Found 195 structures.
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1. Compound ID: 3829
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LIP-(1-2)-+
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a-L-6dTalp3Me-(1-3)-L-Ser-(1-2)-L-Ser3(%)Me-(1-2)-L-Phe-(1-2)-+
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Lau-(1-2)-+ Lau-(1-2)-+ |
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a-L-Rhap2Me3Me4Me-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-a-L-Quip4Ac-(1-3)-D-aThr1Me |
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Structure type: oligomer
Trivial name: GPL-X-I
Compound class: glycopeptidolipid (GPL)
Contained glycoepitopes: IEDB_136098,IEDB_136105,IEDB_137476,IEDB_137477,IEDB_150900,IEDB_225177,IEDB_534864,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1451
Chatterjee D, Khoo KH "The surface glycopeptidolipids of mycobacteria: structures and biological properties" -
Cellular and Molecular Life Sciences 58(14) (2001) 2018-2042
One of the most important opportunistic pathogens associated with acquired immunodeficiency syndrome (AIDS) is the M. avium complex. M. avium infections are found in up to 70% of individuals in advanced stages of AIDS. It is apparent that M. avium can replicate in host macrophages and persist for long periods. This group of mycobacteria are distinguished by the presence of unique, highly antigenic, surface- located lipids known as the glycopeptidolipids (GPLs). The GPLs are the chemical basis of the 31 distinct serovars of the M. avium complex, and have also been identified in some other species. The M. avium lipids are immunosuppressive and can induce a variety of cytokines that affect general host responses. Despite extensive chemical characterization of the structures of these GPLs, much work is needed to elucidate the molecular mechanism involved in this complex glycosylation pathway and its genetic basis. The challenges for the future lie in explaining the roles of these copious products in the intracellular life and infectivity of mycobacteria. The intention of our review is to offer a concise account of the structures of the M. avium lipids, their putative roles in the host responses, bacterial physiology and pathogenesis, particularly in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). Advances in chemical synthesis of the various haptenic oligosaccharides are also given to demonstrate how these have helped to define the immunogenic determinants. We believe that future research should involve the creation of conditional mutants defective in these lipids for both functional and biosynthesis studies which will complement biological assays using chemically defined or modified neoglycoconjugates
Mycobacteria, neoglycoproteins, glycopeptidolipid (GPL), Mycobacterium avium complex (MAC), haptenic oligosaccharides
NCBI PubMed ID: 11814054Publication DOI: 10.1007/PL00000834Journal NLM ID: 9705402Publisher: Basel: Springer
Correspondence: delphi@lamar.colostate.edu
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA, Institute of Biological Chemistry, Academia Sinica, Taipei (Taiwan)
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2. Compound ID: 4154
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b-D-GlcpA-(1-4)-+
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-4)-a-D-GalpNAc-(1-3)-a-L-Fucp-(1-3)-a-D-Glcp-(1-4)-a-L-Quip-(1-3)-a-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_136045,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_140630,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_423153,IEDB_885822,IEDB_983931,SB_192,SB_86
The structure is contained in the following publication(s):
- Article ID: 1532
Kocharova NA, Bushmarinov IS, Ovchinnikova OG, Toukach FV, Torzewska A, Shashkov AS, Knirel YA, Rozalski A "The structure of the O-polysaccharide from the lipopolysaccharide of Providencia stuartii O44 containing L-quinovose, a 6-deoxy sugar rarely occurring in bacterial polysacharides" -
Carbohydrate Research 340(7) (2005) 1419-1423
The O-polysaccharide (O-antigen) of Providencia stuartii O44:H4 (strain 3768/51) was obtained by mild acid degradation of the lipopolysaccharide and studied by sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy, including 2D (1)H,(1)H COSY, TOCSY, ROESY, and H-detected (1)H,(13)C HSQC, and HMQC-TOCSY experiments. The O-polysaccharide was found to have a branched hexasaccharide repeating unit of the following structure: [Formula: see text].
