Found 18 structures.
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1. Compound ID: 4342
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b-D-Galf-(1-6)-{{{-b-D-Galf-(1-5)-b-D-Galf-(1-6)-}}}+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ |
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Mycolic-(1-5)-+ | {{{-a-D-Araf-(1-5)-}}}/n=7/-a-D-Araf-(1-3)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}a-D-Araf-(1-5)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}a-D-Araf-(1-5)-b-D-Galf-(1-5)-{{{-b-D-Galf-(1-6)-b-D-Galf-(1-5)-}}}/n=3/-a-D-Galf-(1-4)-b-L-Rhap-(1-4)-a-D-GlcpNAc-(1---P---/peptidoglycan/ |
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Structure type: oligomer
Aglycon: peptidoglycan
Trivial name: arabinogalactan
Contained glycoepitopes: IEDB_136095,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_149176,IEDB_150077,IEDB_151531,IEDB_159255,IEDB_190606,IEDB_225177,IEDB_885812,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1629
Li W, Chatterjee D, Lee RE "Rapid structural characterization of the arabinogalactan and lipoarabinomannan in live mycobacterial cells using 2D and 3D HR-MAS NMR: structural changes in the arabinan due to ethambutol treatment and gene mutation are observed" -
Glycobiology 15(2) (2005) 139-151
Mycobacteria possess a unique, highly evolved, carbohydrate- and lipid-rich cell wall that is believed to be important for their survival in hostile environments. Until now, our understanding of mycobacterial cell wall structure has been based upon destructive isolation and fragmentation of individual cell wall components. This study describes the observation of the major cell wall structures in live, intact mycobacteria using 2D and 3D high-resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR). As little as 20 mg (wet weight) of [13C]-enriched cells were required to produce a whole-cell spectra in which discrete cross-peaks corresponding to specific cell wall components could be identified. The most abundant signals of the arabinogalactan (AG) and lipoarabinomannan (LAM) were assigned in the HR-MAS NMR spectra by comparing the 2D and 3D NMR whole-cell spectra with the spectra of purified cellular components. This study confirmed that the structures of the AG and LAM moieties in the cell wall of live mycobacteria are consistent with structural reports in the literature, which were obtained via degradative analysis. Most important, by using intact cells it was possible to directly demonstrate the effects of ethambutol on the mycobacterial cell wall polysaccharides, characterize the effects of embB gene knockout in the M. smegmatis ∆embB mutant, and observe differences in the cell wall structures of two mycobacterial species (M. bovis BCG and M. smegmatis.) Herein, we show that HR-MAS NMR is a powerful, rapid, nondestructive technique to monitor changes in the complex, carbohydrate-rich cell wall of live mycobacterial cells.
Mycobacteria, arabinogalactan, lipoarabinomannan, Mycobacterium smegmatis, HR-MAS NMR, HCCH-TOCSY, Mycobacterium bovis, mycolyl arabinogalactanstructure
NCBI PubMed ID: 15371346Publication DOI: 10.1093/glycob/cwh150Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: relee@utmem.edu
Institutions: Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave. Rm. 327, Memphis, TN 38163, USA
Methods: NMR
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2. Compound ID: 4790
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Mycolic-(1-5)-+
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-?)-Gro |
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Structure type: oligomer
Compound class: glycolipid
Contained glycoepitopes: IEDB_159255
The structure is contained in the following publication(s):
- Article ID: 1794
Watanabe M, Kudoh S, Yamada Y, Iguchi K, Minnikin DE "A new glycolipid from Mycobacterium avium-Mycobacterium intracellulare complex" -
Biochimica et Biophysica Acta 1165 (1993) 53-60
From a nonpolar lipid fraction of Mycobacterium avium--Mycobacterium intracellulare complex cell mass, a new glycolipid was obtained, which was shown to be 5-mycoloyl-β-arabinofuranosyl-(1→2)-5-mycoloyl-α-arabinofuranosyl-(1→1')-glycerol. When examined by TLC, all the 12 strains of this species tested, including clinical isolates, were found to contain this glycolipid. But the glycolipid was not detected in Mycobacterium bovis BCG or Mycobacterium tubrculosis H37Rv.
