.com/read/27895636/genomic-and-transcriptomic-evidence-for-carbohydrate-consumption-among-microorganisms-in-a-cold-seep-brine-pool
#4
Weipeng Zhang, Wei Ding, Bo Yang, Renmao Tian, Shuo Gu, Haiwei Luo, Pei-Yuan Qian
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27890857/structural-insights-into-a-family-39-glycoside-hydrolase-from-the-gut-symbiont-bacteroides-cellulosilyticus-wh2
#5
Ahmad Ali-Ahmad, Marie-Line Garron, Véronique Zamboni, Nicolas Lenfant, Didier Nurizzo, Bernard Henrissat, Jean-Guy Berrin, Yves Bourne, Florence Vincent
Bacteria from the human gut are equipped with an arsenal of carbohydrate-active enzymes that degrade dietary and host-derived glycans. In this study, we present the 2.5Å resolution crystal structure of a member (GH39wh2) from the human gut bacteria Bacteroides cellulosilyticus WH2 representative of a new subgroup within family GH39. Together with 6 other GHs, GH39wh2 belongs to a polysaccharide utilization locus (PUL) that could be involved in detecting, binding and hydrolysing a specific carbohydrate species from the intestinal tract...
November 24, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27888008/extracellular-expression-of-alkali-tolerant-xylanase-from-bacillus-subtilis-lucky9-in-e-coli-and-application-for-xylooligosaccharides-production-from-agro-industrial-waste
#6
Siyuan Chang, Yalan Guo, Bin Wu, Bingfang He
An alkali tolerant xylanase gene from Bacillus subtilis Lucky9 was cloned and extracellular expressed in E. coli BL21. Xylanase amino acid sequence showed 99% identity with xylanase sequence from Bacillus subtilis 168, and was belonged to glycoside hydrolase family 11. The recombinant E. coli (pET-pelB-xynLC9) containing pelB signal peptide produced extracellular xylanase of 436.5U/mL for 8h, which was used arabinose as extra carbon source and inducer for enhancing extracellular production. The extracellular xylanase was determined by SDS-PAGE with a relative molecular mass of 21kDa...
November 22, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27884087/a-protease-peptidase-from-culture-medium-of-flammulina-velutipes-that-acts-on-arabinogalactan-protein
#7
Yoshihisa Yoshimi, Yumi Sugawara, Chiaki Hori, Kiyohiko Igarashi, Satoshi Kaneko, Yoichi Tsumuraya, Toshihisa Kotake
Arabinogalactan-proteins (AGPs) are highly diverse plant proteoglycans found on the plant cell surface. AGPs have large arabinogalactan (AG) moieties attached to a core-protein rich in hydroxyproline (Hyp). The AG undergoes hydrolysis by various glycoside hydrolases, most of which have been identified, whereas the core-proteins is presumably degraded by unknown proteases/peptidases secreted from fungi and bacteria in nature. Although several enzymes hydrolyzing other Hyp-rich proteins are known, the enzymes acting on the core-proteins of AGPs remain to be identified...
November 25, 2016: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27881540/genome-sequence-of-salegentibacter-salarius-kctc-12974-isolated-from-a-marine-solar-saltern-of-the-yellow-sea-in-south-korea
#8
Yongle Xu, Jihua Liu, Qiang Zheng, Yanting Liu, Nianzhi Jiao
Salegentibacter salarius KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea in South Korea. Here, we report the draft genome sequence of Salegentibacter salarius KCTC 12974. Various glycoside hydrolase genes in even numbers in the genome reflect the ecological adaption of KCTC 12974 to its habitat.
November 23, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27872187/galactomannan-catabolism-conferred-by-a-polysaccharide-utilisation-locus-of-bacteroides-ovatus-enzyme-synergy-and-crystal-structure-of-a-%C3%AE-mannanase
#9
Viktoria Bågenholm, Sumitha K Reddy, Hanene Bouraoui, Johan Morrill, Evelina Kulcinskaja, Constance M Bahr, Oskar Aurelius, Theresa Rogers, Yao Xiao, Derek T Logan, Eric C Martens, Nicole M Koropatkin, Henrik Stålbrand
A recently identified polysaccharide utilisation locus (PUL) from Bacteroides ovatus ATCC8483 is transcriptionally upregulated during growth on galacto- and glucomannans. It encodes two putative glycoside hydrolase family 26 (GH26) β-mannanases, BoMan26A and BoMan26B, and a GH36 α-galactosidase, BoGal36A. The PUL also includes two glycan binding proteins, confirmed by β-mannan affinity electrophoresis. When this PUL was deleted, B. ovatus was no longer able to grow on locust bean galactomannan. BoMan26A primarily formed mannobiose from mannan polysaccharides...
