9L3P | pdb_00009l3p

Crystal structure of endo-processive xyloglucanase Xeg5A E285A from Aspergillus oryzae with GLLX/L

• PDB DOI: https://doi.org/10.2210/pdb9L3P/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2024-12-19 Released: 2025-06-25 
• Deposition Author(s): Nakamichi, Y., Shimada, N., Watanabe, M., Fujii, T., Matsuzawa, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structural insights into substrate recognition of tri-modular xyloglucanase from Aspergillus oryzae.

Nakamichi, Y., Shimada, N., Watanabe, M., Fujii, T., Yaoi, K., Matsuzawa, T.

(2025) J Struct Biol 217: 108213-108213

• PubMed: 40414580 
• DOI: https://doi.org/10.1016/j.jsb.2025.108213
• Primary Citation Related Structures: 
  9L3D, 9L3J, 9L3O, 9L3P


• PubMed Abstract: 
  

  Xeg5A from Aspergillus oryzae belongs to glycoside hydrolase family 5 subfamily 4. This enzyme has been characterized as a xyloglucan-specific endo-β-1,4-glucanase (xyloglucanase) that cleaves the main chain of xyloglucan at both unbranched and xylosylated glucosyl residues in an endo-processive mode of action. X-ray crystallography revealed that Xeg5A is a tri-modular enzyme composed of a catalytic, an Ig-like, and a C-terminal CBM46-like domains. Xeg5A structures complexed with branched xyloglucan oligosaccharides at subsites -4 to +4 showed that the recognition of xyloglucan side-chain moieties is important for Xeg5A activity. The crystal structure also provided structural insights into the role of the CBM46-like domain in contributing to regiospecificity and, possibly, processivity.

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Organizational Affiliation: 
• Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kita-gun, Kagawa 761-0701, Japan.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kita-gun, Kagawa 761-0701, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.91 kDa 
• Atom Count: 4,671 
• Modeled Residue Count: 549 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase superfamily	A	648	Aspergillus oryzae RIB40	Mutation(s): 1  Gene Names: Ao3042_05083
UniProt
Find proteins for I8IVP5 (Aspergillus oryzae (strain 3.042)) Explore I8IVP5  Go to UniProtKB:  I8IVP5
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G10756ZZ GlyCosmos: G10756ZZ GlyGen: G10756ZZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G01760ZU GlyCosmos: G01760ZU GlyGen: G01760ZU

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose	D	9		N/A

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose	E	3		N/A
Glycosylation Resources
GlyTouCan: G95959IY GlyCosmos: G95959IY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	H [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.596	α = 90
b = 116.463	β = 90
c = 105.418	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Nakamichi, Y., Shimada, N., Watanabe, M., Fujii, T., Matsuzawa, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release