NCBI PubMed ID: 1420348Journal NLM ID: 0217513Publisher: Elsevier
Institutions: Research Institute of BCG, Tokyo, Japan
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3. Compound ID: 5966
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Mycolic-(1-5)-+
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-a-D-Araf |
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Structure type: oligomer
Contained glycoepitopes: IEDB_1309625,IEDB_134619,IEDB_159255,IEDB_857717,IEDB_857718
The structure is contained in the following publication(s):
- Article ID: 2655
McNeil M, Daffé M, Brennan PJ "Location of the mycolyl ester substituents in the cell walls of mycobacteria" -
Journal of Biological Chemistry 266 (1991) 13217-13223
The question of the precise location of mycolic acids, the single most distinctive cell wall entity of members of the Mycobacterium genus, has now been addressed. The free hydroxyl functions of the arabinogalactan component of the mycobacterial cell wall were O-methylated under conditions in which the mycolyl esters were not cleaved. Subsequent replacement of the mycolyl functions with O-ethyl groups resulted in an acid- and base-stable differentially O-alkylated surrogate polysaccharide, more amenable to analysis. Complete hydrolysis, reduction, acetylation, and gas chromatography/mass spectrometry revealed the unexpected finding that the mycolyl substituents were selectively and equally distributed on the 5-hydroxyl functions of terminal- and 2-linked arabinofuranosyl (Araf) residues. Further analysis of the O-alkylated cell wall through partial acid hydrolysis, NaB[2H]4 reduction, pentadeuterioethylation, and gas chromatography/mass spectrometry demonstrated that the mycolyl units are clustered in groups of four on the previously recognized nonreducing terminal pentaarabinosyl unit [β-Araf-(1→2)-α-Araf)2-3,5-α-Araf. However, only about two-thirds of the available pentasaccharide units are so substituted. Thus, the antigenicity of the arabinan component of mycobacterial cell walls may be explained by the fact that about one-third of the pentaarabinosyl units are not mycolyated and are available for interaction with the immune system. On the other hand, the extreme hydrophobicity and impenetrability of the mycobacterial cell may be explained by the same motif also acting as the fulerum for massive esterified paraffin residues. New fundamental information on the structure of mycobacterial cell walls will aid in our comprehension of its impenetrability to antibiotics and role in immunopathogenesis and persistence of disease.
NCBI PubMed ID: 1906464Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523
Methods: GC-MS
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4. Compound ID: 6384
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Mycolic-(1-5)-+
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-b-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ |
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Mycolic-(1-5)-+ | |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-b-D-Araf-(1-5)-a-D-Araf-(1-3)-a-D-Araf-(1-3)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1--/rest of molecule/ |
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Structure type: oligomer
Aglycon: rest of molecule
Contained glycoepitopes: IEDB_159255
The structure is contained in the following publication(s):
- Article ID: 1691
Brennan PJ, Nikaido H "The envelope of mycobacteria" -
Annual Review of Biochemistry 64 (1995) 29-63
Mycobacteria, members of which cause tuberculosis and leprosy, produce cell walls of unusually low permeability, which contribute to their resistance to therapeutic agents. Their cell walls contain large amounts of C60-C90 fatty acids, mycolic acids, that are covalently linked to arabinogalactan. Recent studies clarified the unusual structures of arabinogalactan as well as of extractable cell wall lipids, such as trehalose-based lipooligosaccharides, phenolic glycolipids, and glycopeptidolipids. Most of the hydrocarbon chains of these lipids assemble to produce an asymmetric bilayer of exceptional thickness. Structural considerations suggest that the fluidity is exceptionally low in the innermost part of bilayer, gradually increasing toward the outer surface. Differences in mycolic acid structure may affect the fluidity and permeability of the bilayer, and may explain the different sensitivity levels of various mycobacterial species to lipophilic inhibitors. Hydrophilic nutrients and inhibitors, in contrast, traverse the cell wall presumably through channels of recently discovered porins.
