Found 39 structures.
Displayed structures from 1 to 15
Next 15 structure(s)
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1. Compound ID: 8943
Structure type: monomer
Trivial name: UDP-xylose
Contained glycoepitopes: IEDB_114701,IEDB_140434,IEDB_167188,IEDB_174332
The structure is contained in the following publication(s):
- Article ID: 3854
Gu X, Glushka J, Yin Y, Xu Y, Denny T, Smith J, Jiang Y, Bar-Peled M "Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family" -
Journal of Biological Chemistry 285(12) (2010) 9030-9040
The UDP-sugar interconverting enzymes involved in UDP-GlcA metabolism are well described in eukaryotes but less is known in prokaryotes. Here we identify and characterize a gene (RsU4kpxs) from Ralstonia solanacearum str. GMI1000, which encodes a dual function enzyme not previously described. One activity is to decarboxylate UDP-glucuronic acid to UDP-β-L-threo-pentopyranosyl-4''-ulose in the presence of NAD(+). The second activity converts UDP-β-L-threo-pentopyranosyl-4''-ulose and NADH to UDP-xylose and NAD(+), albeit at a lower rate. Our data also suggest that following decarboxylation, there is stereospecific protonation at the C5 pro-R position. The identification of the R. solanacearum enzyme enables us to propose that the ancestral enzyme of UDP-xylose synthase and UDP-apiose/UDP-xylose synthase was diverged to two distinct enzymatic activities in early bacteria. This separation gave rise to the current UDP-xylose synthase in animal, fungus, and plant as well as to the plant Uaxs and bacterial ArnA and U4kpxs homologs.
Gene Expression Regulation, enzyme, Ralstonia solanacearum, bioinformatics, Uridine Diphosphate Sugars, Uridine diphosphate Xylose, Alcohol Oxidoreductases
NCBI PubMed ID: 20118241Publication DOI: 10.1074/jbc.M109.066803Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: peled@ccrc.uga.edu
Institutions: Department of Biochemistry and Molecular Biology, and the Institute of Bioinformatics, Universityof Georgia, Complex Carbohydrate Research Center, Athens, GA, USA, USA
Methods: 1H NMR, NMR-2D, NMR-1D, genetic methods, biochemical methods, HPLC
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2. Compound ID: 14288
|
/Variants 0/-D-GlcpA-(1-4)-D-Gal-(1-4)-D-Glcp-(1-4)-Xyl
/Variants 0/ is:
D-GlcpA-(1-6)-
OR (exclusively)
D-GlcpA-(1-4)- |
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Structure type: oligomer
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_167188,IEDB_174332,IEDB_190606,IEDB_423153,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 5627
Dembitsky VM, Rezanka T "Metabolites produced by nitrogen-fixing Nostoc species" -
Folia Microbiologica 50(5) (2005) 363-391
This paper provides a comprehensive overview of metabolites, including lipids and lipid-like compounds, boron-containing macrocycles, arsenolipids, oligopeptides and amino acid derivatives, produced by cyanobacteria of the genus Nostoc
cyanobacteria, lipids, metabolites, Nostoc
NCBI PubMed ID: 16475497Publication DOI: 10.1007/bf02931419Journal NLM ID: 0376757Publisher: New York: Springer
Correspondence: rezanka@biomed.cas.cz
Institutions: Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech, Department of Organic Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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3. Compound ID: 14289
|
/Variants 0/-D-Glcp-(1-4)-D-Gal-(1-4)-D-Glcp-(1-4)-Xyl
/Variants 0/ is:
D-GlcpA-(1-6)-
OR (exclusively)
D-GlcpA-(1-4)- |
Show graphically |
Structure type: oligomer
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136044,IEDB_136095,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_167188,IEDB_174332,IEDB_190606,IEDB_423153,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 5627
Dembitsky VM, Rezanka T "Metabolites produced by nitrogen-fixing Nostoc species" -
Folia Microbiologica 50(5) (2005) 363-391
This paper provides a comprehensive overview of metabolites, including lipids and lipid-like compounds, boron-containing macrocycles, arsenolipids, oligopeptides and amino acid derivatives, produced by cyanobacteria of the genus Nostoc
cyanobacteria, lipids, metabolites, Nostoc
NCBI PubMed ID: 16475497Publication DOI: 10.1007/bf02931419Journal NLM ID: 0376757Publisher: New York: Springer
Correspondence: rezanka@biomed.cas.cz
Institutions: Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech, Department of Organic Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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4. Compound ID: 19448
|
Fuc-(1-?)-Xyl-(1-?)-+
|
Fuc-(1-?)-Xyl-(1-?)-+ |
| |