Lipopolysaccharide, structure, Bacterial, O-polysaccharide, O polysaccharide, Providencia, sugar, PDF, polysacharide
NCBI PubMed ID: 15854616Journal NLM ID: 0043535Publisher: Elsevier
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology and Immunology, University of Lodz, PL 90-237 Lodz, Poland
Methods: methylation, NMR, sugar analysis
- Article ID: 4291
De Castro C, Kenyon JJ, Cunneen MM, Molinaro A, Holst O, Skurnik M, Reeves PR "The O-specific polysaccharide structure and gene cluster of serotype O:12 of the Yersinia pseudotuberculosis complex, and the identification of a novel L-quinovose biosynthesis gene" -
Glycobiology 23(3) (2013) 346-353
A major virulence factor for Yersinia pseudotuberculosis is the lipopolysaccharide including the O-polysaccharide. Currently, the O-polysaccharide based serotyping scheme for Y. pseudotuberculosis includes 21 known O-serotypes, with genetic and structural data available for 17 of them. The completion of the O-antigen structures and genetics of this species will enable the visualisation of relationships between O-serotypes and allow for analysis of the evolutionary processes within the species that give rise to new serotypes. Here we present the O-antigen structure and gene cluster of serotype O:12 thus adding one more to the set of completed serotypes, and show that this serotype is present in both Y. pseudotuberculosis and the newly identified Y. similis species. The O:12 structure is shown to include two rare sugars: 4-C[(R)-1-hydroxyethyl]-3,6,dideoxy-D-xylo-hexose (D-yersiniose) and 6-deoxy-L-glucopyranose (L-quinovose). We have identified a novel putative GDP-L-fucose 4-epimerase gene and propose a pathway for the synthesis of GDP-L-quinovose, which extends the known GDP-L-fucose pathway.
O-specific polysaccharide, Yersinia pseudotuberculosis, yersiniose, quinovose, Yersinia similis
NCBI PubMed ID: 23077132Publication DOI: 10.1093/glycob/cws145Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: decastro@unina.it
Institutions: Department of Chemical Sciences, University Federico II of Naples, Naples, Italy., Department of Chemical Sciences, University Federico II of Naples, Naples, Italy
Methods: 13C NMR, 1H NMR, DNA sequencing, sugar analysis, DNA techniques, mild acid hydrolysis, NMR-1D
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4362
Ovchinnikova OG, Liu B, Guo D, Kocharova NA, Shashkov AS, Chen M, Feng L, Rozalski A, Knirel YA, Wang L "Localization and molecular characterization of putative O-antigen gene clusters of Providencia species" -
Microbiology 158(4) (2012) 1024-1036
Enterobacteria of the genus Providencia are opportunistic human pathogens associated with urinary tract and wound infections, as well as enteric diseases. The lipopolysaccharide (LPS) O antigen confers major antigenic variability upon the cell surface and is used for serotyping of Gram-negative bacteria. Recently, Providencia O antigen structures have been extensively studied, but no data on the location and organization of the O antigen gene cluster have been reported. In this study, the four Providencia genome sequences available were analysed, and the putative O antigen gene cluster was identified in the polymorphic locus between the cpxA and yibK genes. This finding provided the necessary information for designing primers, and cloning and sequencing the O antigen gene clusters from five more Providencia alcalifaciens strains. The gene functions predicted in silico were in agreement with the known O antigen structures; furthermore, annotation of the genes involved in the three-step synthesis of GDP-colitose (gmd, colD and colC) was supported by cloning and biochemical characterization of the corresponding enzymes. In one strain (P. alcalifaciens O39), no polysaccharide product of the gene cluster in the cpxA-yibK locus was found, and hence genes for synthesis of the existing O antigen are located elsewhere in the genome. In addition to the putative O antigen synthesis genes, homologues of wza, wzb, wzc and (in three strains) wzi, required for the surface expression of capsular polysaccharides, were found upstream of yibK in all species except Providencia rustigianii, suggesting that the LPS of these species may be attributed to the so-called K LPS (K(LPS)). The data obtained open a way for development of a PCR-based typing method for identification of Providencia isolates.
