scholarly journals The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides

2016 ◽  
Vol 82 (17) ◽  
pp. 5116-5124 ◽  
Author(s):  
Susana V. Valenzuela ◽  
Sergi Lopez ◽  
Peter Biely ◽  
Julia Sanz-Aparicio ◽  
F. I. Javier Pastor
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Glycoside Hydrolase Family ◽  
Biomass Valorization ◽  
Content Type ◽  
Paenibacillus Barcinonensis ◽  
Catalytic Cleft ◽  
Hydrolase Family ◽  
Minor Activity

ABSTRACTA GH8 family enzyme involved in xylan depolymerization has been characterized. The enzyme, Rex8A, is a reducing-end xylose-releasing exo-oligoxylanase (Rex) that efficiently hydrolyzes xylooligosaccharides and shows minor activity on polymeric xylan. Rex8A hydrolyzes xylooligomers of 3 to 6 xylose units to xylose and xylobiose in long-term incubations. Kinetic constants of Rex8A were determined on xylotriose, showing aKmof 1.64 ± 0.03 mM and akcatvalue of 118.8 s−1. Besides linear xylooligosaccharides, the enzyme hydrolyzed decorated xylooligomers. The catalytic activity on branched xylooligosaccharides, i.e., the release of xylose from the reducing end, is a newly described trait of xylose-releasing exo-oligoxylanases, as the exo-activity on these substrates has not been reported for the few of these enzymes characterized to date. Modeling of the three-dimensional (3D) structure of Rex8A shows an (α/α)6barrel fold where the loops connecting the α-helices contour the active site. These loops, which show high sequence diversity among GH8 enzymes, shape a catalytic cleft with a −2 subsite that can accommodate methyl-glucuronic acid decorations. The hydrolytic ability of Rex8A on branched oligomers can be crucial for the complete depolymerization of highly substituted xylans, which is indispensable to accomplish biomass deconstruction and to generate efficient catalysts.IMPORTANCEA GH8 family enzyme involved in xylan depolymerization has been characterized. The Rex8A enzyme fromPaenibacillus barcinonensisis involved in depolymerization of glucuronoxylan, a major component of the lignocellulosic substrates. The study shows that Rex8A is a reducing-end xylose-releasing exo-oligoxylanase that efficiently hydrolyzes xylose from neutral and acidic xylooligosaccharides generated by the action of other xylanases also secreted by the strain. The activity of a Rex enzyme on branched xylooligosaccharides has not been described to date. This report provides original and useful information on the properties of a new example of the rarely studied Rex enzymes. Depolymerization of highly substituted xylans is crucial for biomass valorization as a platform for generation of biofuels, chemicals, and solvents.

Development and characterization of three-dimensional woven fabric for ultra violet protection

2018 ◽  
Vol 30 (4) ◽  
pp. 536-547
Author(s):  
Adeela Nasreen ◽  
Muhammad Umair ◽  
Khubab Shaker ◽  
Syed Talha Ali Hamdani ◽  
Yasir Nawab
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Air Permeability ◽  
Woven Fabrics ◽  
Woven Fabric ◽  
Protection Factor ◽  
Content Type ◽  
Ultraviolet Protection Factor ◽  
Ultraviolet Protection

Purpose The purpose of this paper is to investigate the effect of materials, three dimensional (3D) structure and number of fabric layers on ultraviolet protection factor (UPF), air permeability and thickness of fabrics. Design/methodology/approach Total 24 fabrics samples were developed using two 3D structures and two weft materials. In warp direction cotton (CT) yarn and in weft direction polypropylene (PP) and polyester (PET) were used. Air permeability, thickness and UPF testings were performed and relationship among fabric layers, air permeability, thickness and UPF was developed. Findings UPF and thickness of fabrics increases with number of fabric layers, whereas air permeability decreases with the increase in number of fabric layers. Furthermore, change of multilayer structure from angle interlock to orthogonal interlock having same base weave does not give significant effect on UPF. However, change of material from polyester (PET) to polypropylene (PP) has a dominant effect on UPF. Minimum of three layers of cotton/polyester fabric, without any aid of ultraviolet radiation (UV) resistant coating, are required to achieve good. Cotton/polyester fabrics are more appropriate for outdoor application due to their long-term resistance with sunlight exposure. Originality/value Long-term exposure to UV is detrimental. So, there is need of proper selection of material and fabric to achieve ultraviolet protection. 3D fabrics have yarns in X, Y as well as in Z directions which provide better ultraviolet protection as compared to two dimensional (2D) fabrics. In literature, mostly work was done on ultraviolet protection of 2D fabrics and surface coating of fabrics. There is limited work found on UPF of 3D woven fabrics.