NCBI PubMed ID: 7574484Journal NLM ID: 2985150RInstitutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA
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5. Compound ID: 6394
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Mycolic-(?-5)-+
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Mycolic-(?-5)-b-D-Araf-(1-2)-b-D-Araf-(1-5)-+
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Mycolic-(?-5)-+ |
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Mycolic-(?-5)-b-D-Araf-(1-2)-b-D-Araf-(1-3)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-+
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Mycolic-(?-5)-+ |
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Mycolic-(?-5)-b-D-Araf-(1-2)-b-D-Araf-(1-5)-+ |
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Mycolic-(?-5)-+ | |
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Mycolic-(?-5)-b-D-Araf-(1-2)-b-D-Araf-(1-3)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-3)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-b-D-Araf-(1-5)-D-Ara |
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Structure type: oligomer
Contained glycoepitopes: IEDB_159255,IEDB_581506
The structure is contained in the following publication(s):
- Article ID: 1777
Besra GS, Khoo KH, McNeil MR, Dell A, Morris HR, Brennan PJ "A new interpretation of the structure of the mycolyl-arabinogalactan complex of Mycobacterium tuberculosis as revealed through characterization of oligoglycosylalditol fragments by fast-atom bombardment mass spectrometry and 1H nuclear magnetic resonance spectroscopy" -
Biochemistry 34 (1995) 4257-4266
Previous structural analysis of small oligosaccharide fragments had allowed the recognition of several small structural motifs within arabinogalactan, the dominant cell was structural polysaccharide of Mycobacterium tuberculosis. To determine how these motifs are connected to one another to form the complete polymer, oligosaccharide fragments containing up to 26 glycosyl residues were released by gentle acid hydrolysis of the per-O-methylated arabinogalactan, converted to fully per-O-alkylated oligoglycosylalditols, and purified by high-performance liquid chromatography, and the molecular weights and alkylation patterns of the resultant oligoglycosyl fragments were determined by fast atom bombardment mass spectrometry. The results, combined with previous studies, allowed further understanding of the intricate structural features of the nonreducing ends of arabinogalactan. Thus, the extended nonreducing ends of the arabinan were shown to consist of a tricosaarabinoside (23-mer). We reason that three such arabinan motifs are attached to the homogalactan component or arabinogalactan, which was previously shown to consist of alternating 5- and 6-linked β-D-galactofuranosyl residues. Using the same approach as applied to the arabinan branches, an extended stretch of the galactan was isolated that consisted of at least 23 alternating β-1,6 and β-1,5 D-Galf residues, devoid of any branching, demonstrating that the points of attachment of the arabinan chains to galactan are close to the reducing end of galactan, which itself is linked to peptidoglycan via the linker disaccharide phosphate L-Rhap-(1→3)-α-D-GlcNAc-P. By nuclear magnetic resonance analysis, the L-Rhap was shown to be in the alpha configuration. The long-chain α-alkyl-β-hydroxy mycolic acids, known to occupy the 5-positions of both the terminal β-D-Araf and internal 2-α-D-Araf residues of the terminal branched pentaarabinosyl motif, are now shown to be nonacylated at the beta-hydroxy function. Lack of acylation points to intramolecular hydrogen bonding between the beta-hydroxyl and carbonyl functions of the mycolic acid, providing a highly ordered arrangement of mycolic acids in accord with evolving models of the orientation of the cell wall polymers in mycobacterial cell walls. A revised model is proposed for the composition and orientation of the mycolyl-arabinogalactan in the cell walls of M. tuberculosis, which should increase our understanding of cell wall hydrophobicity, impermeability, and role in disease pathogenesis.