Lipopolysaccharide, Providencia alcalifaciens, O-antigen gene cluster, O-Polysaccharide structure
NCBI PubMed ID: 22282517Publication DOI: 10.1099/mic.0.055210-0Journal NLM ID: 0376646Publisher: Washington, DC: Kluwer Academic/Plenum Publishers
Correspondence: wanglei@nankai.edu.cn; yknirel@gmail.com
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, 300457 Tianjin, PR China
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, DNA sequencing, SDS-PAGE, glycosyltransferase assays, 31P NMR, ESI-MS, genetic methods, HPLC
- Article ID: 4589
Ovchinnikova OG, Rozalski A, Liu B, Knirel YA "O-Antigens of bacteria of the genus Providencia: structure, serology, genetics, and biosynthesis" -
Biochemistry (Moscow) 78(7) (2013) 798-817
The genus Providencia consists of eight species of opportunistic pathogenic enterobacteria that can cause enteric diseases and urinary tract infections. The existing combined serological classification scheme of three species, P. alcalifaciens, P. stuartii, and P. rustigianii, is based on the specificity of O-antigens (O-polysaccharides) and comprises 63 O-serogroups. Differences between serogroups are related to polymorphism at a specific genome locus, the O-antigen gene cluster, responsible for O-antigen biosynthesis. This review presents data on structures of 36 O-antigens of Providencia, many of which contain unusual monosaccharides and non-carbohydrate components. The structural data correlate with the immunospecificity of the O-antigens and enable substantiation on a molecular level of serological relationships within the genus Providencia and between strains of Providencia and bacteria of the genera Proteus, Escherichia, and Salmonella. Peculiar features of the O-antigen gene cluster organization in 10 Providencia serogroups and biosynthetic pathways of nucleotide precursors of specific monosaccharide components of the O-antigens also are discussed.
Lipopolysaccharide, biosynthesis, O-antigen, gene cluster, Providencia, serological specificity
NCBI PubMed ID: 24010842Publication DOI: 10.1134/S0006297913070110Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: olga.ovchinnikova@gmail.com
Institutions: ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, 300457 Tianjin, P. R. China
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3. Compound ID: 9964
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b-L-Olip3NAc-(1-3)-+
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b-L-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-Quip-(1-2)-+ |
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Structure type: oligomer
Trivial name: viridopentaose A
The structure is contained in the following publication(s):
- Article ID: 4151
Harada K, Ito S, Suzuki M "Structural investigation of an antibiotic sporaviridin. IV. Structural revision of viridopentaoses" -
Tetrahedron Letters 23 (1982) 2479-2480
Structures of viridopentaose A, B and C are revised as 4A, 4B and 4C, respectively, by 1H-NMR (360 MHz) spectra and chemical degradations.
Publication DOI: 10.1016/S0040-4039(00)87373-6Journal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 1H NMR, chemical degradation
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4. Compound ID: 9965
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b-L-Olip3NAc-(1-3)-+
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b-L-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-Glcp-(1-2)-+ |
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Structure type: oligomer
Trivial name: viridopentaose C
Contained glycoepitopes: IEDB_142488,IEDB_146664,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 4151
Harada K, Ito S, Suzuki M "Structural investigation of an antibiotic sporaviridin. IV. Structural revision of viridopentaoses" -
Tetrahedron Letters 23 (1982) 2479-2480
Structures of viridopentaose A, B and C are revised as 4A, 4B and 4C, respectively, by 1H-NMR (360 MHz) spectra and chemical degradations.