-4)-a-D-Manp-(1-4)-a-D-Manp-(1-4)-a-D-Manp-(1- |
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Structure type: structural motif or average structure
Compound class: glucan
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_130701,IEDB_136045,IEDB_140116,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_149135,IEDB_152206,IEDB_152214,IEDB_167188,IEDB_174332,IEDB_174333,IEDB_76933,IEDB_983930,SB_44,SB_67,SB_72,SB_86
The structure is contained in the following publication(s):
- Article ID: 7670
Wang J, Cao B, Zhao H, Feng J "Emerging roles of Ganoderma lucidum in anti-aging" -
Aging and Disease 8(6) (2017) 691-707
Ganoderma lucidum is a white-rot fungus that has been viewed as a traditional Chinese tonic for promoting health and longevity. It has been revealed that several extractions from Ganoderma lucidum, such as Ethanol extract, aqueous extract, mycelia extract, water soluble extract of the culture medium of Ganoderma lucidum mycelia, Ganodermasides A, B, C, D, and some bioactive components of Ganoderma lucidum, including Reishi Polysaccharide Fraction 3, Ganoderma lucidum polysaccharides I, II, III, IV, Ganoderma lucidum peptide, Ganoderma polysaccharide peptide, total G. lucidum triterpenes and Ganoderic acid C1 could exert lifespan elongation or related activities. Although the use of Ganoderma lucidum as an elixir has been around for thousands of years, studies revealing its effect of lifespan extension are only the tip of the iceberg. Besides which, the kinds of extractions or components being comfrimed to be anti-aging are too few compared with the large amounts of Ganoderma lucidum extractions or constituients being discovered. This review aims to lay the ground for fully elucidating the potential mechanisms of Ganoderma lucidum underlying anti-aging effect and its clinical application.
Antioxidant, immunomodulation, Ganoderma lucidum, anti-aging, anti-neurodegeneration
NCBI PubMed ID: 29344411Publication DOI: 10.14336/AD.2017.0410Journal NLM ID: 101540533Publisher: California: JKL International
Correspondence: Feng J
; Zhao H
Institutions: Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, China, Cerebrovascular Diseases Research Institute, Xuanwu Hospital of Capital Medical University, Beijing, China
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5. Compound ID: 19657
|
Xyl-(1-21)-Subst
Subst = fomitoside E aglycon = SMILES C[C@]([C@]1(C)CC2)(CC[C@@H]1[C@@H](C/C=C/{25}C(C)(O)C){21}C(O)=O)C3=C2[C@]4(C)[C@](CC3)([H])C(C)(C)[C@H](OC(C)=O)CC4 |
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Structure type: monomer
Compound class: triterpenoid glycoside
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332
The structure is contained in the following publication(s):
- Article ID: 7749
Chen HP, Liu JK "Secondary metabolites from higher fungi" -
Progress in the Chemistry of Organic Natural Products 106 (2017) 1-201
Secondary metabolites of higher fungi (mushrooms) are an underexplored resource compared to plant-derived secondary metabolites. An increasing interest in mushroom natural products has been noted in recent years. This chapter gives a comprehensive overview of the secondary metabolites from higher fungi, with 765 references highlighting the isolation, structure elucidation, biological activities, chemical syntheses, and biosynthesis of pigments, nitrogen-containing compounds, and terpenoids from mushrooms. Mushroom toxins are also included in each section.In a section on pigments of higher fungi, pigments are classified into four categories, namely, those from the shikimate-chorismate, acetate-malonate, and mevalonate biosynthetic pathways, and pigments containing nitrogen, with 145 references covering the years 2010-2016.In a section on other nitrogen-containing compounds of higher fungi, compounds are categorized primarily into nitrogen heterocycles, nucleosides, non-protein amino acids, cyclic peptides, and sphingolipids, with 65 references covering the years 2010-2016. In turn, in a section describing terpenoids of higher fungi, the sesquiterpenoids and diterpenoids are thoroughly elaborated, spanning the years 2001-2016, and 2009-2016, respectively. The divergent biosynthetic pathways from farnesyl pyrophosphate to sesquiterpenoids are also described. Selected triterpenoids with novel structures and promising biological activities, including lanostanes and ergostanes, are reported from the genus Ganoderma, and the fungi Antrodia cinnamomea and Poria cocos. In addition, cucurbitanes and saponaceolides are also compiled in this section.
