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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_114703,IEDB_149136,IEDB_581505,IEDB_591403

• Article ID: 1661
  Xu Q, Klees J, Teyral J, Capen R, Huang M, Sturgess AW, Hennessey JP, Washabaugh M, Sitrin R, Abeygunawardana C "Quantitative nuclear magnetic resonance analysis and characterization of the derivatized Haemophilus influenzae type b polysaccharide intermediate for PedvaxHIB" - Analytical Biochemistry 337(2) (2005) 235-245
  

  PedvaxHIB is a pediatric vaccine that protects children from severe disease caused by the gram-negative bacterium Haemophilus influenzae type b (Hib). The vaccine is made by chemically conjugating Hib capsular polysaccharide to the outer membrane protein complex of Neisseria meningitidis. The protein-conjugated vaccine has proven to be extremely effective in preventing invasive Hib disease in infants and young children. This paper presents the nuclear magnetic resonance (NMR) methodology for the quantitative characterization of derivatized polysaccharide and its validation closely following ICH guidelines. The assay has been shown to be precise and accurate (relative standard deviation [RSD]

  NMR, polysaccharide, derivatization, Quantitative analysis, PRP

  NCBI PubMed ID: 15691503
  Publication DOI: 10.1016/j.ab.2004.11.019
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Correspondence: qiuwei_xu@merck.com
  Institutions: Merck Research Laboratory, Merck & Co., Inc., West Point, PA 19486, USA
  Methods: NMR
  
   
  
  Haemophilus influenzae b
  CSDB ID 10649 (all data & tools)

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Structure type: monomer
Contained glycoepitopes: IEDB_149136,IEDB_581504,IEDB_581505

• Article ID: 3270
  De Leon GP, Elowe NH, Koteva KP, Valvano MA, Wright GD "An In Vitro Screen of Bacterial Lipopolysaccharide Biosynthetic Enzymes Identifies an Inhibitor of ADP-Heptose Biosynthesis" - Chemistry and Biology 13(4) (2006) 437-441
  

  The lipopolysaccharide (LPS)-rich outer membrane of gram-negative bacteria provides a protective barrier that insulates these organisms from the action of numerous antibiotics. Breach of the LPS layer can therefore provide access to the cell interior to otherwise impermeant toxic molecules and can expose vulnerable binding sites for immune system components such as complement. Inhibition of LPS biosynthesis, leading to a truncated LPS molecule, is an alternative strategy for antibacterial drug development in which this vital cellular structure is weakened. A significant challenge for in vitro screens of small molecules for inhibition of LPS biosynthesis is the difficulty in accessing the complex carbohydrate substrates. We have optimized an assay of the enzymes required for LPS heptose biosynthesis that simultaneously surveys five enzyme activities by using commercially available substrates and report its use in a small-molecule screen that identifies an inhibitor of heptose synthesis

  Lipopolysaccharide, biosynthesis, synthesis, LPS, structure, heptose, alternative, biosynthetic, Bacterial, carbohydrate, cell, molecule, Research, complex, bacteria, activity, biochemistry, Gram-negative bacteria, enzyme, gram negative bacteria, Gram-negative, cellular, inhibition, component, binding, binding site, site, Enzymes, action, membrane, substrate, heptose biosynthesis, protective, outer membrane, PDF, assay, immune, immune system, in vitro, use, challenge, development, drug, layer, complement, inhibitor, antibiotic, antimicrobial, antibacterial, toxic, Binding Sites, antibiotics, barrier

  NCBI PubMed ID: 16632256
  Journal NLM ID: 9500160
  Publisher: Maryland Heights, MO: Elsevier
  Correspondence: wrightge@mcmaster.ca
  Institutions: Antimicrobial Research Centre Department of Biochemistry and Biomedical Sciences McMaster University Hamilton, Hamilton, ON, Canada, Infectious Diseases Research Group Siebens-Drake Research Institute Department of Microbiology and Immunology The University of Western Ontario London, Ontario N6A 5C1 Canada
  Methods: biochemical methods
  
   
  
  Escherichia coli
  CSDB ID 20418 (all data & tools)

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Structure type: monomer
Compound class: phosphoglycan
Contained glycoepitopes: IEDB_149136,IEDB_581505

• Article ID: 7013
  Clasquin MF, Melamud E, Singer A, Gooding JR, Xu X, Dong A, Cui H, Campagna SR, Savchenko A, Yakunin AF, Rabinowitz JD, Caudy AA "Riboneogenesis in yeast" - Cell 145(6) (2011) 969-980
  