Publication DOI: 10.1016/S0040-4039(00)87373-6Journal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 1H NMR, chemical degradation
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5. Compound ID: 9966
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b-L-Olip3NAc-(1-3)-+
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b-L-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-QuipNAc-(1-2)-+ |
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Structure type: oligomer
Trivial name: viridopentaose B
The structure is contained in the following publication(s):
- Article ID: 4151
Harada K, Ito S, Suzuki M "Structural investigation of an antibiotic sporaviridin. IV. Structural revision of viridopentaoses" -
Tetrahedron Letters 23 (1982) 2479-2480
Structures of viridopentaose A, B and C are revised as 4A, 4B and 4C, respectively, by 1H-NMR (360 MHz) spectra and chemical degradations.
Publication DOI: 10.1016/S0040-4039(00)87373-6Journal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 1H NMR, chemical degradation
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6. Compound ID: 9982
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b-D-Olip3NAc-(1-3)-+
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b-D-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-Quip-(1-2)-+ |
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Structure type: oligomer
Trivial name: viridopentaose A
The structure is contained in the following publication(s):
- Article ID: 4158
Kimura I, Yamamoto K, Harada K, Suzuki M "Structural investigation of the antibiotic sporaviridin XII. Isolation of the pseudoaglycons from N-acetylsporaviridins under basic conditions" -
Tetrahedron Letters 28 (1987) 1917-1920
N-acetylsporaviridins (N-Ac-SVD) are composed of six components whose molecular weights are all about 2200. Treatment of each component of N-Ac-SVD with 1.8-diazabicyclo [5,4,0] undesen-7 (DBU) gave two pseudoaglycones and one of three viridopentaoses A, B and C.
Publication DOI: 10.1016/S0040-4039(00)96009-XJournal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 13C NMR, IR, DBU treatment, SIMS
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7. Compound ID: 9984
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b-D-Olip3NAc-(1-3)-+
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b-D-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-Glcp-(1-2)-+ |
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Structure type: oligomer
Trivial name: viridopentaose C
Contained glycoepitopes: IEDB_142488,IEDB_146664,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 4158
Kimura I, Yamamoto K, Harada K, Suzuki M "Structural investigation of the antibiotic sporaviridin XII. Isolation of the pseudoaglycons from N-acetylsporaviridins under basic conditions" -
Tetrahedron Letters 28 (1987) 1917-1920
N-acetylsporaviridins (N-Ac-SVD) are composed of six components whose molecular weights are all about 2200. Treatment of each component of N-Ac-SVD with 1.8-diazabicyclo [5,4,0] undesen-7 (DBU) gave two pseudoaglycones and one of three viridopentaoses A, B and C.
Publication DOI: 10.1016/S0040-4039(00)96009-XJournal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 13C NMR, IR, DBU treatment, SIMS
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8. Compound ID: 9985
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b-D-Quip4NAc-(1-2)-+
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b-D-Olip3NAc-(1-3)-b-D-Quip-(1-4)-D-Qui
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b-D-Olip3NAc-(1-3)-+ |
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Structure type: oligomer
Trivial name: viridopentaose B
The structure is contained in the following publication(s):
- Article ID: 4158
Kimura I, Yamamoto K, Harada K, Suzuki M "Structural investigation of the antibiotic sporaviridin XII. Isolation of the pseudoaglycons from N-acetylsporaviridins under basic conditions" -
Tetrahedron Letters 28 (1987) 1917-1920
N-acetylsporaviridins (N-Ac-SVD) are composed of six components whose molecular weights are all about 2200. Treatment of each component of N-Ac-SVD with 1.8-diazabicyclo [5,4,0] undesen-7 (DBU) gave two pseudoaglycones and one of three viridopentaoses A, B and C.