biosynthesis, biological activity, chemical synthesis, mushrooms, secondary metabolites, higher fungi, triterpenoids, diterpenoids, mushroom toxins, nitrogen-containing compounds, pigments, sesquiterpenoids
NCBI PubMed ID: 28762089Publication DOI: 10.1007/978-3-319-59542-9_1Journal NLM ID: 101605200Publisher: Wien: Springer
Correspondence: liujikai@mail.scuec.edu.cn
Institutions: State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
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6. Compound ID: 19882
|
Xyl-(1-?)-Fuc-(1-?)-+
|
Xyl-(1-?)-Fuc-(1-?)-+ |
| |
-4)-a-D-Manp-(1-4)-a-D-Manp-(1-4)-a-D-Manp-(1- |
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Structure type: structural motif or average structure
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_130701,IEDB_136045,IEDB_140116,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_149135,IEDB_152206,IEDB_152214,IEDB_167188,IEDB_174332,IEDB_174333,IEDB_76933,IEDB_983930,SB_44,SB_67,SB_72,SB_86
The structure is contained in the following publication(s):
- Article ID: 7858
Wang YY, Khoo KH, Chen ST, Lin CC, Wong CH, Lin CH "Studies on the immuno-modulating and antitumor activities of Ganoderma lucidum (Reishi) polysaccharides: functional and proteomic analyses of a fucose-containing glycoprotein fraction responsible for the activities" -
Bioorganic and Medicinal Chemistry 10(4) (2002) 1057-1062
A fucose-containing glycoprotein fraction which stimulates spleen cell proliferation and cytokine expression has been identified from the water-soluble extract of Ganoderma lucidum. Proteomic analysis of mouse spleen cells treated with this glycoprotein fraction showed approximately 50% change of the proteome. Further studies on the activities of this glycoprotein fraction through selective proteolysis and glycosidic cleavage indicate that a fucose containing polysaccharide fraction is responsible for stimulating the expression of cytokines, especially IL-1, IL-2 and INF-gamma.
polysaccharides, glycoprotein, proliferation, Ganoderma lucidum
NCBI PubMed ID: 11836115Publication DOI: 10.1016/s0968-0896(01)00377-7Journal NLM ID: 9413298Publisher: Elsevier
Correspondence: wong@scripps.edu
Institutions: Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, Laboratory of Bioorganic Chemistry, Institute of Chemistry, Academia Sinica, Taipei, Taiwan
Methods: GC-MS, amino acid analysis, MALDI-TOF MS, biological assays, methanolysis, electrophoresis, enzymatic digestion, extraction, acetylation, gel filtration chromatography, derivatization, anthrone-sulfuric acid assay, MTT
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7. Compound ID: 19966
|
Xyl-(1-?)-{{{-a-D-Manp-(1-2)-}}}?%a-D-Manp-(1-2)-+
|
-6)-a-D-Manp-(1- |
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Structure type: structural motif or average structure
Trivial name: xylomannan
Compound class: xylomannan
Contained glycoepitopes: IEDB_114701,IEDB_130701,IEDB_136104,IEDB_140116,IEDB_141793,IEDB_141795,IEDB_141828,IEDB_141829,IEDB_141830,IEDB_141831,IEDB_141832,IEDB_141833,IEDB_141834,IEDB_143632,IEDB_144983,IEDB_152206,IEDB_153220,IEDB_153762,IEDB_153763,IEDB_164480,IEDB_167188,IEDB_174332,IEDB_76933,IEDB_857732,IEDB_857735,IEDB_983930,SB_136,SB_191,SB_196,SB_198,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 7902
Free SJ "Fungal cell wall organization and biosynthesis" -
Advances in Genetics 81 (2013) 33-82
The composition and organization of the cell walls from Saccharomyces cerevisiae, Candida albicans, Aspergillus fumigatus, Schizosaccharomyces pombe, Neurospora crassa, and Cryptococcus neoformans are compared and contrasted. These cell walls contain chitin, chitosan, β-1,3-glucan, β-1,6-glucan, mixed β-1,3-/β-1,4-glucan, α-1,3-glucan, melanin, and glycoproteins as major constituents. A comparison of these cell walls shows that there is a great deal of variability in fungal cell wall composition and organization. However, in all cases, the cell wall components are cross-linked together to generate a cell wall matrix. The biosynthesis and properties of each of the major cell wall components are discussed. The chitin and glucans are synthesized and extruded into the cell wall space by plasma membrane-associated chitin synthases and glucan synthases. The glycoproteins are synthesized by ER-associated ribosomes and pass through the canonical secretory pathway. Over half of the major cell wall proteins are modified by the addition of a glycosylphosphatidylinositol anchor. The cell wall glycoproteins are also modified by the addition of O-linked oligosaccharides, and their N-linked oligosaccharides are extensively modified during their passage through the secretory pathway. These cell wall glycoprotein posttranslational modifications are essential for cross-linking the proteins into the cell wall matrix. Cross-linking the cell wall components together is essential for cell wall integrity. The activities of four groups of cross-linking enzymes are discussed. Cell wall proteins function as cross-linking enzymes, structural elements, adhesins, and environmental stress sensors and protect the cell from environmental changes.
