Degradation pathway of plant complex-type N-glycans: identification and characterization of a key α1,3-fucosidase from glycoside hydrolase family 29

2018 ◽  
Vol 475 (1) ◽  
pp. 305-317 ◽  
Author(s):  
Shun Kato ◽  
Megumi Hayashi ◽  
Mai Kitagawa ◽  
Hiroyuki Kajiura ◽  
Megumi Maeda ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Degradation Pathway ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Complex Type ◽  
Gene Encoding ◽  
Mannose Residue ◽  
Growth Features ◽  
Identification And Characterization

Plant complex-type N-glycans are characterized by the presence of α1,3-linked fucose towards the proximal N-acetylglucosamine residue and β1,2-linked xylose towards the β-mannose residue. These glycans are ultimately degraded by the activity of several glycoside hydrolases. However, the degradation pathway of plant complex-type N-glycans has not been entirely elucidated because the gene encoding α1,3-fucosidase, a glycoside hydrolase acting on plant complex-type N-glycans, has not yet been identified, and its substrate specificity remains to be determined. In the present study, we found that AtFUC1 (an Arabidopsis GH29 α-fucosidase) is an α1,3-fucosidase acting on plant complex-type N-glycans. This fucosidase has been known to act on α1,4-fucoside linkage in the Lewis A epitope of plant complex-type N-glycans. We found that this glycoside hydrolase specifically acted on GlcNAcβ1–4(Fucα1–3)GlcNAc, a degradation product of plant complex-type N-glycans, by sequential actions of vacuolar α-mannosidase, β1,2-xylosidase, and endo-β-mannosidase. The AtFUC1-deficient mutant showed no distinct phenotypic plant growth features; however, it accumulated GlcNAcβ1–4(Fucα1–3)GlcNAc, a substrate of AtFUC1. These results showed that AtFUC1 is an α1,3-fucosidase acting on plant complex-type N-glycans and elucidated the degradation pathway of plant complex-type N-glycans.

scholarly journals Molecular Cloning and Characterization of Bifidobacterium bifidum 1,2-α-l-Fucosidase (AfcA), a Novel Inverting Glycosidase (Glycoside Hydrolase Family 95)

2004 ◽  
Vol 186 (15) ◽  
pp. 4885-4893 ◽  
Author(s):  
Takane Katayama ◽  
Akiko Sakuma ◽  
Takatoshi Kimura ◽  
Yutaka Makimura ◽  
Jun Hiratake ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genomic Library ◽  
Bifidobacterium Bifidum ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Sugar Chain ◽  
Hydrolysis Of

ABSTRACT A genomic library of Bifidobacterium bifidum constructed in Escherichia coli was screened for the ability to hydrolyze the α-(1→2) linkage of 2′-fucosyllactose, and a gene encoding 1,2-α-l-fucosidase (AfcA) was isolated. The afcA gene was found to comprise 1,959 amino acid residues with a predicted molecular mass of 205 kDa and containing a signal peptide and a membrane anchor at the N and C termini, respectively. A domain responsible for fucosidase activity (the Fuc domain; amino acid residues 577 to 1474) was localized by deletion analysis and then purified as a hexahistidine-tagged protein. The recombinant Fuc domain specifically hydrolyzed the terminal α-(1→2)-fucosidic linkages of various oligosaccharides and a sugar chain of a glycoprotein. The stereochemical course of the hydrolysis of 2′-fucosyllactose was determined to be inversion by using 1H nuclear magnetic resonance. The primary structure of the Fuc domain exhibited no similarity to those of any glycoside hydrolases (GHs) but showed high similarity to those of several hypothetical proteins in a database. Thus, it was revealed that the AfcA protein constitutes a novel inverting GH family (GH family 95).

Purification, Identification, and Characterization of a Glycoside Hydrolase Family 11-Xylanase with High Activity from Aspergillus niger VTCC 017

2021 ◽  
Author(s):  
Thi Mai Anh Dao ◽  
Nguyen Tien Cuong ◽  
Thi Trung Nguyen ◽  
Nguyen Phuong Dai Nguyen ◽  
Do Thi Tuyen
Keyword(s):  
Aspergillus Niger ◽  
High Activity ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Identification And Characterization ◽  
Hydrolase Family

scholarly journals Cloning of the Novel Gene Encoding β-Agarase C from a Marine Bacterium, Vibrio sp. Strain PO-303, and Characterization of the Gene Product