A novel dextranase gene from the marine bacterium Bacillus aquimaris S5 and its expression and characteristics

2021 ◽  
Vol 368 (3) ◽  
Author(s):  
Dongxue Dong ◽  
Xuelian Wang ◽  
Tian Deng ◽  
Zhe Ning ◽  
Xiaopeng Tian ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Marine Bacterium ◽  
3D Structure ◽  
Great Promise ◽  
Glycoside Hydrolase Family ◽  
Alpha Helices ◽  
Random Coils ◽  
Pharmaceutical Industries ◽  
Bacterium Bacillus ◽  
Hydrolase Family

ABSTRACT Dextranase specifically hydrolyzes dextran and is used to produce functional isomalto-saccharide prebiotics. Moreover, dextranase is used as an additive in mouthwash to remove dental plaque. We cloned and expressed the dextranase gene of the marine bacterium Bacillus aquimaris S5. The length of the BaDex gene was 1788 bp, encoding 573 amino acids. Using bioinformatics to predict and analyze the amino acid sequence of BaDex, we found the isoelectric point and instability coefficient to be 4.55 and 29.22, respectively. The average hydrophilicity (GRAVY) was −0.662. The secondary structure of BaDex consisted of 145 alpha helices, accounting for 25.31% of the protein; 126 extended strands, accounting for 21.99%; and 282 random coils, accounting for 49.21%. The 3D structure of the BaDex protein was predicted and simulated using SWISS-MODEL, and BaDex was classified as a Glycoside Hydrolase Family 66 protein. The optimal temperature and pH for BaDex activity were 40°C and 6.0, respectively. The hydrolysates had excellent antioxidant activity, and 8 U/mL of BaDex could remove 80% of dental plaque in MBRC experiment. This recombinant protein thus has great promise for applications in the food and pharmaceutical industries.

scholarly journals Characterization of Glycoside Hydrolase Family 5 Proteins in Schizosaccharomyces pombe

2010 ◽  
Vol 9 (11) ◽  
pp. 1650-1660 ◽  
Author(s):  
Encarnación Dueñas-Santero ◽  
Ana Belén Martín-Cuadrado ◽  
Thierry Fontaine ◽  
Jean-Paul Latgé ◽  
Francisco del Rey ◽  
...  
Keyword(s):  
Cell Wall ◽  
Schizosaccharomyces Pombe ◽  
Protein Characterization ◽  
Wall Material ◽  
Glycoside Hydrolase Family ◽  
Content Type ◽  
Hydrolysis Of ◽  
Controlled Hydrolysis ◽  
Hydrolase Family

ABSTRACT In yeast, enzymes with β-glucanase activity are thought to be necessary in morphogenetic events that require controlled hydrolysis of the cell wall. Comparison of the sequence of the Saccharomyces cerevisiae exo-β(1,3)-glucanase Exg1 with the Schizosaccharomyces pombe genome allowed the identification of three genes that were named exg1 + (locus SPBC1105.05), exg2 + (SPAC12B10.11), and exg3 + (SPBC2D10.05). The three proteins have different localizations: Exg1 is secreted to the periplasmic space, Exg2 is a membrane protein, and Exg3 is a cytoplasmic protein. Characterization of the biochemical activity of the proteins indicated that Exg1 and Exg3 are active only against β(1,6)-glucans while no activity was detected for Exg2. Interestingly, Exg1 cleaves the glucans with an endohydrolytic mode of action. exg1 + showed periodic expression during the cell cycle, with a maximum coinciding with the septation process, and its expression was dependent on the transcription factor Sep1. The Exg1 protein localizes to the septum region in a pattern that was different from that of the endo-β(1,3)-glucanase Eng1. Overexpression of Exg2 resulted in an increase in cell wall material at the poles and in the septum, but the putative catalytic activity of the protein was not required for this effect.

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 Alkaloids as Inhibitors of Malate Synthase from Paracoccidioides spp.: Receptor-Ligand Interaction-Based Virtual Screening and Molecular Docking Studies, Antifungal Activity, and the Adhesion Process

2015 ◽  
Vol 59 (9) ◽  
pp. 5581-5594 ◽  
Author(s):  
Fausto Guimaraes Costa ◽  
Benedito Rodrigues da Silva Neto ◽  
Ricardo Lemes Gonçalves ◽  
Roosevelt Alves da Silva ◽  
Cecília Maria Alves de Oliveira ◽  
...  
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Docking Studies ◽  
Malate Synthase ◽  
Human Pathogens ◽  
Ligand Interaction ◽  
Content Type ◽  
Extracellular Matrix Components ◽  
Paracoccidioides Spp