Candida albicans, Aspergillus fumigatus, Saccharomyces cerevisiae, fungal cell wall, Schizosaccharomyces pombe, Neurospora crassa, cell wall biogenesis, glucan; chitin, Cryptococcus neoformas
NCBI PubMed ID: 23419716Publication DOI: 10.1016/B978-0-12-407677-8.00002-6Journal NLM ID: 0370421Publisher: San Diego, CA: Academic Press
Correspondence: free@buffalo.edu
Institutions: Department of Biological Sciences, SUNY University at Buffalo, Buffalo, NY, USA
Methods: MS, electrophoresis, enzymatic digestion, microscopy
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8. Compound ID: 20492
|
Subst-(7-4)-Xylp-(1-4)-Subst1
Subst = 3,4,5-trihydroxybenzoic acid = SMILES O{7}C(C1=CC(O)=C(O)C(O)=C1)=O;
Subst1 = 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione = SMILES O{4}C1=CC(C(OC2={53}C(O){54}C(O)=C3)=O)=C(C2=C3C(O4)=O)C4={3}C1O |
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Structure type: monomer
; 584.9888 [M-H]-
C26H18O16
Compound class: phenolic glycoside
Contained glycoepitopes: IEDB_114701,IEDB_167188,IEDB_174332
The structure is contained in the following publication(s):
- Article ID: 8161
Imai K, Yamauchi K, Mitsunaga T "Extractives of Quercus crispula sapwood infected by the pathogenic fungus Raffaelea quercivora II: isolation and identification of phenolic compounds from infected sapwood" -
Mokuzai Gakkai Shi = Journal of the Japan Wood Research Society 59(6) (2013) 517-521
There has been a mass mortality of oak trees in the area along the coast of the Japan Sea. This phenomenon is caused by the ambrosia beetle Platypus quercivorus, which carries the ambrosia fungus Raffaelea quercivora. Extractives of a necrotic brownish coloration formed in the infected sapwood of Quercus crispula were investigated. The methanol extract of the damaged sapwood of Q. crispula was concentrated in vacuo and centrifuged to yield precipitates and the supernatant. The precipitates were subjected to Sephadex LH-20 column chromatography and preparative HPLC to describe a novel ellagic acid derivative (1). The 10 % methanol water-soluble part of the supernatant was subjected to medium-pressure ODS column chromatography and preparative HPLC, respectively, to analyze a known lignan (2). Sulfuric acid hydrolysis of (1) yielded an ellagic acid and a gallic acid. NMR and LC-TOF/MS indicated that an ellagic acid and a gallic acid bonded to a xylose with glycosidic and ester bonds, respectively. Compound (1) was identified as 4,5-dihydroxy-6-(3,7,8-trihydroxy-5,10-dihydro-chromeno[5,4,3-cde]chromen-2-yloxy)-tetrahydro-pyran-3-yl ester, and compound (2) was identified as (-)-lyoniresinol. The presence of (-)-lyoniresinol from damaged sapwood indicated that infection of R. quercivora may cause the formation of a pseudo-heartwood in the sapwood of Q. crispula.
