9L3O | pdb_00009l3o

Crystal structure of endo-processive xyloglucanase Xeg5A from Aspergillus oryzae with XXLG

PDB DOI: https://doi.org/10.2210/pdb9L3O/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae RIB40
Expression System: Komagataella pastoris
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2025.108213
Primary Citation of 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.

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.

Macromolecule Content

Total Structure Weight: 155.23 kDa
Atom Count: 9,964
Modeled Residue Count: 1,100
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase superfamily	A, B	648	Aspergillus oryzae RIB40	Mutation(s): 0 Gene Names: Ao3042_05083
UniProt
Find proteins for I8IVP5 (Aspergillus oryzae (strain 3.042)) Explore I8IVP5 Go to UniProtKB: I8IVP5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I8IVP5
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	C, F	10		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G27421EI GlyCosmos: G27421EI GlyGen: G27421EI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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	D, H	7		N-Glycosylation	Interactions Focus chain D Focus chain H Interactions & Density Focus chain D Focus chain H
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E	8		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G18071YH GlyCosmos: G18071YH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J	3		N-Glycosylation	Interactions Focus chain G Focus chain J Interactions & Density Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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)-beta-D-glucopyranose	I	7		N/A	Interactions Focus chain I Interactions & Density Focus chain I

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	M [auth A] N [auth A] O [auth A] P [auth A] U [auth B] M [auth A], N [auth A], O [auth A], P [auth A], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain X [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain X [auth B]	Q [auth A], X [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain Q [auth A] Focus chain X [auth B] Interactions & Density Focus chain Q [auth A] Focus chain X [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	L [auth A], T [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain T [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	R [auth A], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain S [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain S [auth A]	AA [auth B], S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain S [auth A] Interactions & Density Focus chain AA [auth B] Focus chain S [auth A]