8IC8

Exo-alpha-D-arabinofuranosidase from Microbacterium arabinogalactanolyticum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.

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.

(2023) Nat Commun 14: 5803-5803

  • DOI: https://doi.org/10.1038/s41467-023-41431-2
  • Primary Citation of Related Structures:  
    8HHV, 8IC1, 8IC6, 8IC7, 8IC8

  • 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.


  • Organizational Affiliation

    Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exo-alpha-D-arabinofuranosidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
378Microbacterium arabinogalactanolyticumMutation(s): 0 
Gene Names: BGN97_09235
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.109α = 90
b = 207.538β = 90
c = 253.88γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
BUCCANEERmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H00929
Japan Society for the Promotion of Science (JSPS)Japan15H02443
Japan Society for the Promotion of Science (JSPS)Japan26660083
Japan Society for the Promotion of Science (JSPS)Japan24380053

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Database references