8IC7 | pdb_00008ic7

exo-beta-D-arabinofuranosidase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with beta-D-arabinofuranose

PDB DOI: https://doi.org/10.2210/pdb8IC7/pdb

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

Deposited: 2023-02-11 Released: 2023-08-16
Deposition Author(s): Fukushima, R., Kashima, T., Ishiwata, A., Fujita, K., Fushinobu, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.182 (Depositor), 0.183 (DCC)
R-Value Work:
0.159 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 37726269 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 191.83 kDa
Atom Count: 14,948
Modeled Residue Count: 1,708
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exo-beta-D-arabinofuranosidase	A [auth B], B [auth A]	867	Microbacterium arabinogalactanolyticum	Mutation(s): 0 Gene Names: MIAR_33170
UniProt
Find proteins for A0AAJ6N6D6 (Microbacterium arabinogalactanolyticum) Explore A0AAJ6N6D6 Go to UniProtKB: A0AAJ6N6D6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAJ6N6D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BXX (Subject of Investigation/LOI) Query on BXX Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Y [auth A] SDF format, chain P [auth B] SDF format, chain AA [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain P [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain P [auth B] mmCIF format, chain AA [auth A]	AA [auth A], M [auth B], N [auth B], P [auth B], Y [auth A]	beta-D-arabinofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-SQOUGZDYSA-N		Interactions Focus chain AA [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Y [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain O [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain O [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain O [auth B]	O [auth B], Z [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain O [auth B] Focus chain Z [auth A] Interactions & Density Focus chain O [auth B] Focus chain Z [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain X [auth A] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain X [auth A] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain X [auth A] mmCIF format, chain L [auth B]	K [auth B], L [auth B], X [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain X [auth A] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain X [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain J [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.182 (Depositor), 0.183 (DCC)
R-Value Work: 0.159 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.763	α = 90
b = 97.249	β = 101.25
c = 139.681	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

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