November 21, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27872074/glycoside-hydrolases-degrade-polymicrobial-bacterial-biofilms-in-wounds
#10
Derek Fleming, Laura Chahin, Kendra Rumbaugh
The persistent nature of chronic wounds leaves them highly susceptible to invasion by a variety of pathogens that have the ability to construct an Extracellular Polymeric Substance (EPS). This EPS makes the bacterial population, or biofilm, up to one-thousand-fold more antibiotic tolerant than planktonic cells, and makes wound healing extremely difficult. Thus, compounds which have the ability to degrade biofilms, but not host tissue components, are highly sought-after for clinical applications. In this study, we examined the efficacy of two glycoside hydrolases, alpha-amylase and cellulase, which break down complex polysaccharides, to effectively disrupt Staphylococcus aureus and Pseudomonas aeruginosa mono-culture and co-culture biofilms...
November 21, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27871388/the-family-22-carbohydrate-binding-module-of-bifunctional-xylanase-%C3%AE-glucanase-xyn10e-from-paenibacillus-curdlanolyticus-b-6-has-an-important-role-in-lignocellulose-degradation
#11
Junjarus Sermsathanaswadi, Sirilak Baramee, Chakrit Tachaapaikoon, Patthra Pason, Khanok Ratanakhanokchai, Akihiko Kosugi
A newly isolated endo-β-1,4-xylanase (Xyn10E) from Paenibacillus curdlanolyticus B-6 has a modular structure consisting of a family 22 carbohydrate-binding module (CBM), a glycoside hydrolase (GH) family 10 catalytic domain, two fibronectin type III (Fn3) domains, and a family 3 CBM at the C-terminus. Intact Xyn10E (rXyn10E), CBM22-deleted Xyn10E (X-CBM3), CBM3-deleted Xyn10E (X-CBM22), and GH10 catalytic domain only (X-GH10) were expressed in Escherichia coli. rXyn10E showed bifunctional degradation activity toward xylan and β-glucan and also degraded microcrystalline cellulose...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27871383/allosteric-properties-of-geobacillus-maltogenic-amylase
#12
Parvaneh Rahmati, Reza H Sajedi, Parichehr Zamani, Hossein Rahmani, Khosro Khajeh
Maltogenic amylases (MAases, EC 3.2.1.133) have been gotten much attention due to their various applications in industry and commercial processes. MAases belong to subfamily 20 of glycoside hydrolase family 13 (NPase or CDases subfamily) and they have important differences with other members of the family. This enzyme consists of two subunits which form two active sites in the dimer form by binding of the central domain of each subunit to the N domain of the next one (domain-swapping dimeric structure). Allosterism is a possible way of regulating enzymatic activity and no evidence has been found regarding to the cooperativity and correlation between MAases subunits, therefore in this study the allosteric behavior of MAases from a native strain (Geobacillus sp...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27871378/deciphering-the-factors-defining-the-ph-dependence-of-a-commercial-glycoside-hydrolase-family-8-enzyme
#13
Mário Barroca, Gustavo Santos, Björn Johansson, Florian Gillotin, Georges Feller, Tony Collins
A prerequisite to the use of any enzyme in any industrial process is an understanding of its activity and stability under process conditions. Glycoside hydrolase family 8 enzymes include many important biotechnological biocatalysts yet little is known of the performance of these with respect to pH. A better understanding of this parameter and its relationship to structure and function in these enzymes will allow for an improved use of these in industry as well as an enhanced ability in their engineering and optimisation for a particular application...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27866295/characterization-of-a-neutral-recombinant-xylanase-from-thermoactinospora-rubra-yim-77501-t
#14
Yi-Rui Yin, Qing-Wen Hu, Wen-Dong Xian, Feng Zhang, En-Min Zhou, Hong Ming, Min Xiao, Xiao-Yang Zhi, Wen-Jun Li
A xylanase gene (TrXyn10) from Thermoactinospora rubra YIM 77501(T) was cloned and expressed in Escherichia coli. The amino acid sequence displayed 78% homology with Microbispora mesophila xylanase (WP_062413927.1). The recombinant xylanase (TrXyn10), with MW 46.1 kDa, could hydrolyse beechwood, birchwood and oatspelt xylan. Based on the sequence, enzymatic properties and tertiary structure of the protein, TrXyn10 belongs to glycoside hydrolase family 10 (GH10). The optimal pH and temperature for the recombinant enzyme were determined to be 7...