Publication DOI: 10.1016/S0040-4039(00)96009-XJournal NLM ID: 2984819RPublisher: Elsevier
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
Methods: 13C NMR, IR, DBU treatment, SIMS
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9. Compound ID: 9996
Structure type: oligomer
Trivial name: aculexitiose
The structure is contained in the following publication(s):
- Article ID: 4165
Murata H, Kojima N, Harada K, Suzuki M, Ikemoto T, Shibuya T, Haneishi T, Torikata A "Structural elucidation of aculeximycin. I. Further purification and glycosidic bond cleavage of aculeximycin" -
The Journal of Antibiotics 42 (1989) 691-700
A new insecticidal antibiotic, aculeximycin (ACM), was produced by an actinomycete identified as Streptosporangium albidum. ACM has been successfully isolated from culture filtrate by a combination of Diaion HP-20, Amberlite CG-50, reversed phase silica gel and Sephadex LH-20 chromatographies. It was found that ACM is a basic glycosidic antibiotic with a molecular weight of 1,672 including five monosaccharide units, three double bonds and a hemiketal ring by preliminary spectral analyses. Treatment of ACM with 1,8-diazabicyclo[5,4,0]undecene-7 caused a glycosidic bond cleavage to give aculexitriose, pseudoaglycones I and II.
NCBI PubMed ID: 2722683Journal NLM ID: 0151115Publisher: London: Nature Publishing Group
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
- Article ID: 4166
Murata H, Harada K, Suzuki M, Ikemoto T, Shibuya T, Haneishi T, Torikata A "Structural elucidation of aculeximycin. II. Structures of carbohydrate moieties" -
The Journal of Antibiotics 42 (1989) 701-710
Treatment of aculeximycin with 2% 1,8-diazabicyclo[5,4,0]undecene-7 (DBU)-methanol yielded three products, aculexitriose, pseudoaglycones I and II. The structural elucidation of aculexitriose was carried out by spectral analyses (MS, NMR (1H-1H 2D NMR spectroscopy, nuclear Overhauser effect] and chemical degradations of aculexitriose and its derivatives. The structure of aculexitriose was established to be a branched trisaccharide, O-6-deoxy-β-D-glucopyranosyl-(1→2)-O-[3-amino-2,3,6-trideoxy-β- D- arabino-hexopyranosyl-(1→3)]-6-deoxy-D-glucopyranose. On the other hand the pseudoaglycones I and II were stereoisomers with respect to a chiral center newly formed by the DBU reaction. The pseudoaglycones contain one neutral sugar and one amino sugar, which turned out to be D-mannose and L-vancosamine, respectively.
NCBI PubMed ID: 2722684Journal NLM ID: 0151115Publisher: London: Nature Publishing Group
Institutions: Faculty of Pharmacy, Meijo University, Nagoya, Japan
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10. Compound ID: 10337
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b-Yerp-(1-4)-+
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-3)-a-D-Galp-(1-4)-a-L-Quip-(1-3)-b-D-GlcpNAc-(1-
Yer = 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-D-xylo-hexose (yersiniose A) |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_151528,IEDB_151531,IEDB_190606,SB_173,SB_7
The structure is contained in the following publication(s):
- Article ID: 4291
De Castro C, Kenyon JJ, Cunneen MM, Molinaro A, Holst O, Skurnik M, Reeves PR "The O-specific polysaccharide structure and gene cluster of serotype O:12 of the Yersinia pseudotuberculosis complex, and the identification of a novel L-quinovose biosynthesis gene" -
Glycobiology 23(3) (2013) 346-353
A major virulence factor for Yersinia pseudotuberculosis is the lipopolysaccharide including the O-polysaccharide. Currently, the O-polysaccharide based serotyping scheme for Y. pseudotuberculosis includes 21 known O-serotypes, with genetic and structural data available for 17 of them. The completion of the O-antigen structures and genetics of this species will enable the visualisation of relationships between O-serotypes and allow for analysis of the evolutionary processes within the species that give rise to new serotypes. Here we present the O-antigen structure and gene cluster of serotype O:12 thus adding one more to the set of completed serotypes, and show that this serotype is present in both Y. pseudotuberculosis and the newly identified Y. similis species. The O:12 structure is shown to include two rare sugars: 4-C[(R)-1-hydroxyethyl]-3,6,dideoxy-D-xylo-hexose (D-yersiniose) and 6-deoxy-L-glucopyranose (L-quinovose). We have identified a novel putative GDP-L-fucose 4-epimerase gene and propose a pathway for the synthesis of GDP-L-quinovose, which extends the known GDP-L-fucose pathway.