infection, Quercus crispula, Raffaelea quercivora, (-)-lyoniresinol, tannin
Publication DOI: 10.1007/s10086-013-1366-yJournal NLM ID: 101165750Publisher: Nihon Mokuzai Gakkai
Correspondence: Mitsunaga T
Institutions: Department of Applied Life Science, Faculty of Applied Biological Science, Gifu University, Gifu, Japan
Methods: 13C NMR, 1H NMR, FAB-MS, HPLC, HMBC, COSY, LC-TOF/MS
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9. Compound ID: 21339
|
L-Xylp-(1-4)-+ L-Xylp-(1-4)-+ L-Xylp-(1-4)-+ L-Xylp-(1-4)-+
| | | |
-3)-a-L-Fucp-(1-3)-a-D-Galp2Me-(1-3)-a-L-Fucp-(1-3)-a-D-Galp2Me-(1-3)-a-L-Fucp-(1-3)-a-D-Galp-(1-3)-a-L-Fucp-(1-3)-a-D-Galp2Me-(1-3)-a-L-Fucp-(1-3)-a-D-Galp2Ac-(1-3)-a-L-Fucp-(1- |
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Structure type: polymer chemical repeating unit
; 25950
Compound class: fucoxylogalactan
Contained glycoepitopes: IEDB_136045,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_151528,IEDB_152214,IEDB_174333,IEDB_190606,SB_36,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 8599
Chang CC, Cheng JJ, Lee IJ, Lu MK "Purification, structural elucidation, and anti-inflammatory activity of xylosyl galactofucan from Armillaria mellea" -
Carbohydrate Polymers 114 (2018) 584-591
A xylosyl 1,3-galactofucan (AMPS-III) was isolated and identified as a novel anti-inflammatory agent from an edible fungus, Armillaria mellea. The characteristics chemical structure of AMPS-III including the linkages of compositional monosaccharides and structure of the repeat unit were depicted and elucidated by proton, carbon and two-dimensional nuclear magnetic resonance techniques. AMPS-III was chemically proposed to have a partial 4-O-xylosylated 1,3-linked α-D-galactosyl-interlaced α-L-fucan composed of a pentadecasaccharide repeat unit with a molecular mass approximately 13 kDa. AMPS-III significantly suppressed the release of tumor necrosis factor-α (TNF-α) and cytokine monocyte chemotactic protein-1 (MCP-1) in RAW264.7 macrophages and EAhy926 following LPS and TNF-α induction. The results provide helpful evidences for application of AMPS-III as anti-inflammatory food supplements.
polysaccharides, Armillaria mellea, anti-inflammation, galactofucan
NCBI PubMed ID: 29452183Publication DOI: 10.1016/j.ijbiomac.2018.02.033Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: Chang CC
; Lu MK
Institutions: Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, China, School of Pharmacy, College of Medicine, National Taiwan University, Taipei, China, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, China
Methods: 13C NMR, 1H NMR, HPSEC, statistical analysis, TOCSY, cytokine production, phenol-sulfuric acid assay, DQF-COSY, HMBC, centrifugation, NOESY, HSQC, TFA hydrolysis
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10. Compound ID: 21833
|
a-D-Manp-(1-3)-+
|
Xylp-(1--P--?)--+ |
| |
?%a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-6)-a-D-Manp-(1-6)-+
|
a-D-Manp-(1-2)-+ ?%a-D-Manp-(1-3)-a-D-Manp-(1-2)-a-D-Manp-(1-2)-+ |
| | |
{{{-a-D-Manp-(1-6)-}}}/n=2/-?%a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-6)-a-D-Man-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc
|
Xylp-(1-?)-+ |
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Structure type: structural motif or average structure
Contained glycoepitopes: IEDB_114701,IEDB_123886,IEDB_123887,IEDB_130701,IEDB_135813,IEDB_136104,IEDB_137340,IEDB_137485,IEDB_140116,IEDB_140434,IEDB_141111,IEDB_141793,IEDB_141807,IEDB_141828,IEDB_141829,IEDB_141830,IEDB_141831,IEDB_141832,IEDB_143632,IEDB_144983,IEDB_145668,IEDB_148491,IEDB_148492,IEDB_151079,IEDB_151531,IEDB_152206,IEDB_153212,IEDB_153220,IEDB_164174,IEDB_164175,IEDB_164176,IEDB_167188,IEDB_174332,IEDB_174840,IEDB_187201,IEDB_187238,IEDB_187239,IEDB_423157,IEDB_429156,IEDB_474450,IEDB_540671,IEDB_548907,IEDB_76933,IEDB_857734,IEDB_857735,IEDB_983930,SB_136,SB_191,SB_196,SB_197,SB_198,SB_33,SB_44,SB_53,SB_67,SB_72,SB_73,SB_74,SB_77,SB_85
The structure is contained in the following publication(s):
- Article ID: 8809
Thak EJ, Kim J, Lee DJ, Kim JY, Kang HA "Structural analysis of N-/O-glycans assembled on proteins in yeasts" -
Journal of Microbiology 56(1) (2018) 11-23
Protein glycosylation, the most universal and diverse post-translational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species-and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.
