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39 results for “glycosyltransferase”
Diffraction images used to solve the structures published in the article "A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites"
<p>Raw diffraction images used for generating the structures published in the article A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites" (available <a href="https://doi.org/10.1016/j.chom.2019.08.009">here</a>). The software used for the processing of each dataset is listed in their respective PDB entries.</p> <p> </p> <p>If you find this useful, please contact me at <a href="mailto:lukasz.sobala@hirszfeld.pl">lukasz.sobala@hirszfeld.pl</a>, I am just interested in how these data are used!</p>
Exploring the in Vitro Operating Window of Glycosyltransferase PtUGT1 from Polygonum tinctorium for a Biocatalytic Route to Indigo Dye
<p>The eobiotic compound indican lends itself to a compelling biocatalytic dyeing strategy for denim, in which the formation of corrosive byproducts is avoided. However, the efficient and scalable production of indican remains a key bottleneck. This work focuses on the <em>in vitro</em> characterization of <em>Pt</em>UGT1, a glycosyltransferase from <em>Polygonum tinctorium</em> that catalyzes the formation of indican via the glycosylation of indoxyl. Here, the buffer composition and enzyme concentration were identified as key parameters for enzyme activity and stability. The short lifetime of the enzyme under reaction conditions initiated an immobilization study. As a consequence, an amino-functionalized methacrylate resin was identified as a highly functional option for efficient immobilization of <em>Pt</em>UGT1, allowing immobilization yields of >98% for enzyme loadings up to 7.6 wt %. We further report a stabilization factor of 47 and significantly improved overall biocatalytic productivity. The straightforward handling and reuse of the described heterogeneous biocatalyst is demonstrated.</p>
Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during evolution. Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied GTs. Our studies provide an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation.
Data from: UDP-glycosyltransferases act as key determinants of host plant range in generalist and specialist Spodoptera species
Open the record for dataset details and reuse information.
Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
Open the record for dataset details and reuse information.
Fig. 1 in Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system
Fig. 1. Rapid screening of plant glycosyltransferases using the LET-based-TX-TL system. We can either use long primers which contain a promoter, a ribosome binding site, and a terminator to generate expressible linear DNAs or use short primers to amplify the targeted gene fragments and then ligate them with a promoter, a ribosome binding site, a terminator, and a backbone; then another pair of primers is used to generate expressible linear DNAs. Afterward, combine TX-TL extracts, buffers, and expressible linear DNAs to start protein expression. Then this TX-TL mixture is directly added with substrates (such as quercetin) to start glycosylation reactions. Finally, UPLC-MS is used to analyze the reaction mixture to examine whether targeted products (such as isoquercitrin) are generated.
Fig. 2 in Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system
Fig. 2. UPLC-MS analysis of isoquercitrin converted from quercetin by AtUGTs expressed in TX-TL. (A) A glycosylation reaction catalyzed by a UDP-glucose glycosyltransferase. (B) The chromatogram of the blank sample, which only has 50% methanol solvent. (C) The chromatogram of the negative group, which has TX-TL, quercetin, UDPglucose but no additional DNA. (D) The chromatogram of the quercetin standard. (E) The chromatogram of the isoquercitrin standard. (F–O) Chromatograms of products from the catalysis of quercetin by different AtUGTs (the final concentrations of the linear DNAs used for each AtUGTs are listed below in brackets): (F) AT1G07250 (32.25 nM), (G) AT1G07260 (29.24 nM), (H) AT2G36790 (20.64 nM), (I) AT2G15480 (29.98 nM), (J) AT2G15490 (29.50 nM), (K) AT3G16520 (25.03 nM), (L) AT3G21750 (23.7 nM), (M) AT3G46660 (24.14 nM), (N) AT4G15280 (24.47 nM), and (O) AT4G34138 (22.52 nM), see Supplementary Fig. S4 for the duplicate group. The y axis indicates ion signal abundance relative to the highest signal in each chromatogram (%). The numbers in the top right of each chromatogram (for instance 3.38e7 in [E]) indicate the ion counts represented by "100" relative abundance. The retention time of the isoquercitrin standard is 4.0 min, and the red arrow in each figure indicates the retention time of the product isoquercitrin. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system
Fig. 4. UPLC-MS analysis of isoquercitrin converted from quercetin by ArUGTs using heterologous expression. (A) The SDS-PAGE gel of heterologous expression of ArUGTs AR14572, AR11662, and AR43718 protein. The theoretical molecular weights of AR14572 protein, AR11662 protein, and AR43718 protein are 80.1 kDa, 79.8 kDa, and 80.4 kDa, respectively. (B) The chromatogram of isoquercitrin standard. (C–E) Chromatograms of products from the catalysis of quercetin by different ArUGTs using heterologous expression: (C) AR14572, (D) AR11662, and (E) AR43718, see Supplementary Fig. S6 for the duplicate group. The y axis indicates ion signal abundance relative to the highest signal in each chromatogram (%). The numbers in the top right of each chromatogram (for instance 4.56e6 in [B]) indicate the ion counts represented by "100" relative abundance. The retention time of the isoquercitrin standard is 3.93 min, and the red arrow in each figure indicates the retention time of the product isoquercitrin. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5. A in Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system
Fig. 5. A phylogenetic tree based on protein sequences of six ArUGTs: AR06047, AR06981, AR07558, AR11662, AR14572, and AR43718. The phylogenetic tree is constructed using MEGA. Numbers at the forks are bootstrap values from 100 replicates.