O-specific polysaccharide, Yersinia pseudotuberculosis, yersiniose, quinovose, Yersinia similis
NCBI PubMed ID: 23077132Publication DOI: 10.1093/glycob/cws145Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: decastro@unina.it
Institutions: Department of Chemical Sciences, University Federico II of Naples, Naples, Italy., Department of Chemical Sciences, University Federico II of Naples, Naples, Italy
Methods: 13C NMR, 1H NMR, DNA sequencing, sugar analysis, DNA techniques, mild acid hydrolysis, NMR-1D
- Article ID: 5010
Kenyon JJ, Cunneen MM, Reeves PR "Genetics and evolution of Yersinia pseudotuberculosis O-specific polysaccharides: a novel pattern of O-antigen diversity" -
FEMS Microbiology Reviews 41(2) (2017) 200-217
O-antigen polysaccharide is a major immunogenic feature of the lipopolysaccharide of Gram-negative bacteria, and most species produce a large variety of forms that differ substantially from one another. There are 18 known O-antigen forms in the Yersinia pseudotuberculosis complex, which are typical in being composed of multiple copies of a short oligosaccharide called an O unit. The O-antigen gene clusters are located between the hemH and gsk genes, and are atypical as 15 of them are closely related, each having one of five downstream gene modules for alternative main-chain synthesis, and one of seven upstream modules for alternative side-branch sugar synthesis. As a result, many of the genes are in more than one gene cluster. The gene order in each module is such that, in general, the earlier a gene product functions in O-unit synthesis, the closer the gene is to the 5 end for side-branch modules or the 3 end for main-chain modules. We propose a model whereby natural selection could generate the observed pattern in gene order, a pattern that has also been observed in other species.
Lipopolysaccharide, serotype, O antigen, gene cluster, O-specific polysaccharide, Yersinia pseudotuberculosis, O-antigen polysaccharide
NCBI PubMed ID: 28364730Publication DOI: 10.1093/femsre/fux002Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: peter.reeves@sydney.edu.au
Institutions: School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia, Institute of Health and Biomedical Innovation, Queensland University of Technology. Brisbane, QLD 4001, Australia
Methods: function analysis of gene clusters
- Article ID: 6089
Knirel YA, Anisimov AP, Kislichkina AA, Kondakova AN, Bystrova OV, Vagaiskaya AS, Shatalin KY, Shashkov AS, Dentovskaya SV "Lipopolysaccharide of the Yersinia pseudotuberculosis Complex" -
Biomolecules 11(10) (2021) 1410
Lipopolysaccharide (LPS), localized in the outer leaflet of the outer membrane, serves as the major surface component of the Gram-negative bacterial cell envelope responsible for the activation of the host's innate immune system. Variations of the LPS structure utilized by Gram-negative bacteria promote survival by providing resistance to components of the innate immune system and preventing recognition by TLR4. This review summarizes studies of the biosynthesis of Yersinia pseudotuberculosis complex LPSs, and the roles of their structural components in molecular mechanisms of yersiniae pathogenesis and immunogenesis.