2006 ◽  
Vol 72 (9) ◽  
pp. 6399-6401 ◽  
Author(s):  
Jinhua Dong ◽  
Shinnosuke Hashikawa ◽  
Takafumi Konishi ◽  
Yutaka Tamaru ◽  
Toshiyoshi Araki
Keyword(s):  
Amino Acid ◽  
Gene Product ◽  
Glycoside Hydrolase ◽  
Marine Bacterium ◽  
Glycoside Hydrolase Family ◽  
The Novel ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Hydrolase Family

ABSTRACT The β-agarase C gene (agaC) of a marine bacterium, Vibrio sp. strain PO-303, consisted of 1,437 bp encoding 478 amino acid residues. β-Agarase C was identified as the first β-agarase that cannot hydrolyze neoagarooctaose and smaller neoagarooligosaccharides and was assigned to a novel glycoside hydrolase family.

scholarly journals Identification and Characterization of a Mucilaginibacter sp. Strain QM49 β-Glucosidase and Its Use in the Production of the Pharmaceutically Active Minor Ginsenosides (S)-Rh1and (S)-Rg2

2013 ◽  
Vol 79 (19) ◽  
pp. 5788-5798 ◽  
Author(s):  
Chang-Hao Cui ◽  
Qing-Mei Liu ◽  
Jin-Kwang Kim ◽  
Bong-Hyun Sung ◽  
Song-Gun Kim ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Vector System ◽  
Glycoside Hydrolase Family ◽  
Scale Production ◽  
Amino Acid Residues ◽  
Content Type ◽  
Silica Column ◽  
Identification And Characterization ◽  
Hydrolase Family

ABSTRACTHere, we isolated and characterized a new ginsenoside-transforming β-glucosidase (BglQM) fromMucilaginibactersp. strain QM49 that shows biotransformation activity for various major ginsenosides. The gene responsible for this activity,bglQM, consists of 2,346 bp and is predicted to encode 781 amino acid residues. This enzyme has a molecular mass of 85.6 kDa. Sequence analysis of BglQM revealed that it could be classified into glycoside hydrolase family 3. The enzyme was overexpressed inEscherichia coliBL21(DE3) using a maltose binding protein (MBP)-fused pMAL-c2x vector system containing the tobacco etch virus (TEV) proteolytic cleavage site. Overexpressed recombinant BglQM could efficiently transform the protopanaxatriol-type ginsenosides Re and Rg1into (S)-Rg2and (S)-Rh1, respectively, by hydrolyzing one glucose moiety attached to the C-20 position at pH 8.0 and 30°C. TheKmvalues forp-nitrophenyl-β-d-glucopyranoside, Re, and Rg1were 37.0 ± 0.4 μM and 3.22 ± 0.15 and 1.48 ± 0.09 mM, respectively, and theVmaxvalues were 33.4 ± 0.6 μmol min−1mg−1of protein and 19.2 ± 0.2 and 28.8 ± 0.27 nmol min−1mg−1of protein, respectively. A crude protopanaxatriol-type ginsenoside mixture (PPTGM) was treated with BglQM, followed by silica column purification, to produce (S)-Rh1and (S)-Rg2at chromatographic purities of 98% ± 0.5% and 97% ± 1.2%, respectively. This is the first report of gram-scale production of (S)-Rh1and (S)-Rg2from PPTGM using a novel ginsenoside-transforming β-glucosidase of glycoside hydrolase family 3.

scholarly journals A novel β-xylosidase structure fromGeobacillus thermoglucosidasius: the first crystal structure of a glycoside hydrolase family GH52 enzyme reveals unpredicted similarity to other glycoside hydrolase folds

2014 ◽  
Vol 70 (5) ◽  
pp. 1366-1374 ◽  
Author(s):  
Giannina Espina ◽  
Kirstin Eley ◽  
Guillaume Pompidor ◽  
Thomas R. Schneider ◽  
Susan J. Crennell ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Glycoside Hydrolase ◽  
Thermophilic Bacterium ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Gene Encoding ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
The Family ◽  
Hydrolase Family

