8IC6

exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris

Summary for 8IC6

• Entry DOI: 10.2210/pdb8ic6/pdb
• Descriptor: exo-beta-D-arabinanase, MAGNESIUM ION, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (7 entities in total)
• Functional Keywords: glycoside hydrolase, hydrolase
• Biological source: Microbacterium arabinogalactanolyticum
• Total number of polymer chains: 2
• Total formula weight: 191592.59

Authors

Fukushima, R.,Kashima, T.,Ishiwata, A.,Fujita, K.,Fushinobu, S. (deposition date: 2023-02-10, release date: 2023-08-16, Last modification date: 2023-09-27)

Primary citation

Shimokawa, M.,Ishiwata, A.,Kashima, T.,Nakashima, C.,Li, J.,Fukushima, R.,Sawai, N.,Nakamori, M.,Tanaka, Y.,Kudo, A.,Morikami, S.,Iwanaga, N.,Akai, G.,Shimizu, N.,Arakawa, T.,Yamada, C.,Kitahara, K.,Tanaka, K.,Ito, Y.,Fushinobu, S.,Fujita, K.
Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.
Nat Commun, 14:5803-5803, 2023

PubMed Abstract: 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.

PubMed: 37726269
DOI: 10.1038/s41467-023-41431-2

Experimental method

X-RAY DIFFRACTION (1.75 Å)