core, Pathogenesis, lipid A, Yersinia pseudotuberculosis, lipopolysaccharide (LPS), Yersinia pestis, Plague, pathogenicity factor
NCBI PubMed ID: 34680043Publication DOI: 10.3390/biom11101410Journal NLM ID: 101596414Publisher: Basel, Switzerland: MDPI
Correspondence: Y.A. Knirel
; S.V. Dentovskaya
Institutions: Laboratory of Carbohydrate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Laboratory for Plague Microbiology, Especially Dangerous Infections Department, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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11. Compound ID: 10941
Structure type: monomer
Trivial name: GDP-L-quinovose
Contained glycoepitopes: IEDB_141493,IEDB_149170,IEDB_190357
The structure is contained in the following publication(s):
- Article ID: 4436
Maki M, Renkonen R "Biosynthesis of 6-deoxyhexose glycans in bacteria" -
Glycobiology 14(3) (2004) 1R-15R
After the breakthroughs in genomic sequencing, one of the next challenges remains to understand the molecular biology of other classes of biomolecules, such as protein and lipids, many of which carry specific glycomodification when mediating their biological functions. This review focuses on the 6-deoxyhexose biosynthesis of cell surface glycans of three Gram-negative pathogens, Helicobacter pylori, Pseudomonas aeruginosa, and Actinobacillus actinomycetemcomitans serotype a. 6-Deoxysugars are important functional components of cell surface glycans, and their biosynthetic pathways might be suitable targets for novel interventions of antibacterial chemotherapy.
rhamnose, fucose, nucleotide sugars, 6-deoxy-talose
NCBI PubMed ID: 14693916Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: risto.renkonen@helsinki.fi
Institutions: Rational Drug Design Program and Department of Bacteriology and Immunology, Biomedicum and Haartman Institute, PO Box 63, FIN-00014 University of Helsinki, Helsinki, Finland
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12. Compound ID: 11280
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a-D-GalpNAc-(1-3)-+
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L-Ala-(2-6)-+ |
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-4)-b-D-GlcpA-(1-4)-a-L-Fucp-(1-4)-a-D-Glcp-(1-4)-a-D-Quip-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_140630,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_423153,IEDB_885822,IEDB_983931,SB_192,SB_86
The structure is contained in the following publication(s):
- Article ID: 4548
Katzenellenbogen E, Kocharova NA, Shashkov AS, Gyrska-Fraczek S, Bogulska M, Gamian A, Knirel YA "Structure of the O-polysaccharide of Edwardsiella tarda PCM 1150 containing an amide of D-glucuronic acid with L-alanine" -
Carbohydrate Research 368 (2013) 84-88
Mild acid degradation of the lipopolysaccharide of Edwardsiella tarda PCM 1150 afforded an O-polysaccharide, which was isolated by GPC on Sephadex G-50 and studied by sugar and methylation analyses along with 1D and 2D 1H and 13C NMR spectroscopies, including experiments performed in a 9:1 H2O/D2O mixture to detect NH protons and their correlations with CH protons. The O-polysaccharide was found to contain an amide of d-glucuronic acid with l-alanine (d-GlcA6Ala) and the following structure of the branched hexasaccharide repeating unit was established: →4)-β-D-GlcpA6Ala-(1→4)-α-L-Fucp-(1→4)-α-D-Glcp-(1→4)-α-D-Quip-(1→3)-β-D-GlcpNAc-(1→3<←1)-α-D-GalpNAc.
Lipopolysaccharide, O-antigen, bacterial polysaccharide structure, Edwardsiella tarda, D-Glucuronoyl-L-alanine
NCBI PubMed ID: 23348241Publication DOI: 10.1016/j.carres.2012.12.016Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: E. Katzenellenbogen
Institutions: L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, sugar analysis, acid hydrolysis, GLC
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13. Compound ID: 13469
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R-Pyr-(2-6:2-4)-b-D-Manp-(1-4)-b-D-Quip-(1-2)-a-D-Manp6Ac-(1-3)-+
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-4)-b-D-Quip-(1-4)-b-D-Quip-(1- |
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Structure type: structural motif or average structure
Trivial name: xanthan
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130701,IEDB_137485,IEDB_144983,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 5349
Singh RS, Saini GK "Biosynthesis of pullulan and its applications in food and pharmaceutical industry" -
Book: Microorganisms in Sustainable Agriculture and Biotechnology (2012) Chapter 24, 509-553
Pullulan is a water-soluble polysaccharide produced by yeast-like fungus Aureobasidium pullulans. It is a regularly repeating copolymer with the chemical structure {→6)-α-D-glucopyranosyl-(1→4)-α-D-glucopyranosyl-(1→4)-α-D-glucopyranosyl-(1→}n and viewed as a succession of α-(1→6)-linked (1→4)-α-D-triglucosides i.e. maltotriose (G3). Pullulan has a wide range of commercial applications in biomedical and food industries. Because of its strictly linear structure, pullulan is also a very valuable tool in basic research as well as a well-defined model substance. This chapter focuses on the current literature on pullulan mainly its microbial sources, structural geometry, fermentative production, biosynthesis aspects, peculiar characteristics and varied applications.