NCBI PubMed ID: 7703239Journal NLM ID: 0370623Publisher: American Chemical Society
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA
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6. Compound ID: 10017
Structure type: oligomer
Trivial name: trehalose dicorynomycolate
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_159255,IEDB_186966,IEDB_742521,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 4171
Datta AK, Takayama K "Isolation and purification of trehalose 6-mono- and 6,6'-di corynomycolates from Corynebacterium matruchotii. Structural characterization by 1H NMR" -
Carbohydrate Research 245 (1993) 151-158
NCBI PubMed ID: 8358747Publication DOI: 10.1016/0008-6215(93)80068-PJournal NLM ID: 0043535Publisher: Elsevier
Institutions: Mycobacteriology Research Laboratory, William S. Middleton Memorial Veterans Hospital, Madison, WI
Methods: 1H NMR, EI-MS, TLC, melting point determination
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7. Compound ID: 10018
Structure type: oligomer
Trivial name: trehalose monocorynomycolate, trehalose monomycolate
Compound class: glycolipid
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_159255,IEDB_186966,IEDB_742521,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 4171
Datta AK, Takayama K "Isolation and purification of trehalose 6-mono- and 6,6'-di corynomycolates from Corynebacterium matruchotii. Structural characterization by 1H NMR" -
Carbohydrate Research 245 (1993) 151-158
NCBI PubMed ID: 8358747Publication DOI: 10.1016/0008-6215(93)80068-PJournal NLM ID: 0043535Publisher: Elsevier
Institutions: Mycobacteriology Research Laboratory, William S. Middleton Memorial Veterans Hospital, Madison, WI
Methods: 1H NMR, EI-MS, TLC, melting point determination
- Article ID: 5612
Kuyukina MS, Ivshina IB, Baeva TA, Kochina OA, Gein SV, Chereshnev VA "Trehalolipid biosurfactants from nonpathogenic Rhodococcus actinobacteria with diverse immunomodulatory activities" -
New Biotechnology 32(6) (2015) 559-568
Actinobacteria of the genus Rhodococcus produce trehalolipid biosurfactants with versatile biochemical properties and low toxicity. In recent years, these biosurfactants are increasingly studied as possible biomedical agents with expressed immunological activities. Applications of trehalolipids from Rhodococcus, predominantly cell-bound, in biomedicine are also attractive because their cost drawback could be less significant for high-value products. The review summarizes recent findings in immunomodulatory activities of trehalolipid biosurfactants from nonpathogenic Rhodococcus and related actinobacteria and compares their biomedical potential with well-known immunomodifying properties of trehalose dimycolates from Mycobacterium tuberculosis. Molecular mechanisms of trehalolipid interactions with immunocompetent cells are also discussed
Rhodococcus, immunological activity, trehalose lipids
NCBI PubMed ID: 25796474Publication DOI: 10.1016/j.nbt.2015.03.006Journal NLM ID: 101465345Publisher: Amsterdam: Elsevier
Correspondence: kuyukina@iegm.ru
Institutions: Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia, Microbiology and Immunology Department, Perm State University, Perm, Russia, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
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8. Compound ID: 11211
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Mycolic-(1-5)-+
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=2/-a-D-Araf-(1-5)-+
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Mycolic-(1-5)-+ |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ |
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Mycolic-(1-5)-+ | |
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Mycolic-(1-5)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=2/-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=13/-+
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/Variants 0/-+ |
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b-D-Galf-(1-5)-{{{-b-D-Galf-(1-6)-b-D-Galf-(1-5)-}}}/n=10/-b-D-Galf-(1-6)-b-D-Galf-(1-5)-{{{-b-D-Galf-(1-6)-b-D-Galf-(1-5)-}}}/n=3/-b-D-Galf-(1-4)-a-L-Rhap-(1-3)-a-D-GlcpNAc-(1---P---/peptidoglycan/
/Variants 0/ is:
Suc-(1-2)-
OR (exclusively)
D-GalpN-(1-2)- |
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Structure type: structural motif or average structure
Aglycon: peptidoglycan
Trivial name: mycolyl arabinogalactan
Compound class: LPS
Contained glycoepitopes: IEDB_136095,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_141807,IEDB_149176,IEDB_150077,IEDB_151531,IEDB_159255,IEDB_190606,IEDB_225177,IEDB_885812,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 4525
Grzegorzewicz AE, Jackson M "Subfractionation and analysis of the cell envelope (lipo)polysaccharides of Mycobacterium tuberculosis" -
Book: Methods in Molecular Biology (2013) Vol. 966, 309-324
The cell envelope of Mycobacterium tuberculosis, the causative agent of tuberculosis in humans, is the source of carbohydrates of exceptional structure which play essential roles in the physiology of the bacterium and in its interactions with the host during infection. Much of what is known about their biosynthesis was derived from the phenotypic analysis of knockout or conditional knockout mutants of mycobacteria generated by random or specific insertional mutagenesis. Here, we describe the current techniques used to subfractionate M. tuberculosis cells and investigate major quantitative and qualitative changes in their cell envelope (lipo)polysaccharides.
