scholarly journals Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family

2011 ◽  
Vol 77 (23) ◽  
pp. 8350-8354 ◽  
Author(s):  
Yuichi Sakamoto ◽  
Keiko Nakade ◽  
Naotake Konno
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Fruiting Body ◽  
Glycoside Hydrolase ◽  
Lentinula Edodes ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Product Analysis ◽  
Content Type ◽  
Hydrolase Family

ABSTRACTThe cell wall of the fruiting body of the mushroomLentinula edodesis degraded after harvesting by enzymes such as β-1,3-glucanase. In this study, a novel endo-type β-1,3-glucanase, GLU1, was purified fromL. edodesfruiting bodies after harvesting. The gene encoding it,glu1, was isolated by rapid amplification of cDNA ends (RACE)-PCR using primers designed from the N-terminal amino acid sequence of GLU1. The putative amino acid sequence of the mature protein contained 247 amino acid residues with a molecular mass of 26 kDa and a pI of 3.87, and recombinant GLU1 expressed inPichia pastorisexhibited β-1,3-glucanase activity. GLU1 catalyzed depolymerization of glucans composed of β-1,3-linked main chains, and reaction product analysis by thin-layer chromatography (TLC) clearly indicated that the enzyme had an endolytic mode. However, the amino acid sequence of GLU1 showed no significant similarity to known glycoside hydrolases. GLU1 has similarity to several hypothetical proteins in fungi, and GLU1 and highly similar proteins should be classified as a novel glycoside hydrolase family (GH128).

scholarly journals Purification, characterization and gene cloning of two α-l-arabinofuranosidases from Streptomyces chartreusis GS901

2000 ◽  
Vol 346 (1) ◽  
pp. 9-15 ◽  
Author(s):  
Noriki MATSUO ◽  
Satoshi KANEKO ◽  
Atsushi KUNO ◽  
Hideyuki KOBAYASHI ◽  
Isao KUSAKABE
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Glycoside Hydrolase ◽  
Catalytic Domain ◽  
Gum Arabic ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Amino Acid Sequencing ◽  
Molecular Masses ◽  
Hydrolase Family

α-L-Arabinofuranosidases I and II were purified from the culture filtrate of Streptomyces chartreusis GS901 and were found to have molecular masses of 80 and 37 kDa and pI values of 6.6 and 7.5 respectively. Both enzymes demonstrated slight reactivity towards arabinoxylan and arabinogalactan as substrates but did not hydrolyse gum arabic or arabinoxylo-oligosaccharides. α-L-Arabinofuranosidase I hydrolysed all of the α-linkage types that normally occur between two α-L-arabinofuranosyl residues, with the following decreasing order of reactivity being observed for the respective disaccharide linkages: α-(1 → 2) α-(1 → 3) α-(1 → 5). This enzyme cleaved the (1 → 3) linkages of the arabinosyl side-chains of methyl 3,5-di-O-α-L-arabinofuranosyl-α-L-arabinofuranoside in preference to the (1 → 5) linkages. α-L-Arabinofuranosidase I hydrolysed approx. 30% of the arabinan but hydrolysed hardly any linear arabinan. In contrast, α-L-Arabinofuranosidase II hydrolysed only (1 → 5)-arabinofuranobioside among the regioisomeric methyl arabinobiosides and did not hydrolyse the arabinotrioside. Linear 1 → 5-linked arabinan was a good substrate for this enzyme, but it hydrolysed hardly any of the arabinan. Synergism between the two enzymes was observed in the conversion of arabinan and debranched arabinan into arabinose. Complete amino acid sequencing of α-L-arabinofuranosidase I indicated that the enzyme consists of a central catalytic domain that belongs to family 51 of the glycoside hydrolases and additionally that unknown functional domains exist in the N-terminal and C-terminal regions. The amino acid sequence of α-L-arabinofuranosidase II indicated that this enzyme belongs to family 43 of the glycoside hydrolase family and, as this is the first report of an exo-1,5-α-L-arabinofuranosidase, it represents a novel type of enzyme.

scholarly journals A Novel Glycoside Hydrolase Family 5 β-1,3-1,6-Endoglucanase from Saccharophagus degradans 2-40Tand Its Transglycosylase Activity

2016 ◽  
Vol 82 (14) ◽  
pp. 4340-4349 ◽  
Author(s):  
Damao Wang ◽  
Do Hyoung Kim ◽  
Nari Seo ◽  
Eun Ju Yun ◽  
Hyun Joo An ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Marine Bacterium ◽  
Enzymatic Reaction ◽  
Glycoside Hydrolase Family ◽  
Reaction Products ◽  
Brown Macroalgae ◽  
Fungal Cell ◽  
Content Type ◽  
Saccharophagus Degradans ◽  
Hydrolase Family