biosynthesis, structure, fermentative production, pullulan, Aureobasidium pullulans, food and biomedical applications
Publication DOI: 10.1007/978-94-007-2214-9_24Publisher: Springer Science+Business Media B.V.
Correspondence: rssingh11@lycos.com
Editors: Satyanarayana T, Johri BN
Institutions: Carbohydrate and Protein Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala, India
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14. Compound ID: 14150
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Subst-(11-3)-a-L-Quip
Subst = 12-hydroxysaphenic acid = SMILES C{12}C(O)c2cccc3nc1c({11}C(=O)O)cccc1nc23 |
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Structure type: monomer
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5582
Pathirana C, Jensen PR, Dwight R, Fenical W "Rare phenazine L-quinovose esters from a marine actinomycete" -
Journal of Organic Chemistry 57(2) (1992) 740-742
A study of the shallow sediments in Bodega Bay, CA, resulted in the isolation of a filamentous bacterium (isolate CNB-253, an unknown Streptomyces sp.) which was found to produce compounds with broad-screen antibacterial activity. Subsequent fermentation in saltwater-based media, followed by EtOAc extraction of the whole broth, vacuum flash chromatographic purification of the extract, and HPLC purification led to the isolation of four new alkaloid esters of the rare phenazine class
Streptomyces, antibacterial activity, phenazine esters
Publication DOI: 10.1021/jo00028a060Journal NLM ID: 2985193RPublisher: Columbus, OH: American Chemical Society
Institutions: Scripps Institution of Oceanography, University of California, San Diego, USA
Methods: 13C NMR, 1H NMR, IR, acid hydrolysis, HPLC, extraction, optical rotation measurement, acetylation, CD, CC, cell growth, LR-ESI-MS, HR-CI-MS
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15. Compound ID: 14151
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Subst-(11-3)-b-L-Quip
Subst = 12-hydroxysaphenic acid = SMILES C{12}C(O)c2cccc3nc1c({11}C(=O)O)cccc1nc23 |
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Structure type: monomer
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5582
Pathirana C, Jensen PR, Dwight R, Fenical W "Rare phenazine L-quinovose esters from a marine actinomycete" -
Journal of Organic Chemistry 57(2) (1992) 740-742
A study of the shallow sediments in Bodega Bay, CA, resulted in the isolation of a filamentous bacterium (isolate CNB-253, an unknown Streptomyces sp.) which was found to produce compounds with broad-screen antibacterial activity. Subsequent fermentation in saltwater-based media, followed by EtOAc extraction of the whole broth, vacuum flash chromatographic purification of the extract, and HPLC purification led to the isolation of four new alkaloid esters of the rare phenazine class
Streptomyces, antibacterial activity, phenazine esters
Publication DOI: 10.1021/jo00028a060Journal NLM ID: 2985193RPublisher: Columbus, OH: American Chemical Society
Institutions: Scripps Institution of Oceanography, University of California, San Diego, USA
Methods: 13C NMR, 1H NMR, IR, acid hydrolysis, HPLC, extraction, optical rotation measurement, acetylation, CD, CC, cell growth, LR-ESI-MS, HR-CI-MS
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