capsule, arabinogalactan, lipoarabinomannan, Mycobacterium tuberculosis, glucan, lipomannan
NCBI PubMed ID: 23299743Publication DOI: 10.1007/978-1-62703-245-2_19Publisher: Totowa, NJ: Humana Press
Correspondence: Mary.Jackson@colostate.edu
Editors: Holst O, Walker JM, Beck A
Institutions: Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
Methods: mild acid hydrolysis, alkaline degradation, biochemical methods, HPLC, SDS-Tricine-PAGE
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9. Compound ID: 11284
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Mycolic-(1-?)-+
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Mycolic-(1-?)-a-D-Araf-(1-2)-a-D-Araf-(1-5)-+
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Mycolic-(1-?)-+ | ANY-(1-3)-+ b-D-Galf-(1-6)-+ ANY-(1-4)-+
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Mycolic-(1-?)-a-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}a-D-Araf-(1-5)-b-D-Galf-(1-5)-{{{-b-D-Galf-(1-6)-b-D-Galf-(1-5)-}}}/n=30/-b-D-Galf-(1-6)-b-D-Galf-(1-5)-b-D-Galf-(1-4)-a-L-Rhap-(1-3)-a-D-GlcpNAc-(1--P--6)--b-Murp2Ac-(1-4)-b-D-GlcpNAc-(1--/peptidogycan/
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PEP-(2-8)-+ |
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Structure type: oligomer
Aglycon: peptidogycan
Trivial name: mycolyl arabinogalactan complex
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_136095,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_149176,IEDB_150077,IEDB_151531,IEDB_159255,IEDB_190606,IEDB_225177,IEDB_241115,IEDB_423183,IEDB_885812,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 4551
Knirel YA, Valvano MA "Bacterial polysaccharide structure and biosynthesis" -
Book: Encyclopedia of Biophysics (2013) 162-168
no abstract
carbohydrates, polysaccharide, glycan, extracellular polysaccharide, exoglycan, exopolysaccharide
Publication DOI: 10.1007/978-3-642-16712-6_91Publisher: Springer
Correspondence: knirel@ioc.ac.ru; mvalvano@uwo.ca
Editors: Roberts GCK
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1 Canada
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10. Compound ID: 12879
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b-D-Araf-(1-2)-a-D-Araf-(1-5)-+
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b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-+
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b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ |
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b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=2/-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=12/-a-D-Araf-(1-5)-+
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?%Suc-(1-2)-+ |
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Mycolic-(1-?)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ |
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Mycolic-(1-?)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=2/-a-D-Araf-(1-5)-+ |
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Mycolic-(1-?)-b-D-Araf-(1-2)-a-D-Araf-(1-5)-+ | |
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Mycolic-(1-?)-b-D-Araf-(1-2)-a-D-Araf-(1-3)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=2/-a-D-Araf-(1-3)-a-D-Araf-(1-5)-a-D-Araf-(1-5)-{{{-a-D-Araf-(1-5)-}}}/n=12/-a-D-Araf-(1-5)-+ |
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?%a-D-GalpN-(1-2)-+ | |
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Subst1-(1-?)-Subst2-(1-?)-b-D-Galf-(1-5)-{{{-b-D-Galf-(1-6)-b-D-Galf-(1-5)-}}}/n=2/-b-D-Galf-(1-6)-b-D-Galf-(1-5)-b-D-Galf-(1-6)-b-D-Galf-(1-5)-b-D-Galf-(1-6)-{{{-b-D-Galf-(1-5)-}}}/n=4/-b-D-Galf-(1-5)-b-D-Galf
Subst1 = peptidoglycan;
Subst2 = linker |
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Structure type: structural motif or average structure
Trivial name: arabinogalactan
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_1309625,IEDB_134619,IEDB_136095,IEDB_137472,IEDB_137473,IEDB_149137,IEDB_149176,IEDB_159255,IEDB_190606,IEDB_857717,IEDB_857718,IEDB_857720,IEDB_885812
The structure is contained in the following publication(s):
- Article ID: 5123
Angala SK, Palčeková Z, Belardinelli JM, Jackson M "Covalent modifications of polysaccharides in mycobacteria" -
Nature Chemical Biology 14(3) (2018) 193-198
Mycobacteria produce carbohydrates of exceptional structures that are covalently modified by unique substituents, whose functional characterization could expand our understanding of how mycobacteria adapt to their environment.