ABSTRACTIn this study, we characterized Gly5M, originating from a marine bacterium, as a novel β-1,3-1,6-endoglucanase in glycoside hydrolase family 5 (GH5) in the Carbohydrate-Active enZyme database. Thegly5Mgene encodes Gly5M, a newly characterized enzyme from GH5 subfamily 47 (GH5_47) inSaccharophagus degradans2-40T. Thegly5Mgene was cloned and overexpressed inEscherichia coli. Through analysis of the enzymatic reaction products by thin-layer chromatography, high-performance liquid chromatography, and matrix-assisted laser desorption ionization–tandem time of flight mass spectrometry, Gly5M was identified as a novel β-1,3-endoglucanase (EC 3.2.1.39) and bacterial β-1,6-glucanase (EC 3.2.1.75) in GH5. The β-1,3-endoglucanase and β-1,6-endoglucanase activities were detected by using laminarin (a β-1,3-glucan with β-1,6-glycosidic linkages derived from brown macroalgae) and pustulan (a β-1,6-glucan derived from fungal cell walls) as the substrates, respectively. This enzyme also showed transglycosylase activity toward β-1,3-oligosaccharides when laminarioligosaccharides were used as the substrates. Since laminarin is the major form of glucan storage in brown macroalgae, Gly5M could be used to produce glucose and laminarioligosaccharides, using brown macroalgae, for industrial purposes.IMPORTANCEIn this study, we have discovered a novel β-1,3-1,6-endoglucanase with a unique transglycosylase activity, namely, Gly5M, from a marine bacterium,Saccharophagus degradans2-40T. Gly5M was identified as the newly found β-1,3-endoglucanase and bacterial β-1,6-glucanase in GH5. Gly5M is capable of cleaving glycosidic linkages of both β-1,3-glucans and β-1,6-glucans. Gly5M also possesses a transglycosylase activity toward β-1,3-oligosacchrides. Due to the broad specificity of Gly5M, this enzyme can be used to produce glucose or high-value β-1,3- and/or β-1,6-oligosaccharides.

scholarly journals Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Ao Li ◽  
Elisabeth Laville ◽  
Laurence Tarquis ◽  
Vincent Lombard ◽  
David Ropartz ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Sequence Similarity ◽  
Gut Bacteria ◽  
Glycoside Hydrolase Family ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Content Type ◽  
Multiple Sequence Alignments ◽  
Hydrolase Family

Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.

scholarly journals Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)

2018 ◽  
Vol 293 (47) ◽  
pp. 18138-18150 ◽  
Author(s):  
Léa Chuzel ◽  
Mehul B. Ganatra ◽  
Erdmann Rapp ◽  
Bernard Henrissat ◽  
Christopher H. Taron
Keyword(s):  
Glycoside Hydrolase ◽  
Catalytic Mechanism ◽  
Recombinant Expression ◽  
Biochemical Property ◽  
Environmental Dna ◽  
Thermal Spring ◽  
Sialic Acid Residue ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Hydrolase Family

Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.

scholarly journals Epoxyalkyl glycosides of d-xylose and xylo-oligosaccharides are active-site markers of xylanases from glycoside hydrolase family 11, not from family 10

2000 ◽  
Vol 347 (3) ◽  
pp. 865-873 ◽  
Author(s):  
Patricia NTARIMA ◽  
Wim NERINCKX ◽  
Klaus KLARSKOV ◽  
Bart DEVREESE ◽  
Mahalingeshwara K. BHAT ◽  
...  
Keyword(s):  
Active Site ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolases ◽  
Thermomyces Lanuginosus ◽  
Glycoside Hydrolase Family ◽  
Active Site Residues ◽  
X Ray ◽  
Order Of Magnitude ◽  
Site Markers ◽  
Hydrolase Family

A series of Ω-epoxyalkyl glycosides of D-xylopyranose, xylobiose and xylotriose were tested as potential active-site-directed inhibitors of xylanases from glycoside hydrolase families 10 and 11. Whereas family-10 enzymes (Thermoascus aurantiacus Xyn and Clostridium thermocellum Xyn Z) are resistant to electrophilic attack of active-site carboxyl residues, glycoside hydrolases of family 11 (Thermomyces lanuginosus Xyn and Trichoderma reesei Xyn II) are irreversibly inhibited. The apparent inactivation and association constants (ki, 1/Ki) are one order of magnitude higher for the xylobiose and xylotriose derivatives. The effects of the aglycone chain length can clearly be described. Xylobiose and n-alkyl β-D-xylopyranosides are competitive ligands and provide protection against inactivation. MS measurements showed 1:1 stoichiometries in most labelling experiments. Electrospray ionization MS/MS analysis revealed the nucleophile Glu86 as the modified residue in the T. lanuginosus xylanase when 2,3-epoxypropyl β-D-xylopyranoside was used, whereas the acid/base catalyst Glu178 was modified by the 3,4-epoxybutyl derivative. The active-site residues Glu86 and Glu177 in T. reesei Xyn II are similarly modified, confirming earlier X-ray crystallographic data [Havukainen, Törrönen, Laitinen and Rouvinen (1996) Biochemistry 35, 9617-9624]. The inability of the Ω-epoxyalkyl xylo(oligo)saccharide derivatives to inactivate family-10 enzymes is discussed in terms of different ligand-subsite interactions.