protein glycosylation, structure analysis, yeast, N-/O-glycans
NCBI PubMed ID: 29299842Publication DOI: 10.1007/s12275-018-7468-xJournal NLM ID: 9703165Publisher: Seoul: Microbiological Society of Korea
Correspondence: Kang HA
Institutions: Department of Life Science, Chung-Ang University, Seoul, Republic of Korea, Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
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11. Compound ID: 23485
|
a-D-Manp-(1-2)-a-D-Manp-(1-6)-+
|
a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)-+
|
a-D-Manp-(1-3)-+ |
| |
D-Manp-(1-?)-+ | |
| | |
Xyl-(1--P--?)--a-D-Manp-(1-6)-a-D-Manp-(1-6)-a-D-Manp-(1-?)-b-D-GlcpNAc-(1-?)-a-D-GlcpNAc-(1--/MP84 (Cda3) protein/
|
Xyl-(1-?)-+ |
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Structure type: oligomer
Aglycon: MP84 (Cda3) protein
Trivial name: cell wall mannoprotein
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_130701,IEDB_135813,IEDB_136104,IEDB_137340,IEDB_137485,IEDB_140116,IEDB_140434,IEDB_141793,IEDB_141807,IEDB_141828,IEDB_141829,IEDB_141830,IEDB_141831,IEDB_143632,IEDB_144983,IEDB_144995,IEDB_145668,IEDB_151079,IEDB_151531,IEDB_152206,IEDB_153220,IEDB_153762,IEDB_164174,IEDB_164479,IEDB_167188,IEDB_174332,IEDB_241100,IEDB_474450,IEDB_76933,IEDB_857733,IEDB_857734,IEDB_983930,SB_136,SB_191,SB_196,SB_197,SB_198,SB_44,SB_53,SB_55,SB_67,SB_72,SB_73,SB_74,SB_77,SB_85
The structure is contained in the following publication(s):
- Article ID: 9632
Lee SB, Mota C, Thak EJ, Kim J, Son YJ, Oh DB, Kang HA "Effects of altered N-glycan structures of Cryptococcus neoformans mannoproteins, MP98 (Cda2) and MP84 (Cda3), on interaction with host cells" -
Scientific Reports 13(1) (2023) 1175
Cryptococcus neoformans is an opportunistic human fungal pathogen causing lethal meningoencephalitis. It has several cell wall mannoproteins (MPs) identified as immunoreactive antigens. To investigate the structure and function of N-glycans assembled on cryptococcal cell wall MPs in host cell interactions, we purified MP98 (Cda2) and MP84 (Cda3) expressed in wild-type (WT) and N-glycosylation-defective alg3 mutant (alg3Δ) strains. HPLC and MALDI-TOF analysis of the MP proteins from the WT revealed protein-specific glycan structures with different extents of hypermannosylation and xylose/xylose phosphate addition. In alg3Δ, MP98 and MP84 had truncated core N-glycans, containing mostly five and seven mannoses (M5 and M7 forms), respectively. In vitro adhesion and uptake assays indicated that the altered core N-glycans did not affect adhesion affinities to host cells although the capacity to induce the immune response of bone-marrow derived dendritic cells (BMDCs) decreased. Intriguingly, the removal of all N-glycosylation sites on MP84 increased adhesion to host cells and enhanced the induction of cytokine secretion from BMDCs compared with that on MP84 carrying WT N-glycans. Therefore, the structure-dependent effects of N-glycans suggested their complex roles in modulating the interaction of MPs with host cells to avoid nonspecific adherence to host cells and host immune response hyperactivation.