polysaccharides, modification, Mycobacteria, covalent, arabinogalactan (AG), lipoarabinomannan (LAM), lipomannan (LM)
NCBI PubMed ID: 29443974Publication DOI: 10.1038/nchembio.2571Journal NLM ID: 101231976Publisher: New York, NY: Nature Publishing Group
Correspondence: Mary.Jackson@ColoState.EDU
Institutions: Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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11. Compound ID: 13562
Structure type: fragment of a bigger structure
Compound class: arabinan
Contained glycoepitopes: IEDB_159255
The structure is contained in the following publication(s):
- Article ID: 5391
Eppe G, El Bkassiny S, Vincent SP "Galactofuranose biosynthesis: discovery, mechanisms and therapeutic relevance" -
Book: Carbohydrates in Drug Design and Discovery(series: RSC Drug Discovery Series) (2015) Vol. 43, Chapter 9, 209-241
Galactofuranose, the atypical and thermodynamically disfavored form of D-galactose, has in reality a very old history in chemistry and biochemistry. Indeed, synthetic methods to produce galactofuranosides selectively date back to the beginning of the 20th century. Moreover, in 1937, Haworth et al. found that the extracellular polysaccharide ‘‘galactocarolose’’ produced by Penicillium charlesii contains galactose in a furanose configuration. The search for biosynthetic precursors rapidly began and, in 1970, it was found that when galactocarolose biosynthesis was inhibited, UDP-galactofuranose (UDP-Galf) accumulated. UDP-Galf was thus identified as a likely biosynthetic precursor of galactofuranosides. One year later, while studying the T1 antigen of Salmonella typhimurium, Nikaido and Sarvas speculated that UDP-galactopyranose (UDP-Galp) was the precursor of UDP-Galf. However, the first gene that, unambiguously, could be attributed to the conversion of UDP-Galp into its furanose form was only identified and cloned in 1996 and the first galactofuranosyltransferase was discovered at the very beginning of the 21st century. As we will detail below, the Galf-processing enzymes happen to proceed through unique or rarely occurring mechanisms. Meanwhile, galactofuranose moieties have also been identified in the cell wall of major pathogens. Therefore, interest into the biosynthesis of galactofuranose and the search for glycomimetics of galactofuranose have grown rapidly in recent years. The purpose of this chapter is to give an overview of the fundamental aspects of the galactofuranose biosynthesis, from the biological occurrence to the search for inhibitors. Several review articles partially covering some aspects of this topic have been published in the literature and will be cited in each paragraph.
biosynthesis, bacteria, galactofuranose, fungi, reaction mechanics
Publication DOI: 10.1039/9781849739993-00209Publisher: Royal Society of Chemistry
Correspondence: stephane.vincent@unamur.be
Editors: Jesús Jiménez-Barbero J, Canada FJ, Martín-Santamaría S
Institutions: University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique, Namur, Belgium
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12. Compound ID: 13566
Structure type: fragment of a bigger structure
Compound class: arabinan
Contained glycoepitopes: IEDB_159255
The structure is contained in the following publication(s):
- Article ID: 5391
Eppe G, El Bkassiny S, Vincent SP "Galactofuranose biosynthesis: discovery, mechanisms and therapeutic relevance" -
Book: Carbohydrates in Drug Design and Discovery(series: RSC Drug Discovery Series) (2015) Vol. 43, Chapter 9, 209-241
Galactofuranose, the atypical and thermodynamically disfavored form of D-galactose, has in reality a very old history in chemistry and biochemistry. Indeed, synthetic methods to produce galactofuranosides selectively date back to the beginning of the 20th century. Moreover, in 1937, Haworth et al. found that the extracellular polysaccharide ‘‘galactocarolose’’ produced by Penicillium charlesii contains galactose in a furanose configuration. The search for biosynthetic precursors rapidly began and, in 1970, it was found that when galactocarolose biosynthesis was inhibited, UDP-galactofuranose (UDP-Galf) accumulated. UDP-Galf was thus identified as a likely biosynthetic precursor of galactofuranosides. One year later, while studying the T1 antigen of Salmonella typhimurium, Nikaido and Sarvas speculated that UDP-galactopyranose (UDP-Galp) was the precursor of UDP-Galf. However, the first gene that, unambiguously, could be attributed to the conversion of UDP-Galp into its furanose form was only identified and cloned in 1996 and the first galactofuranosyltransferase was discovered at the very beginning of the 21st century. As we will detail below, the Galf-processing enzymes happen to proceed through unique or rarely occurring mechanisms. Meanwhile, galactofuranose moieties have also been identified in the cell wall of major pathogens. Therefore, interest into the biosynthesis of galactofuranose and the search for glycomimetics of galactofuranose have grown rapidly in recent years. The purpose of this chapter is to give an overview of the fundamental aspects of the galactofuranose biosynthesis, from the biological occurrence to the search for inhibitors. Several review articles partially covering some aspects of this topic have been published in the literature and will be cited in each paragraph.
