Journal: BMC Bioinformatics

Article Title: AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

doi: 10.1186/1471-2105-13-229

Figure Lengend Snippet: Feature comparison of different conversion tools (As of April 2012)

Article Snippet: The Clone/Gene ID Converter [ ], MatchMiner [ ], the Gene name converter in GeneMerge [ ], RESOURCERER [ ] and GeneLynx [ ] are additional ID conversion tools.

Techniques: Comparison, Generated, Expressing, Sequencing

Journal: BMC Bioinformatics

Article Title: AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

doi: 10.1186/1471-2105-13-229

Figure Lengend Snippet: ID converter tools, data sources and availability

Article Snippet: The Clone/Gene ID Converter [ ], MatchMiner [ ], the Gene name converter in GeneMerge [ ], RESOURCERER [ ] and GeneLynx [ ] are additional ID conversion tools.

Techniques:

Journal: Nature Communications

Article Title: Molecular basis for bacterial N -glycosylation by a soluble HMW1C-like N -glycosyltransferase

doi: 10.1038/s41467-023-41238-1

Figure Lengend Snippet: a Scheme illustrating the general reaction of NGTs. b Glycosylation kinetics of Aa NGT using UDP-Glc and the peptide FGNWTT. c Plots comparing the initial velocities of Aa NGT in the presence of different sugar nucleotides. Additional kinetic data are given in Supplementary Table . All experiments were obtained in duplicate ( n = 2 independent experiments). d ITC data for the binding of UDP to Aa NGT. Top: raw thermogram (thermal power versus time). Bottom: binding isotherm (normalized heats versus molar ratio). The experiment was repeated at least 2 times independently with similar results, and one representative plot for each experiment is shown. e Graph depicting the K d s for the nucleotides (see Supplementary Table for all ITC data). Source data are provided as a Source Data file.

Article Snippet: Aa NGT mutants (R177A, H214A, D215A, and R177A-H214A-D215A) were generated by GenScript via site-directed mutagenesis using the vector pMALC2x-10HistTAG-PP- AaNGT .

Techniques: Glycoproteomics, Binding Assay

Journal: Nature Communications

Article Title: Molecular basis for bacterial N -glycosylation by a soluble HMW1C-like N -glycosyltransferase

doi: 10.1038/s41467-023-41238-1

Figure Lengend Snippet: a Ribbon structure of the Aa NGT complexed to UDP and FG N WTT. The N-terminal AAD, the N-terminal Rossmann and C-terminal Rossmann fold subdomains are colored in cyan, yellow and orange, respectively. The UDP nucleotide is depicted with gray carbon atoms whereas the peptide is shown as green carbon atoms. In b Close-up view of the active site showing the bound UDP and FG N WTT, UDP-Gal, and UDP-2F-Glc in the different complexes. Electron density maps are Fo–Fc (blue) contoured at 2.2 σ for all ligands. Except for the first N-terminal residue (Phe1 -2 ) of FG N WTT, the density for the peptide and nucleotides were well defined. c A close-up view of the surface representation of the Aa NGT active site is displayed, with the same colors as in panel a .

Article Snippet: Aa NGT mutants (R177A, H214A, D215A, and R177A-H214A-D215A) were generated by GenScript via site-directed mutagenesis using the vector pMALC2x-10HistTAG-PP- AaNGT .

Techniques: Residue

Journal: Nature Communications

Article Title: Molecular basis for bacterial N -glycosylation by a soluble HMW1C-like N -glycosyltransferase

doi: 10.1038/s41467-023-41238-1

Figure Lengend Snippet: a View of the active sites of Aa NGT-UDP-2F-Glc (upper-left panel), Aa NGT-UDP-Gal (upper-right panel), and Aa NGT-UDP-FG N WTT (lower-left panel) complexes. Residues are colored according to their location in the different domains and subdomains of Aa NGT, with the same color scheme as used in Fig. . The nucleotides UDP and the peptide are shown as gray and green carbon atoms, respectively. Hydrogen bond interactions are displayed as dotted black lines. b Superposition of the different ligands with UDP-Gal as yellow carbon/phosphate atoms, UDP-2F-Glc as orange carbon/phosphate atoms, UDP as gray carbon/phosphate atoms, and FG N WTT as green carbon atoms. c Glycosylation kinetics of Aa NGT and mutants, measured against variable concentrations of the peptide FG N WTT and using a saturated concentration of UDP-Glc. Additional kinetic data are provided in Supplementary Table . All experiments were obtained in duplicate ( n = 2 independent experiments). Source data are provided as a Source Data file.

Article Snippet: Aa NGT mutants (R177A, H214A, D215A, and R177A-H214A-D215A) were generated by GenScript via site-directed mutagenesis using the vector pMALC2x-10HistTAG-PP- AaNGT .

Techniques: Glycoproteomics, Concentration Assay