8IC1 | pdb_00008ic1

endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides

• PDB DOI: https://doi.org/10.2210/pdb8IC1/pdb

• Classification: HYDROLASE
• Organism(s): Microbacterium arabinogalactanolyticum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-10 Released: 2023-08-16 
• Deposition Author(s): Li, J., Nakashima, C., Ishiwata, A., Fujita, K., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.159 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

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

• PubMed: 37726269 
• DOI: https://doi.org/10.1038/s41467-023-41431-2
• Primary Citation 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.

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Organizational Affiliation: 
• 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.
Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan. [e-mail].
CRIIM, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan. [e-mail].
Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 221.46 kDa 
• Atom Count: 16,610 
• Modeled Residue Count: 1,916 
• Deposited Residue Count: 1,952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endo-alpha-D-arabinanase	A, B, C, D	488	Microbacterium arabinogalactanolyticum	Mutation(s): 0  Gene Names: MIAR_33230
UniProt
Find proteins for A0AAJ6N6D4 (Microbacterium arabinogalactanolyticum) Explore A0AAJ6N6D4  Go to UniProtKB:  A0AAJ6N6D4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose	E, I	4		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose	F, G, H, J	3		N/A
Glycosylation Resources
GlyTouCan: G28026DF GlyCosmos: G28026DF

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	W [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
OYO (Subject of Investigation/LOI)	BA [auth B], LA [auth C], R [auth A], UA [auth D]	(3~{a}~{S},5~{R},6~{R},6~{a}~{S})-5-(hydroxymethyl)-2,2-dimethyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]dioxol-6-ol C8 H14 O5 JAUQZVBVVJJRKM-JWXFUTCRSA-N
PGE	EA [auth C], L [auth A], M [auth A], NA [auth D], T [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	FA [auth C], GA [auth C], N [auth A], PA [auth D], QA [auth D], X [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth B], CA [auth B], DA [auth C], HA [auth C], K [auth A], KA [auth C], MA [auth D], OA [auth D], Q [auth A], S [auth B], TA [auth D], U [auth B], V [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	JA [auth C], P [auth A], SA [auth D], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	IA [auth C], O [auth A], RA [auth D], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.159 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.708	α = 90
b = 137.731	β = 90
c = 148.589	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Li, J., Nakashima, C., Ishiwata, A., Fujita, K., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15H02443
Japan Society for the Promotion of Science (JSPS)	Japan	26660083
Japan Society for the Promotion of Science (JSPS)	Japan	24380053

Revision History  

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