ABSTRACTParacoccidioidesis the agent of paracoccidioidomycosis. Malate synthase plays a crucial role in the pathogenicity and virulence of various fungi, such as those that are human pathogens. Thus, an inhibitor of this enzyme may be used as a powerful antifungal without side effects in patients once these enzymes are absent in humans. Here, we searched for compounds with inhibitory capacity against the malate synthase ofParacoccidioidesspecies (PbMLS). The three-dimensional (3D) structure ofPbMLS was determined using the I-TASSER server. Compounds were selected from the ZINC database. Based on the mechanism underlying the interaction of the compounds withPbMLS, it was possible to identify β-carboline moiety as a standard key structure. The compounds with β-carboline moiety that are available in our laboratories were investigated. A total of nine alkaloid compounds were selected. The primary mechanisms of interaction of the alkaloid compounds in the binding pocket ofPbMLS were identified and compared with the mechanism of interaction of acetyl coenzyme A (acetyl-CoA). We discovered that the amphipathic nature of the compounds, concomitant with the presence of β-carboline moiety, was crucial for their stability in the binding pocket ofPbMLS. In addition, the importance of a critical balance of the polar and nonpolar contacts of the compounds in this region was observed. Four β-carboline alkaloid compounds showed the ability to inhibit recombinantPbMLS (PbMLSr) activity,Paracoccidioidesspecies growth, and adhesion of the fungus andPbMLSr to the extracellular matrix components. The cytotoxicity of the alkaloids was also evaluated.

Contribution of roughness parameters in the scuffing performance of metallic surfaces

2017 ◽  
Vol 69 (4) ◽  
pp. 507-515 ◽  
Author(s):  
Lukasz Wojciechowski ◽  
Radomir Majchrowski ◽  
Thomas G. Mathia
Keyword(s):  
Boundary Lubrication ◽  
Three Dimensional ◽  
Evaluation Study ◽  
Statistical Correlation ◽  
Morphological Parameters ◽  
Metallic Surfaces ◽  
Double Blind ◽  
Content Type ◽  
Lubrication Conditions

Purpose Boundary lubrication cannot provide long-term protection against scuffing. Therefore, it is fundamental to recognise the breaking point of the boundary layer that activates scuffing. Based on this assumption, three-dimensional (3D) morphologies of surfaces were characterised, and the fundamental conditions of the scuffing process were investigated to identify the transition from boundary lubrication conditions to catastrophic wear. Design/methodology/approach A series of systematic tribological double-blind experiments were carried out using a poorly lubricated cylinder/plane interface to model the tribological inverse problem in a boundary lubrication situation. Areal morphological analysis was performed, with the help of an optical interferometer, on a millimetric area corresponding to the contact surface during experimental tribological investigations. The statistical correlation between scuffing and the selected morphological parameters was evaluated. This evaluation study consisted of determining the linear, logarithmic, exponential, polynomial (of degree 2) or power dependency between time to scuffing and morphological parameters. Findings A clear, statistically confirmed relationship was observed between selected morphological parameters of the surface (Spd, Sha, Str, Sz) and its scuffing performance. Originality/value 3D morphological parameters that best specified the technological scuffing performance of metallic surfaces were selected and proposed.

Fabrication of nanocellulose/PEGDA hydrogel by 3D printing

2018 ◽  
Vol 24 (8) ◽  
pp. 1265-1271 ◽  
Author(s):  
Aimin Tang ◽  
Qinwen Wang ◽  
Shan Zhao ◽  
Wangyu Liu
Keyword(s):  
Additive Manufacturing ◽  
3D Printing ◽  
3D Structure ◽  
Three Dimensional ◽  
Aqueous Dispersion ◽  
Compression Modulus ◽  
Content Type ◽  
Precise Control ◽  
Light Curing ◽  
Equilibrium Swelling Ratio

Purpose Nanocellulose is characterised by favourable biocompatibility, degradability, nanostructure effect, high modulus and high tensile strength and has been widely applied in various fields. The current research in the field of new nanocellulose materials mainly focuses on the hydrogel, aerogel and the tissue engineering scaffold. All of these are three-dimensional (3D) porous materials, but conventional manufacturing technology fails to realise precise control. Therefore, the method of preparing structural materials using 3D printing and adopting the nanocellulose as the 3D printing material has been proposed. Then, how to realise 3D printing of nanocellulose is the problem that should be solved. Design/methodology/approach By adding the photosensitive component polyethyleneglycol diacrylate (PEGDA) in the aqueous dispersion system of nanocellulose, the nanocellulose was endowed with photosensitivity. Then, nanocellulose/PEGDA hydrogels were prepared by the additive manufacturing of nanocellulose through light curing. Findings The results showed that the nanocellulose/PEGDA hydrogels had a uniform shape and a controllable structure. The nanocellulose supported the scaffold structure in the hydrogels. Prepared with 1.8 per cent nanocellulose through 40 s of light curing, the nanocellulose/PEGDA hydrogels had a maximum compression modulus of 0.91 MPa. The equilibrium swelling ratio of the nanocellulose/PEGDA hydrogel prepared with 1.8 per cent nanocellulose was 13.56, which increased by 44 per cent compared with that of the PEGDA hydrogel without nanocellulose. Originality/value The paper proposed a method for rapidly prototyping the nanocellulose with expected properties, which provided a theoretical basis and technological reference for the 3D additive manufacturing of nanocellulose 3D structure materials with a controlled accurate architecture.

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.

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