scholarly journals Characterization of Glycoside Hydrolase Families 13 and 31 Reveals Expansion and Diversification of α-Amylase Genes in the Phlebotomine Lutzomyia longipalpis and Modulation of Sandfly Glycosidase Activities by Leishmania Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Samara Graciane da Costa-Latgé ◽  
Paul Bates ◽  
Rod Dillon ◽  
Fernando Ariel Genta
Keyword(s):  
Glycoside Hydrolase ◽  
The Body ◽  
Glycoside Hydrolases ◽  
Food Sources ◽  
Leishmania Infection ◽  
Glycoside Hydrolase Family ◽  
Lutzomyia Longipalpis ◽  
Leishmania Mexicana ◽  
Hydrolase Family ◽  
Dipteran Species

Sugar-rich food sources are essential for sandflies to meet their energy demands, achieving more prolonged survival. The digestion of carbohydrates from food is mainly realized by glycoside hydrolases (GH). To identify genes coding for α-glycosidases and α-amylases belonging to Glycoside Hydrolase Family 13 (GH13) and Glycoside Hydrolase Family 31 (GH31) in Lutzomyia longipalpis, we performed an HMMER search against its genome using known sequences from other dipteran species. The sequences retrieved were classified based on BLASTP best hit, analysis of conserved regions by alignment with sequences of proteins with known structure, and phylogenetic analysis comparing with orthologous proteins from other dipteran species. Using RT-PCR analysis, we evaluated the expression of GH13 and GH31 genes, in the gut and rest of the body of females, in four different conditions: non-fed, sugar-fed, blood-fed, and Leishmania mexicana infected females. L. longipalpis has GH13/31 genes that code for enzymes involved in various aspects of sugar metabolism, as carbohydrate digestion, storage, and mobilization of glycogen reserves, proteins involved in transport, control of N-glycosylation quality, as well as others with a putative function in the regulation of myogenesis. These proteins are representatives of GH13 and GH31 families, and their roles seem to be conserved. Most of the enzymes seem to be active with conserved consense sequences, including the expected catalytic residues. α-amylases also demonstrated the presence of calcium and chloride binding sites. L. longipalpis genome shows an expansion in the α-amylase gene family, with two clusters. In contrast, a retraction in the number of α-glucosidases occurred. The expansion of α-amylases is probably related to the specialization of these proteins for different substrates or inhibitors, which might correlate with the higher diversity of plant foods available in the natural habitat of L. longipalpis. The expression of α-glucosidase genes is higher in blood-fed females, suggesting their role in blood digestion. Besides that, in blood-fed females infected with the parasite Leishmania mexicana, these genes were also modulated. Glycoside Hydrolases from families 13 and 31 are essential for the metabolism of L. longipalpis, and GH13 enzymes seem to be involved in the interaction between sandflies and Leishmania.

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 Engineering the Xylan Utilization System in Bacillus subtilis for Production of Acidic Xylooligosaccharides

2013 ◽  
Vol 80 (3) ◽  
pp. 917-927 ◽  
Author(s):  
Mun Su Rhee ◽  
Lusha Wei ◽  
Neha Sawhney ◽  
John D. Rice ◽  
Franz J. St. John ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Veterinary Medicine ◽  
Glycoside Hydrolase ◽  
Parent Strain ◽  
Structure And Function ◽  
Glycoside Hydrolase Family ◽  
Content Type ◽  
Potential Source ◽  
And Function ◽  
Hydrolase Family

ABSTRACTXylans are the predominant polysaccharides in hemicelluloses and an important potential source of biofuels and chemicals. The ability ofBacillus subtilissubsp.subtilisstrain 168 to utilize xylans has been ascribed to secreted glycoside hydrolase family 11 (GH11) and GH30 endoxylanases, encoded by thexynAandxynCgenes, respectively. Both of these enzymes have been defined with respect to structure and function. In this study, the effects of deletion of thexynAandxynCgenes, individually and in combination, were evaluated for xylan utilization and formation of acidic xylooligosaccharides. Parent strain 168 depolymerizes methylglucuronoxylans (MeGXn), releasing the xylobiose and xylotriose utilized for growth and accumulating the aldouronate methylglucuronoxylotriose (MeGX3) with some methylglucuronoxylotetraose (MeGX4). The combined GH11 and GH30 activities process the products generated by their respective actions on MeGXnto release a maximal amount of neutral xylooligosaccharides for assimilation and growth, at the same time forming MeGX3in which the internal xylose is substituted with methylglucuronate (MeG). Deletion ofxynAresults in the accumulation of β-1,4-xylooligosaccharides with degrees of polymerization ranging from 4 to 18 and an average degree of substitution of 1 in 7.2, each with a single MeG linked α-1,2 to the xylose penultimate to the xylose at the reducing terminus. Deletion of thexynCgene results in the accumulation of aldouronates comprised of 4 or more xylose residues in which the MeG may be linked α-1,2 to the xylose penultimate to the nonreducing xylose. TheseB. subtilislines may be used for the production of acidic xylooligosaccharides with applications in human and veterinary medicine.

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.

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