structure, N-glycans, Cryptococcus neoformans, cell wall mannoproteins
NCBI PubMed ID: 36670130Publication DOI: 10.1038/s41598-023-27422-9Journal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: H.A. Kang
Institutions: Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 156-756, South Korea, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea, Department of Biosystems and Bioengineering, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, South Korea
Methods: SDS-PAGE, DNA techniques, Western blotting, MALDI-TOF MS, HPLC, protein detection, cytokine production
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12. Compound ID: 23486
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a-D-Manp-(1-6)-+
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a-D-Manp-(1-6)-+ |
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)-a-D-Manp-(1-?)-b-D-GlcpNAc-(1-?)-a-D-GlcpNAc-(1--/alg3ΔMP84 (Cda3) protein/
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Xyl-(1-?)-+ |
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Structure type: oligomer
Aglycon: alg3ΔMP84 (Cda3) protein
Trivial name: cell wall mannoprotein
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_130701,IEDB_135813,IEDB_136104,IEDB_137340,IEDB_141793,IEDB_141807,IEDB_141830,IEDB_143632,IEDB_144983,IEDB_145668,IEDB_151531,IEDB_152206,IEDB_153220,IEDB_164174,IEDB_167188,IEDB_174332,IEDB_241100,IEDB_983930,SB_136,SB_196,SB_197,SB_198,SB_44,SB_55,SB_67,SB_72,SB_73,SB_74,SB_85
The structure is contained in the following publication(s):
- Article ID: 9632
Lee SB, Mota C, Thak EJ, Kim J, Son YJ, Oh DB, Kang HA "Effects of altered N-glycan structures of Cryptococcus neoformans mannoproteins, MP98 (Cda2) and MP84 (Cda3), on interaction with host cells" -
Scientific Reports 13(1) (2023) 1175
Cryptococcus neoformans is an opportunistic human fungal pathogen causing lethal meningoencephalitis. It has several cell wall mannoproteins (MPs) identified as immunoreactive antigens. To investigate the structure and function of N-glycans assembled on cryptococcal cell wall MPs in host cell interactions, we purified MP98 (Cda2) and MP84 (Cda3) expressed in wild-type (WT) and N-glycosylation-defective alg3 mutant (alg3Δ) strains. HPLC and MALDI-TOF analysis of the MP proteins from the WT revealed protein-specific glycan structures with different extents of hypermannosylation and xylose/xylose phosphate addition. In alg3Δ, MP98 and MP84 had truncated core N-glycans, containing mostly five and seven mannoses (M5 and M7 forms), respectively. In vitro adhesion and uptake assays indicated that the altered core N-glycans did not affect adhesion affinities to host cells although the capacity to induce the immune response of bone-marrow derived dendritic cells (BMDCs) decreased. Intriguingly, the removal of all N-glycosylation sites on MP84 increased adhesion to host cells and enhanced the induction of cytokine secretion from BMDCs compared with that on MP84 carrying WT N-glycans. Therefore, the structure-dependent effects of N-glycans suggested their complex roles in modulating the interaction of MPs with host cells to avoid nonspecific adherence to host cells and host immune response hyperactivation.
structure, N-glycans, Cryptococcus neoformans, cell wall mannoproteins
NCBI PubMed ID: 36670130Publication DOI: 10.1038/s41598-023-27422-9Journal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: H.A. Kang
Institutions: Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 156-756, South Korea, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea, Department of Biosystems and Bioengineering, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, South Korea
Methods: SDS-PAGE, DNA techniques, Western blotting, MALDI-TOF MS, HPLC, protein detection, cytokine production
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13. Compound ID: 24530
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a-GalpA-(1-2)-+
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a-Xylp2Me-(1-3)-+ |
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a-Galp-(1-2)-b-GlcpA-(1-4)-a-Fucp-(1-4)-b-Rhap-(1-5)-Apif
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b-GalpA-(1-3)-+ |
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Structure type: oligomer
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_115136,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_1394181,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_149135,IEDB_151528,IEDB_152214,IEDB_174333,IEDB_190606,IEDB_225177,IEDB_423153,IEDB_885823,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 10073
Stevenson TT, Darvill AG, Albersheim P "Structure of plant cell walls XXIII. Structural features of the plant cell-wall polysaccharide rhamnogalacturonan-II" -
Carbohydrate Research 182 (1988) 207-226
Rhamnogalacturonan-II (RG-II), isolated from the cell walls of suspension-cultured sycamore cells, has been further characterized. End-group analysis of RG-II showed that the polysaccharide contains about 30 glycosyl residues. Some 28 residues have been found as constituents of well characterized oligosaccharide fragments of RG-II. RG-II was treated with lithium metal dissolved in ethylenediamine to degrade the glycosyluronic acid residues. The major product was isolated, characterized, and shown to be the triglycosylalditol α-Xyl-(1→3)-α-Fuc-(1→4)-β-Rha-(1→31)-apiitol. This tetrasaccharide fragment of RG-II has three residues in common with a previously characterized heptasaccharide that had been derived from RG-II by partial hydrolysis with acid. RG-II was found to contain a large number of branched galactosyluronic acid residues that have not yet been identified as components of oligosaccharide fragments, although they are undoubtedly part of an octa(galactosyluronic acid) fragment generated by partial acid hydrolysis. The results of sequential partial acid hydrolysis provided evidence that, in RG-II, the extremely acid-labile 3-deoxy-d-manno-2-octulosonic-acid and 3-deoxy-d-lyxo-2-heptulosaric acid residues are attached to O-3 of 3,4-linked galactosyluronic acid residues, and that the mildly acid-labile apiofuranosyl residues are attached to O-2 of 2,4-linked galactosyluronic acid residues. These and previously published data suggested that RG-II has a highly branched structure, arranged around an α-(1→4)-linked galactosyluronic acid backbone.