Fig. 3 in Rapid screening of glycosyltransferases in plants using a linear DNA expression template based cell-free transcription-translation system
Fig. 3. UPLC-MS analysis of isoquercitrin converted from quercetin by ArUGTs expressed in TX-TL. (A) A glycosylation reaction catalyzed by a UDP-glucose glycosyltransferase. (B) The chromatogram of the blank sample is 50% methanol solvent. (C) The chromatogram of the negative group, which has TXTL, quercetin, UDP-glucose but no additional DNA. (D) The chromatogram of quercetin standard. (E) The chromatogram of isoquercitrin standard. (F–K) Chromatograms of products from the catalysis of quercetin by different ArUGTs (the final concentrations of the linear DNAs used for each ArUGTs are 30 nM): (F) AR14572, (G) AR11662, (H) AR43718, (I) AR06047, (J) AR06981, and (K) AR07558, see Supplementary Fig. S5 for the duplicate group. The y axis indicates ion signal abundance relative to the highest signal in each chromatogram (%). The numbers in the top right of each chromatogram (for instance 2.21e7 in [E]) indicate the ion counts represented by "100" relative abundance. The retention time of the isoquercitrin standard is 4.08 min, and the red arrow in each figure indicates the retention time of the product isoquercitrin. The numbers under the protein names are the peak intensities of the product. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Supplementary Data for: "Molecular basis for bacterial N-glycosylation by a soluble HMW1C-like N-glycosyltransferase"
<p>This data set contains files related to the article "<strong>Molecular basis for bacterial <em>N</em>-glycosylation by a soluble HMW1C-like <em>N</em>-glycosyltransferase</strong>" by Beatriz Piniello, Javier Macías-León, Shun Miyazaki, Ana García-García, Ismael Compañón, Mattia Ghirardello, Víctor Taleb, Billy Veloz, Francisco Corzana, Atsushi Miyagawa, Carme Rovira and Ramón Hurtado-Guerrero.</p> <p>Description of the files:</p> <p><strong>Simulation data:</strong></p> <p>- <strong>classical_md_simulations.zip: </strong>includes the inputs and initial and final structures of the classical MD simulation of AaNGT in complex with UDP-Glc and peptide, for both Asn3 in amide and imidic acid form.</p> <p>- <strong>qmmm_simulations.zip</strong>: includes the inputs for equilibration and metadynamics, and the initial structure extracted from the classical MD. Other relevant structures included in the directories of the pertinent figures (see below). Also includes plots of the CVs for each of the metadynamics.</p> <p><strong>Data related to the figures in the manuscript (data from the plots is in the Source Data file included with the manuscript):</strong></p> <p><strong>- Figure_4.zip: </strong>PDB file of the structure shown.</p> <p>- <strong>Figure_5.zip</strong>: PDB files of the structures shown (MC, TS and P, (already uploaded in v1) and FES file.</p> <p>- <strong>Figure_S6.zip: </strong>PDB files of the structures shown (MC, TS and P).</p> <p>- <strong>Figure_S7.zip: </strong>PDB files of the structures shown (MC, TS and P) for both simulations, and their respective FES files.</p> <p>- <strong>Figure_S9.zip</strong>: PDB file of the structure shown (computational only). It is the same as the structure shown in <strong>Figure 8</strong>.</p> <p>- <strong>Figure_S11.zip</strong>: PDB file of the structure shown.</p> <p>- <strong>Table_S3.zip: </strong>Excel file with the data to obtain the table. TS is given as a single structure in the table and thus not included in the file.</p> <p> </p> <p>More data can be made available upon reasonable request.</p>
Machine-learning model based on glycosyltransferase expression predicts multiple cancer types, subtypes and survival probability
GEO Series GSE254461. Homo sapiens. 57 samples. Type: Expression profiling by high throughput sequencing.
Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity
GEO Series GSE184976. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity
GEO Series GSE184977. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Glycosyltransferase enzyme GCNT3 overexpression effect on SW620 colon cancer cells
GEO Series GSE88792. Homo sapiens. 3 samples. Type: Expression profiling by array.
Transcriptome profiling of glycosyltransferase knockouts using CRISPR in Poplar
GEO Series GSE186781. Populus tremula x Populus alba. 12 samples. Type: Expression profiling by high throughput sequencing.
Targeting N-glycosylation of 4F2hc mediated by glycosyltransferases B3GNT3 sensitizes ferroptosis of pancreatic ductal adenocarcinoma
GEO Series GSE207741. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
The O-glycosyltransferase C1GALT1 promotes EWSR1::FLI1 expression and is a therapeutic target for Ewing sarcoma
GEO Series GSE287721. Homo sapiens. 2 samples. Type: Other.
Exploring the Possibility to Use Glycosyltransferase as a Prognosis Marker of Neuroblastoma
ClinicalTrials.gov study NCT01638572. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Glycosyltransferase Extl1 promotes CCR7-mediated dendritic cell migration to restrain infection and autoimmunity
GEO Series GSE184978. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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