  Glucose is catabolized in yeast via two fundamental routes, glycolysis and the oxidative pentose phosphate pathway, which produces NADPH and the essential nucleotide component ribose-5-phosphate. Here, we describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptulose-1,7-bisphosphate. In the pathway's committed step, sedoheptulose bisphosphate is hydrolyzed to sedoheptulose-7-phosphate by the enzyme sedoheptulose-1,7-bisphosphatase (SHB17), whose activity we identified based on metabolomic analysis of the corresponding knockout strain. The crystal structure of Shb17 in complex with sedoheptulose-1,7-bisphosphate reveals that the substrate binds in the closed furan form in the active site. Sedoheptulose-7-phosphate is ultimately converted by known enzymes of the nonoxidative pentose phosphate pathway to ribose-5-phosphate. Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells.

  riboneogenesis

  NCBI PubMed ID: 21663798
  Publication DOI: 10.1016/j.cell.2011.05.022
  Journal NLM ID: 0413066
  Publisher: Cambridge, MA: Cell Press
  Correspondence: Rabinowitz JD ; Caudy AA
  Institutions: Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, USA, Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada, Department of Chemistry, University of Tennessee, Knoxville, USA, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
  Methods: crystallography, extraction, cell growth, LC-MS/MS, HPLC-MS, enzymatic assay
  
   
  
  Saccharomyces cerevisiae, Saccharomyces cerevisiae shb17Δ
  CSDB ID 43355 (all data & tools)

Show legend Show as text

Structure type: monomer
Compound class: glycoside
Contained glycoepitopes: IEDB_149136,IEDB_581505

• Article ID: 8788
  Suparmin A, Kato T, Takemoto H, Park EY "Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris" - Microbiology Open 8(9) (2019) ID e00836
  

  An entomopathogenic fungus, Cordyceps sp. has been known to produce cordycepin which is a purine nucleoside antimetabolite and antibiotic with potential anticancer, antioxidant and anti-inflammatory activities. Interestingly, Cordyceps militaris produces significantly higher amount in a liquid surface culture than in a submerged culture. The liquid surface culture consists of mycelia growing into the air (aerial mycelia) and mycelia growing toward the bottom into the medium (submerged mycelia). In this study, to clarify roles of aerial and submerged mycelia of C. militaris in the cordycepin production the difference in metabolism between these mycelia was investigated. From transcriptomic analyses of the aerial and submerged mycelia at the culture of 5, 12 and 19 days, the metabolism of the submerged mycelia switched from the oxidative phosphorylation to the fermentation pathway. This activated the pentose phosphate pathway to provide building block materials for the nucleotide biosynthetic pathway. Under hypoxic conditions, the 5-aminolevulinic acid synthase (CCM_01504), delta-aminolevulinic acid dehydratase (CCM_00935), coproporphyrinogen III oxidase (CCM_07483) and cytochrome c oxidase 15 (CCM_05057) genes of heme biosynthesis were significantly upregulated. In addition, the liquid surface culture revealed that metabolite coproporhyrinogen III and glycine, the product and precursor of heme, were increased at 12th day and decreased at 19th day, respectively. These results indicate that the submerged mycelia induce the activation of iron acquisition, the ergosterol biosynthetic pathway, and the iron cluster genes of cordycepin biosynthesis in a hypoxic condition. Even though, the expression of the cluster genes of cordycepin biosynthesis was not significantly different in both types of mycelia.

  Hypoxia, Cordyceps militaris, aerial mycelia, heme biosynthesis, liquid surface culture, submerged mycelia

  NCBI PubMed ID: 30924317
  Publication DOI: 10.1002/mbo3.836
  Journal NLM ID: 101588314
  Publisher: Oxford: Wiley-Blackwell
  Correspondence: park.enoch@shizuoka.ac.jp
  Institutions: Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan, Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan, Instrumental Research Support Office, Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
  Methods: GC-MS, cell growth, RNA sequencing, gene expression, centrifugation, qRT-PCR, HPLC-UV
  
   
  
  Cordyceps militaris NBRC 103,752
  CSDB ID 49929 (all data & tools)

Show legend Show as text

Structure type: monomer
Compound class: glycoside
Contained glycoepitopes: IEDB_149136,IEDB_581505

• Article ID: 11700
  Åstot C, Dolezal K, Moritz T, Sandberg G "Deuterium in vivo labelling of cytokinins in Arabidopsis thaliana analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry" - Journal of Mass Spectrometry 35(1) (2000) 13-22
  