Geobacillus thermoglucosidasiusis a thermophilic bacterium that is able to ferment both C6 and C5 sugars to produce ethanol. During growth on hemicellulose biomass, an intracellular β-xylosidase catalyses the hydrolysis of xylo-oligosaccharides to the monosaccharide xylose, which can then enter the pathways of central metabolism. The gene encoding aG. thermoglucosidasiusβ-xylosidase belonging to CAZy glycoside hydrolase family GH52 has been cloned and expressed inEscherichia coli. The recombinant enzyme has been characterized and a high-resolution (1.7 Å) crystal structure has been determined, resulting in the first reported structure of a GH52 family member. A lower resolution (2.6 Å) structure of the enzyme–substrate complex shows the positioning of the xylobiose substrate to be consistent with the proposed retaining mechanism of the family; additionally, the deep cleft of the active-site pocket, plus the proximity of the neighbouring subunit, afford an explanation for the lack of catalytic activity towards the polymer xylan. Whilst the fold of theG. thermoglucosidasiusβ-xylosidase is completely different from xylosidases in other CAZy families, the enzyme surprisingly shares structural similarities with other glycoside hydrolases, despite having no more than 13% sequence identity.

Identification and Characterization of a Glycoside Hydrolase Family 9 Member from the Digestive Gland of the Snail Achatina fulica

2021 ◽  
Author(s):  
Youssef Bacila Sade ◽  
Camila Silva Gonçalves ◽  
Sandra Mara Naressi Scapin ◽  
Guilherme Luiz Pinheiro ◽  
Roberto Becht Flatschart ◽  
...  
Keyword(s):  
Digestive Gland ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Achatina Fulica ◽  
Glycoside Hydrolase Family 9 ◽  
Identification And Characterization ◽  
Hydrolase Family

scholarly journals Identification and Characterization of a Novel Terrabacter ginsenosidimutans sp. nov. β-Glucosidase That Transforms Ginsenoside Rb1 into the Rare Gypenosides XVII and LXXV

2010 ◽  
Vol 76 (17) ◽  
pp. 5827-5836 ◽  
Author(s):  
Dong-Shan An ◽  
Chang-Hao Cui ◽  
Hyung-Gwan Lee ◽  
Liang Wang ◽  
Sun Chang Kim ◽  
...  
Keyword(s):  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Ginsenoside Rb1 ◽  
E Coli ◽  
Significant Homology ◽  
Pharmacologically Active ◽  
Hydrolysis Of ◽  
Identification And Characterization ◽  
Hydrolase Family

ABSTRACT A new β-glucosidase from a novel strain of Terrabacter ginsenosidimutans (Gsoil 3082T) obtained from the soil of a ginseng farm was characterized, and the gene, bgpA (1,947 bp), was cloned in Escherichia coli. The enzyme catalyzed the conversion of ginsenoside Rb1 {3-O-[β-d-glucopyranosyl-(1-2)-β-d-glucopyranosyl]-20-O-[β-d-glucopyranosyl-(1-6)-β-d-glucopyranosyl]-20(S)-protopanaxadiol} to the more pharmacologically active rare ginsenosides gypenoside XVII {3-O-β-d-glucopyranosyl-20-O-[β-d-glucopyranosyl-(1-6)-β-d-glucopyranosyl]-20(S)-protopanaxadiol}, gypenoside LXXV {20-O-[β-d-glucopyranosyl-(1-6)-β-d-glucopyranosyl]-20(S)-protopanaxadiol}, and C-K [20-O-(β-d-glucopyranosyl)-20(S)-protopanaxadiol]. A BLAST search of the bgpA sequence revealed significant homology to family 3 glycoside hydrolases. Expressed in E. coli, β-glucosidase had apparent Km values of 4.2 ± 0.8 and 0.14 ± 0.05 mM and V max values of 100.6 ± 17.1 and 329 ± 31 μmol·min−1·mg of protein−1 against p-nitrophenyl-β-d-glucopyranoside and Rb1, respectively. The enzyme catalyzed the hydrolysis of the two glucose moieties attached to the C-3 position of ginsenoside Rb1, and the outer glucose attached to the C-20 position at pH 7.0 and 37°C. These cleavages occurred in a defined order, with the outer glucose of C-3 cleaved first, followed by the inner glucose of C-3, and finally the outer glucose of C-20. These results indicated that BgpA selectively and sequentially converts ginsenoside Rb1 to the rare ginsenosides gypenoside XVII, gypenoside LXXV, and then C-K. Herein is the first report of the cloning and characterization of a novel ginsenoside-transforming β-glucosidase of the glycoside hydrolase family 3.