Publication DOI: 10.1016/0008-6215(88)84004-7Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Complex Carbohydrate Research Center and Department of Biochemistry, University of Georgia, Russell Research Center of the United States Department of Agriculture, Athens, Georgia, U.S.A.
Methods: 1H NMR, gel filtration, FAB-MS, partial acid hydrolysis, GC-MS, acid hydrolysis
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14. Compound ID: 24531
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a-Xylp2Me3Me4Me-(1-3)-a-Fucp2Me4Me-(1-4)-b-Rhap2Me3Me-(1-5)-Api1Me2Me3Me4Me-ol |
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Structure type: oligomer
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_130699,IEDB_136045,IEDB_1394181,IEDB_142489,IEDB_144562,IEDB_149135,IEDB_152214,IEDB_174333,IEDB_225177,IEDB_885823,SB_86
The structure is contained in the following publication(s):
- Article ID: 10073
Stevenson TT, Darvill AG, Albersheim P "Structure of plant cell walls XXIII. Structural features of the plant cell-wall polysaccharide rhamnogalacturonan-II" -
Carbohydrate Research 182 (1988) 207-226
Rhamnogalacturonan-II (RG-II), isolated from the cell walls of suspension-cultured sycamore cells, has been further characterized. End-group analysis of RG-II showed that the polysaccharide contains about 30 glycosyl residues. Some 28 residues have been found as constituents of well characterized oligosaccharide fragments of RG-II. RG-II was treated with lithium metal dissolved in ethylenediamine to degrade the glycosyluronic acid residues. The major product was isolated, characterized, and shown to be the triglycosylalditol α-Xyl-(1→3)-α-Fuc-(1→4)-β-Rha-(1→31)-apiitol. This tetrasaccharide fragment of RG-II has three residues in common with a previously characterized heptasaccharide that had been derived from RG-II by partial hydrolysis with acid. RG-II was found to contain a large number of branched galactosyluronic acid residues that have not yet been identified as components of oligosaccharide fragments, although they are undoubtedly part of an octa(galactosyluronic acid) fragment generated by partial acid hydrolysis. The results of sequential partial acid hydrolysis provided evidence that, in RG-II, the extremely acid-labile 3-deoxy-d-manno-2-octulosonic-acid and 3-deoxy-d-lyxo-2-heptulosaric acid residues are attached to O-3 of 3,4-linked galactosyluronic acid residues, and that the mildly acid-labile apiofuranosyl residues are attached to O-2 of 2,4-linked galactosyluronic acid residues. These and previously published data suggested that RG-II has a highly branched structure, arranged around an α-(1→4)-linked galactosyluronic acid backbone.
Publication DOI: 10.1016/0008-6215(88)84004-7Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Complex Carbohydrate Research Center and Department of Biochemistry, University of Georgia, Russell Research Center of the United States Department of Agriculture, Athens, Georgia, U.S.A.
Methods: 1H NMR, gel filtration, FAB-MS, partial acid hydrolysis, GC-MS, acid hydrolysis
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15. Compound ID: 25165
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Galp-(1-2)-Xylp-(1-6)-+
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Glcp-(1-2)-Xylp-(1-6)-+ |
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Glcp-(1-6)-+ | |
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-4)-Glcp-(1-4)-Glcp-(1-4)-Glcp-(1-4)-Glcp-(1- |
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Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_114701,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_140629,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_167188,IEDB_174332,IEDB_190606,IEDB_241101,IEDB_420417,IEDB_420418,IEDB_420419,IEDB_420421,IEDB_423115,IEDB_857742,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 10344
Al-Kaisey MT, Wilkie KCB "The polysaccharides of agricultural lupin seeds" -
Carbohydrate Research 227 (1992) 147-161
The polysaccharides of the seeds of four species of agricultural lupin have been shown to comprise galactans, arabinogalactans, arabinans, rhamnogalacturonans, and galactoxyloglucans. Low molecular weight compounds were present in the mixtures after methylation of the acidic polysaccharides. Three tri-O-acetyl-O-methylhexuronic acids, with one hydroxyl group unsubstituted, formed during methylation, hydrolysis, and acetylation of the acidic polysaccharides, were present in high and variable proportions.
NCBI PubMed ID: 1499028Publication DOI: 10.1016/0008-6215(92)85067-AJournal NLM ID: 0043535Publisher: Elsevier
Institutions: Chemistry Department, University of Aberdeen, Aberdeen, Great Britain
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