biosynthesis, bacteria, galactofuranose, fungi, reaction mechanics
Publication DOI: 10.1039/9781849739993-00209Publisher: Royal Society of Chemistry
Correspondence: stephane.vincent@unamur.be
Editors: Jesús Jiménez-Barbero J, Canada FJ, Martín-Santamaría S
Institutions: University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique, Namur, Belgium
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13. Compound ID: 14249
Structure type: oligomer
Trivial name: trehalose dimycolate
Compound class: glycolipid
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_159255,IEDB_186966,IEDB_742521,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5612
Kuyukina MS, Ivshina IB, Baeva TA, Kochina OA, Gein SV, Chereshnev VA "Trehalolipid biosurfactants from nonpathogenic Rhodococcus actinobacteria with diverse immunomodulatory activities" -
New Biotechnology 32(6) (2015) 559-568
Actinobacteria of the genus Rhodococcus produce trehalolipid biosurfactants with versatile biochemical properties and low toxicity. In recent years, these biosurfactants are increasingly studied as possible biomedical agents with expressed immunological activities. Applications of trehalolipids from Rhodococcus, predominantly cell-bound, in biomedicine are also attractive because their cost drawback could be less significant for high-value products. The review summarizes recent findings in immunomodulatory activities of trehalolipid biosurfactants from nonpathogenic Rhodococcus and related actinobacteria and compares their biomedical potential with well-known immunomodifying properties of trehalose dimycolates from Mycobacterium tuberculosis. Molecular mechanisms of trehalolipid interactions with immunocompetent cells are also discussed
Rhodococcus, immunological activity, trehalose lipids
NCBI PubMed ID: 25796474Publication DOI: 10.1016/j.nbt.2015.03.006Journal NLM ID: 101465345Publisher: Amsterdam: Elsevier
Correspondence: kuyukina@iegm.ru
Institutions: Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia, Microbiology and Immunology Department, Perm State University, Perm, Russia, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Article ID: 5676
Hanashima S, Götze S, Liu Y, Ikeda A, Kojima-Aikawa K, Taniguchi N, Silva DV, Feizi T, Seeberger PH, Yamaguchi Y "Defining the Interaction of human soluble lectin ZG16p and mycobacterial phosphatidylinositol mannosides" -
Chembiochem: a European Journal of Chemical Biology 16(10) (2015) 1502-1511
ZG16p is a soluble mammalian lectin that interacts with mannose and heparan sulfate. Here we describe detailed analysis of the interaction of human ZG16p with mycobacterial phosphatidylinositol mannosides (PIMs) by glycan microarray and NMR. Pathogen-related glycan microarray analysis identified phosphatidylinositol mono- and di-mannosides (PIM1 and PIM2) as novel ligand candidates of ZG16p. Saturation transfer difference (STD) NMR and transferred NOE experiments with chemically synthesized PIM glycans indicate that PIMs preferentially interact with ZG16p by using the mannose residues. The binding site of PIM was identified by chemical-shift perturbation experiments with uniformly 15N-labeled ZG16p. NMR results with docking simulations suggest a binding mode of ZG16p and PIM glycan; this will help to elucidate the physiological role of ZG16p
NMR spectroscopy, chemical synthesis, lectins, carbohydrate microarrays, microarrays, phosphatidyl inositol mannoside
NCBI PubMed ID: 25919894Publication DOI: 10.1002/cbic.201500103Journal NLM ID: 100937360Publisher: Weinheim, Germany: Wiley Interscience
Correspondence: Yamaguchi Y
Institutions: Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany, Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Japan, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany, Glycosciences Laboratory, Department of Medicine, Imperial College London, London, UK, The Glycoscience Institute, Ochanomizu University, Tokyo, Japan, Disease Glycomics Team, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Japan
Methods: 13C NMR, 1H NMR, NMR-2D, DNA cloning, DNA techniques, chemical synthesis, enzymatic digestion, ion-exchange chromatography, molecular modeling, 15N NMR, SEC, CC, binding assays, cell growth, gene expression, sonication, centrifugation
