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Taxonomic group: bacteria / Actinobacteria (Phylum: Actinobacteria)
Associated disease: infection due to Mycobacterium tuberculosis [ICD11: XN1N2

]

NCBI PubMed ID: 37726269
Publication DOI: 10.1038/s41467-023-41431-2
Journal NLM ID: 101528555
Publisher: London: Nature Publishing Group
Correspondence: S. Fushinobu <asfushi

mail.ecc.u-tokyo.ac.jp>; K. Fujita <k4022897

kadai.jp>
Institutions: Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan, Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan, Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, 278-8510, Japan, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan, Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan, Graduate School of Science, Osaka University, Osaka, 560-0043, Japan, CRIIM, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan

The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of D-arabinose, the enantiomer of the typical L-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-D-arabinanases, GH172 exo-α-D-arabinofuranosidase, and GH116 exo-β-D-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex D-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-D-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these D-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.

characterization, enzyme, Mycobacteria, arabinogalactan, lipoarabinomannan, arabinofuranosidase

Structure type: oligomer
Location inside paper: Fig. 1a
Aglycon: mannan core-phoshatidyl-inositol
Trivial name: mannose-capped lipoarabinomannan (MtLAM)
Contained glycoepitopes: IEDB_130701,IEDB_1309625,IEDB_134619,IEDB_136104,IEDB_140116,IEDB_141830,IEDB_143632,IEDB_144983,IEDB_152206,IEDB_857717,IEDB_857718,IEDB_857720,IEDB_857722,IEDB_857723,IEDB_857726,IEDB_857727,IEDB_857728,IEDB_983930,SB_136,SB_196,SB_44,SB_67,SB_72

Methods: 1H NMR, SDS-PAGE, DNA techniques, TLC, enzymatic degradation, HPLC, electron microscopy, crystallography, enzyme assay, HPAEC-PAD, ESI-TOF-MS, genome sequencing, qPCR RT, SEC-MALS/RI, SEC-SAXS

Related record ID(s): 24841, 24842
NCBI Taxonomy refs (TaxIDs): 1773
Show glycosyltransferases

There is only one chemically distinct structure:

O=C(O)CCC(=O)O[C@@H]1[C@@H](OC[C@H]2O[C@H](OC[C@H]3O[C@H](OC[C@H]4O[C@H](OC[C@H]5O[C@H](OC[C@H]6O[C@H](OC[C@H]7O[C@H](OC[C@H]8O[C@H](OC[C@H]9O[C@H](OC[C@H]%10O[C@H](OC[C@H]%11O[C@H](O)[C@@H](O)[C@@H]%11O)[C@@H](O)[C@@H]%10O)[C@@H](O)[C@@H]9O)[C@@H](O)[C@@H]8O)[C@@H](O)[C@@H]7O)[C@@H](O)[C@@H]6O)[C@@H](O)[C@@H]5O[C@H]5O[C@H](CO[C@H]6O[C@H](CO[C@H]7O[C@H](CO[C@H]8O[C@H](CO[C@H]9O[C@H](CO)[C@@H](O)[C@@H]9O[C@@H]9O[C@H](CO[C@H]%10O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%10O[C@H]%10O[C@H](CO)[C@@H](O[C@H]%11O[C@H](CO)[C@@H](O)[C@@H]%11O)[C@H](O)[C@@H]%10O)[C@@H](O)[C@@H]9O)[C@@H](O[C@H]9O[C@H](CO)[C@@H](O)[C@@H]9O[C@@H]9O[C@H](CO)[C@@H](O)[C@@H]9O)[C@@H]8O)[C@@H](O)[C@@H]7O)[C@@H](O)[C@@H]6O)[C@@H](O)[C@@H]5O)[C@@H](O)[C@@H]4O)[C@@H](O)[C@@H]3O)[C@@H](O)[C@@H]2O)O[C@H](CO[C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O[C@@H]2O[C@H](CO[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@@H]2O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O[C@@H]1O[C@H](CO[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at aDAraf: large unit count (13) was reduced to 5

Taxonomic group: bacteria / Actinobacteria (Phylum: Actinobacteria)

NCBI PubMed ID: 37726269
Publication DOI: 10.1038/s41467-023-41431-2
Journal NLM ID: 101528555
Publisher: London: Nature Publishing Group
Correspondence: S. Fushinobu <asfushi

mail.ecc.u-tokyo.ac.jp>; K. Fujita <k4022897

characterization, enzyme, Mycobacteria, arabinogalactan, lipoarabinomannan, arabinofuranosidase

Structure type: oligomer
Location inside paper: Fig. 2a
Aglycon: mannan core-phoshatidyl-inositol
Trivial name: mannose-capped lipoarabinomannan (MsLAM)
Contained glycoepitopes: IEDB_130701,IEDB_1309625,IEDB_134619,IEDB_144983,IEDB_152206,IEDB_474450,IEDB_857717,IEDB_857718,IEDB_857720,IEDB_857722,IEDB_983930,SB_44,SB_67,SB_72

Methods: 1H NMR, SDS-PAGE, DNA techniques, TLC, enzymatic degradation, HPLC, electron microscopy, crystallography, enzyme assay, HPAEC-PAD, ESI-TOF-MS, genome sequencing, qPCR RT, SEC-MALS/RI, SEC-SAXS

Related record ID(s): 22315, 24842
NCBI Taxonomy refs (TaxIDs): 1772
Show glycosyltransferases

There are 4 chemically distinct structures. Please, select:

[1*]OP(=O)(O)O[C@@H]1[C@@H](OC[C@H]2O[C@@H](O[C@@H]3[C@@H](OC[C@H]4O[C@H](OC[C@H]5O[C@H](OC[C@H]6O[C@H](OC[C@H]7O[C@H](OC[C@H]8O[C@H](OC[C@H]9O[C@H](OC[C@H]%10O[C@H](OC[C@H]%11O[C@H](OC[C@H]%12O[C@H](OC[C@H]%13O[C@H](OC[C@H]%14O[C@H](O)[C@@H](O)[C@@H]%14O)[C@@H](O)[C@@H]%13O)[C@@H](O)[C@@H]%12O)[C@@H](O)[C@@H]%11O)[C@@H](O)[C@@H]%10O)[C@@H](O)[C@@H]9O)[C@@H](O)[C@@H]8O[C@H]8O[C@H](CO[C@H]9O[C@H](CO[C@H]%10O[C@H](CO[C@H]%11O[C@H](CO[C@H]%12O[C@H](CO)[C@@H](O)[C@@H]%12O[C@@H]%12O[C@H](CO)[C@@H](O)[C@@H]%12O)[C@@H](O[C@H]%12O[C@H](CO)[C@@H](O)[C@@H]%12O[C@@H]%12O[C@H](CO)[C@@H](O)[C@@H]%12O)[C@@H]%11O)[C@@H](O)[C@@H]%10O)[C@@H](O)[C@@H]9O)[C@@H](O)[C@@H]8O)[C@@H](O)[C@@H]7O)[C@@H](O)[C@@H]6O)[C@@H](O)[C@@H]5O)[C@@H](OC(=O)CCC(=O)O)[C@@H]4O[C@H]4O[C@H](CO)[C@@H](O)[C@@H]4O[C@@H]4O[C@H](CO)[C@@H](O)[C@@H]4O)O[C@H](CO)[C@H]3O)[C@@H](O)[C@@H]2O)O[C@H](CO)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

R1 = INO
Warning = sub-repeat ending at aDAraf: large unit count (13) was reduced to 5

mail.ecc.u-tokyo.ac.jp>; K. Fujita <k4022897

characterization, enzyme, Mycobacteria, arabinogalactan, lipoarabinomannan, arabinofuranosidase

Structure type: oligomer
Location inside paper: Fig. 3a
Aglycon: galactan-linker-peptidoglycan
Trivial name: arabinogalactan (MsAG)
Contained glycoepitopes: IEDB_1309625,IEDB_134619,IEDB_137473,IEDB_159255,IEDB_857717,IEDB_857718,IEDB_857720

Methods: 1H NMR, SDS-PAGE, DNA techniques, TLC, enzymatic degradation, HPLC, electron microscopy, crystallography, enzyme assay, HPAEC-PAD, ESI-TOF-MS, genome sequencing, qPCR RT, SEC-MALS/RI, SEC-SAXS

Related record ID(s): 22315, 24841
NCBI Taxonomy refs (TaxIDs): 1772
Show glycosyltransferases

There are 81 chemically distinct structures. Please, select:

CCCCCCCCCCCCCCCC(O)C(CCCCCCCCCCCCCC)C(=O)O[C@@H]1[C@H](O[C@@H]2[C@@H](OC[C@H]3O[C@H](OC[C@H]4O[C@H](OC[C@H]5O[C@H](OC[C@H]6O[C@H](OC[C@H]7O[C@H](OC[C@H]8O[C@H](OC[C@H]9O[C@H](OC[C@H]%10O[C@H](OC[C@H]%11O[C@H](OC[C@H]%12O[C@H](OC[C@H]%13O[C@H](O)[C@@H](O)[C@@H]%13O)[C@@H](O)[C@@H]%12O)[C@@H](O)[C@@H]%11O)[C@@H](O)[C@@H]%10O)[C@@H](O)[C@@H]9O)[C@@H](O)[C@@H]8O)[C@@H](O)[C@@H]7O[C@H]7O[C@H](CO[C@H]8O[C@H](CO[C@H]9O[C@H](CO[C@H]%10O[C@H](CO[C@H]%11O[C@H](CO)[C@@H](O)[C@@H]%11O[C@@H]%11O[C@H](CO)[C@@H](O)[C@@H]%11OC(=O)C(CCCCCCCCCCCCCC)C(O)CCCCCCCCCCCCCCC)[C@@H](O[C@H]%11O[C@H](CO)[C@@H](O)[C@@H]%11O[C@@H]%11O[C@H](CO)[C@@H](O)[C@@H]%11OC(=O)C(CCCCCCCCCCCCCC)C(O)CCCCCCCCCCCCCCC)[C@@H]%10O[C@H]%10O[C@H](CO)[C@H](O)[C@H](O)[C@H]%10N)[C@@H](O)[C@@H]9O)[C@@H](O)[C@@H]8O)[C@@H](O)[C@@H]7O)[C@@H](O)[C@@H]6O)[C@@H](O)[C@@H]5O)[C@@H](O)[C@@H]4O)[C@@H](OC(=O)CCC(=O)O)[C@@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@@H]3O[C@@H]3O[C@H](CO)[C@@H](O)[C@@H]3OC(=O)C(CCCCCCCCCCCCCC)C(O)CCCCCCCCCCCCCCC)O[C@H](CO)[C@H]2O)O[C@H](CO)[C@H]1O

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at aDAraf: large unit count (13) was reduced to 5