Identification and characterization of the glycoside hydrolase family 18 genes from the entomopathogenic fungus Isaria cicadae genome

2020 ◽  
Vol 66 (4) ◽  
pp. 274-287
Author(s):  
Yao Peng ◽  
Lifang Wang ◽  
Yan Gao ◽  
Liang Ye ◽  
Huihui Xu ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Glycoside Hydrolase Family ◽  
Transcript Levels ◽  
Chitinase Genes ◽  
Fungal Chitinases ◽  
Identification And Characterization

Fungal chitinases play essential roles in chitin degradation, cell wall remodeling, chitin recycling, nutrition acquisition, autolysis, and virulence. In this study, 18 genes of the glycoside hydrolase 18 (GH18) family were identified in the Isaria cicadae genome. Seventeen of the genes belonged to chitinases and one was an endo-β-N-acetylglucosaminidase (ENGase). According to phylogenetic analysis, the 17 chitinases were designated as subgroups A (7 chitinases), B (7), and C (3). The exon–intron organizations of these genes were analyzed. The conserved regions DxxDxDxE and S/AxGG and the domains CBM1, CBM18, and CBM50 were detected in I. cicadae chitinases and ENGase. The results of analysis of expression patterns showed that genes ICchiA1, ICchiA6, ICchiB1, and ICchiB4 had high transcript levels in the different growth conditions or developmental stages. Subgroup A chitinase genes had higher transcript levels than the genes of all other chitinases. Subgroup B chitinase genes (except ICchiB7) presented higher transcript levels in chitin medium compared with other conditions. ICchiC2 and ICchiC3 were mainly transcribed in autolysis medium and in blastospores, respectively. Moreover, ICchiB1 presented higher transcript levels than genes of other chitinases. This work provides an overview of the GH18 chitinases and ENGase in I. cicadae and provides a context for the chitinolytic potential, functions, and biological controls of these enzymes of entomopathogenic fungi.

scholarly journals The thermostable 4,6-α-glucanotransferase of Bacillus coagulans DSM 1 synthesizes isomaltooligosaccharides

Amylase ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 13-22
Author(s):  
Gang Xiang ◽  
Piet L. Buwalda ◽  
Marc J.E.C van der Maarel ◽  
Hans Leemhuis
Keyword(s):  
Bacillus Coagulans ◽  
Glycoside Hydrolase Family ◽  
Rat Intestine ◽  
Glycaemic Response ◽  
Food Ingredient ◽  
Starch Conversion ◽  
Identification And Characterization ◽  
Hydrolase Family

Abstract The 4,6-α-glucanotransferases of the glycoside hydrolase family 70 can convert starch into isomaltooligosaccharides (IMOs). However, no thermostable 4,6-α-glucanotransferases have been reported to date, limiting their applicability in the starch conversion industry. Here we report the identification and characterization of a thermostable 4,6-α-glucanotransferase from Bacillus coagulans DSM 1. The gene was cloned and the recombinant protein, called BcGtfC, was produced in Escherichia coli. BcGtfC is stable up to 66 °C in the presence of substrate. It converts debranched starch into an IMO product with a high percentage of α-1,6-glycosidic linkages and a relatively high molecular weight compared to commercially available IMOs. Importantly, the product is only partly and very slowly digested by rat intestine powder, suggesting that the IMO will provide a low glycaemic response in vivo when applied as food ingredient. Thus, BcGtfC is a thermostable 4,6-α-glucanotransferase suitable for the industrial production of slowly digestible IMOs from starch.

scholarly journals Characterization of Fusarium oxysporum β-1,6-Galactanase, an Enzyme That Hydrolyzes Larch Wood Arabinogalactan

2007 ◽  
Vol 73 (9) ◽  
pp. 3109-3112 ◽  
Author(s):  
Tatsuji Sakamoto ◽  
Yuya Taniguchi ◽  
Shiho Suzuki ◽  
Hideshi Ihara ◽  
Haruhiko Kawasaki
Keyword(s):  
Fusarium Oxysporum ◽  
Glycoside Hydrolase ◽  
Recombinant Enzyme ◽  
Glycoside Hydrolase Family ◽  
Type Ii ◽  
High Similarity ◽  
Degrading Enzyme ◽  
Larch Wood ◽  
Hydrolase Family

ABSTRACT A type II arabinogalactan-degrading enzyme (FoGal1) was purified from Fusarium oxysporum 12S, and the corresponding cDNA was isolated. FoGal1 had high similarity to enzymes of glycoside hydrolase family 5. Treatment of larch wood arabinogalactan with the recombinant enzyme indicated that FoGal1 is a β-1,6-galactanase that preferentially debranches β-1,6-galactobiose from the substrate.

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