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14. Compound ID: 14250
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Mycolic-(1-6)-+
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Mycolic-(1-3)-+ |
| |
Mycolic-(1-2)-a-D-Glcp-(1-1)-a-D-Glcp |
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Structure type: oligomer
Trivial name: trehalose trimycolate
Compound class: glycolipid
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_159255,IEDB_186966,IEDB_742521,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5612
Kuyukina MS, Ivshina IB, Baeva TA, Kochina OA, Gein SV, Chereshnev VA "Trehalolipid biosurfactants from nonpathogenic Rhodococcus actinobacteria with diverse immunomodulatory activities" -
New Biotechnology 32(6) (2015) 559-568
Actinobacteria of the genus Rhodococcus produce trehalolipid biosurfactants with versatile biochemical properties and low toxicity. In recent years, these biosurfactants are increasingly studied as possible biomedical agents with expressed immunological activities. Applications of trehalolipids from Rhodococcus, predominantly cell-bound, in biomedicine are also attractive because their cost drawback could be less significant for high-value products. The review summarizes recent findings in immunomodulatory activities of trehalolipid biosurfactants from nonpathogenic Rhodococcus and related actinobacteria and compares their biomedical potential with well-known immunomodifying properties of trehalose dimycolates from Mycobacterium tuberculosis. Molecular mechanisms of trehalolipid interactions with immunocompetent cells are also discussed
Rhodococcus, immunological activity, trehalose lipids
NCBI PubMed ID: 25796474Publication DOI: 10.1016/j.nbt.2015.03.006Journal NLM ID: 101465345Publisher: Amsterdam: Elsevier
Correspondence: kuyukina@iegm.ru
Institutions: Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia, Microbiology and Immunology Department, Perm State University, Perm, Russia, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
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15. Compound ID: 14372
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Mycolic-(1-6)-a-D-Glcp
Mycolic = mycolic acid = SMILES CCCCCCCCCCCCCCCCCCCCCCCCC({1}C(=O)O)C(O)CCCCCCCCCCCCCCCCCCCC1CC1CCCCCCCCCCCCCCCCC(=O)C(C)CCCCCCCCCCCCCCCC |
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Structure type: monomer
Compound class: O-antigen, glycolipid
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_159255,IEDB_186966,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5697
Van Rhijn I, Moody DB "CD1 and mycobacterial lipids activate human T cells" -
Immunological Reviews 264(1) (2015) 138-153
For decades, proteins were thought to be the sole or at least the dominant source of antigens for T cells. Studies in the 1990s demonstrated that CD1 proteins and mycobacterial lipids form specific targets of human αβ T cells. The molecular basis by which T-cell receptors (TCRs) recognize CD1-lipid complexes is now well understood. Many types of mycobacterial lipids function as antigens in the CD1 system, and new studies done with CD1 tetramers identify T-cell populations in the blood of tuberculosis patients. In human populations, a fundamental difference between the CD1 and major histocompatibility complex systems is that all humans express nearly identical CD1 proteins. Correspondingly, human CD1 responsive T cells show evidence of conserved TCRs. In addition to natural killer T cells and mucosal-associated invariant T (MAIT cells), conserved TCRs define other subsets of human T cells, including germline-encoded mycolyl-reactive (GEM) T cells. The simple immunogenetics of the CD1 system and new investigative tools to measure T-cell responses in humans now creates a situation in which known lipid antigens can be developed as immunodiagnostic and immunotherapeutic reagents for tuberculosis disease
Mycobacterium tuberculosis, T cells, CD1, T-cell receptor, mycolyl lipids
NCBI PubMed ID: 25703557Publication DOI: 10.1111/imr.12253Journal NLM ID: 7702118Publisher: Oxford: Blackwell
Correspondence: bmoody@partners.org
Institutions: Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, USA, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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