  A method was developed for analysing the biosynthetic rate of the cytokinin class of plant hormones. Transgenic, cytokinin-overproducing Arabidopsis thaliana plants were incubated in liquid culture media enriched with 30% deuterium oxide, and incorporation into the different parts of the cytokinin molecule was analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry after precolumn propionylation. The sugar moieties of the cytokinins generally showed a high and independent incorporation, so the analysis in this study focused on the cytokinin base moieties. It was observed that during a 24 h incubation period almost all labelling was incorporated into the side-chain, rather than the adenine moiety. The incorporation dynamics of isopentenyladenosine-5'-monophosphate, zeatinriboside-5'-monophosphate (ZRMP) and zeatin-9-glucoside were investigated through analysis of the cytokinin base fragments in high-resolution selective ion monitoring mode. Using a fractional synthetic rate approach, the biosynthetic rate of ZRMP was determined to be 18 ng/h/g fresh weight, giving a turnover time of 25 h. A method for the mass isotopomer abundance analysis of the cytokinins in the zeatin family, based on selective reaction monitoring, was also developed to gain further sensitivity. Use of this technique showed that there was a higher level of enrichment in zeatin nucleotide than in the corresponding nucleoside, in agreement with the hypothesis that cytokinin nucleotides are primary products in this pathway.

  Fast Atom Bombardment, Arabidopsis thaliana, in vivo labelling, isotopomer, cytokinin biosynthesis

  NCBI PubMed ID: 10633230
  Publication DOI: 10.1002/(SICI)1096-9888(200001)35:1<13::AID-JMS901>3.0.CO;2-I
  Journal NLM ID: 9504818
  Publisher: Chichester, UK: Wiley
  Institutions: Department of Forest Genetics and Plant Physiology, The Swedish University of Agricultural Sciences, Umeå, Sweden
  Methods: HPLC, enzymatic digestion, extraction, isotopic labeling, derivatization, cation-exchange chromatography, immunoafinity chromatography, SRM-MS, HR-SIMS, LC-FAB-MS
  
   
  
  Arabidopsis thaliana
  CSDB ID 64756 (all data & tools)

Show legend Show as text

Structure type: monomer
Compound class: glycoside
Contained glycoepitopes: IEDB_149136,IEDB_581505

• Article ID: 11700
  Åstot C, Dolezal K, Moritz T, Sandberg G "Deuterium in vivo labelling of cytokinins in Arabidopsis thaliana analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry" - Journal of Mass Spectrometry 35(1) (2000) 13-22
  

  A method was developed for analysing the biosynthetic rate of the cytokinin class of plant hormones. Transgenic, cytokinin-overproducing Arabidopsis thaliana plants were incubated in liquid culture media enriched with 30% deuterium oxide, and incorporation into the different parts of the cytokinin molecule was analysed by capillary liquid chromatography/frit-fast atom bombardment mass spectrometry after precolumn propionylation. The sugar moieties of the cytokinins generally showed a high and independent incorporation, so the analysis in this study focused on the cytokinin base moieties. It was observed that during a 24 h incubation period almost all labelling was incorporated into the side-chain, rather than the adenine moiety. The incorporation dynamics of isopentenyladenosine-5'-monophosphate, zeatinriboside-5'-monophosphate (ZRMP) and zeatin-9-glucoside were investigated through analysis of the cytokinin base fragments in high-resolution selective ion monitoring mode. Using a fractional synthetic rate approach, the biosynthetic rate of ZRMP was determined to be 18 ng/h/g fresh weight, giving a turnover time of 25 h. A method for the mass isotopomer abundance analysis of the cytokinins in the zeatin family, based on selective reaction monitoring, was also developed to gain further sensitivity. Use of this technique showed that there was a higher level of enrichment in zeatin nucleotide than in the corresponding nucleoside, in agreement with the hypothesis that cytokinin nucleotides are primary products in this pathway.

  Fast Atom Bombardment, Arabidopsis thaliana, in vivo labelling, isotopomer, cytokinin biosynthesis

  NCBI PubMed ID: 10633230
  Publication DOI: 10.1002/(SICI)1096-9888(200001)35:1<13::AID-JMS901>3.0.CO;2-I
  Journal NLM ID: 9504818
  Publisher: Chichester, UK: Wiley
  Institutions: Department of Forest Genetics and Plant Physiology, The Swedish University of Agricultural Sciences, Umeå, Sweden
  Methods: HPLC, enzymatic digestion, extraction, isotopic labeling, derivatization, cation-exchange chromatography, immunoafinity chromatography, SRM-MS, HR-SIMS, LC-FAB-MS
  
   
  
  Arabidopsis thaliana
  CSDB ID 64757 (all data & tools)