November 19, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27862076/characterization-of-endoglucanase-from-paenibacillus-sp-m33-a-novel-isolate-from-a-freshwater-swamp-forest
#15
Pimpikar Kanchanadumkerng, Makiko Sakka, Kazuo Sakka, Chanpen Wiwat
The newly isolated Paenibacillus sp. M33 from freshwater swamp forest soil in Thailand demonstrated its potential as a cellulose degrader. One of its endoglucanase genes from Paenibacillus sp., celP, was cloned to study the molecular characteristics of its gene product. The celP gene was recognized firstly by degenerate primer designed from Paenibacillus endoglucanase gene, and subsequently identified flanking region by inverse PCR technique. The celP gene consists of an open reading frame of 1707 bp encoding for 569 amino acids including 33-amino acids signal sequence...
November 8, 2016: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/27859885/crystallographic-insight-into-the-evolutionary-origins-of-xyloglucan-endo-transglycosylases-and-endo-hydrolases
#16
Nicholas McGregor, Victor Yin, Ching-Chieh Tung, Filip Van Petegem, Harry Brumer
The xyloglucan endo-transglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodelling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endo-glycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endo-glucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG)...
November 15, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27856750/substrate-recognition-and-catalysis-by-gh47-%C3%AE-mannosidases-involved-in-asn-linked-glycan-maturation-in-the-mammalian-secretory-pathway
#17
Yong Xiang, Khanita Karaveg, Kelley W Moremen
Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation...
November 17, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27856189/n-linked-glycans-are-an-important-component-of-the-processive-machinery-of-cellobiohydrolases
#18
Alexander V Gusakov, Anna S Dotsenko, Aleksandra M Rozhkova, Arkady P Sinitsyn
Cellobiohydrolases (CBHs), belonging to glycoside hydrolase families 6 and 7 (GH6 and GH7), are the major components of cellulase systems of filamentous fungi involved in biodegradation of cellulose in nature. Previous studies demonstrated that N-linked glycans in the catalytic domains of GH7 CBHs significantly affect the enzyme activity against cellulosic substrates. The influence of N-linked glycans on the activity and processivity of recombinant GH6 CBH II from Penicillium verruculosum (PvCel6A) was studied using site-directed mutagenesis of the respective Asn residues...
November 14, 2016: Biochimie
https://www.readbyqxmd.com/read/27854040/expression-and-characterization-of-a-novel-antifungal-exo-%C3%AE-1-3-glucanase-from-chaetomium-cupreum
#19
Cheng Jiang, Jinzhu Song, Hua Cong, Junzheng Zhang, Qian Yang
A novel β-1,3-glucanase gene, designated Ccglu17A, was cloned from the biological control fungus Chaetomium cupreum Ame. Its 1626-bp open reading frame encoded 541 amino acids. The corresponding amino acid sequence showed highest identity (67 %) with a glycoside hydrolase family 17 β-1,3-glucanase from Chaetomium globosum. The recombinant protein Ccglu17A was successfully expressed in Pichia pastoris, and the enzyme was purified to homogeneity with 10.1-fold purification and 47.8 % recovery yield. The protein's molecular mass was approximately 65 kDa, and its maximum activity appeared at pH 5...
November 16, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27854035/biochemical-characterization-of-a-gh43-%C3%AE-xylosidase-from-bacteroides-ovatus
#20
Douglas B Jordan, J Rose Stoller, Charles C Lee, Victor J Chan, Kurt Wagschal
Divalent metal-activated glycoside hydrolase family 43 (GH43) β-xylosidases have been found to have high k cat/K m for xylooligosaccharides and may demonstrate high efficacy in industrial reactors digesting hemicellulose. By searching an amino acid database, we found a Bacteroides ovatus GH43 β-xylosidase termed BoXA that is 81% identical in overall amino acid sequence to a GH43, divalent metal-activated β-xylosidase with high k cat/K m, and also it has 19 of 20 residues in the active site conserved. However, unlike its metal-activated homolog, the B...
November 16, 2016: Applied Biochemistry and Biotechnology
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