9X1I | pdb_00009x1i

Structure of endo-beta-N-acetylglucosaminidase HS

PDB DOI: https://doi.org/10.2210/pdb9X1I/pdb

Classification: HYDROLASE
Organism(s): human oral metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-02 Released: 2026-03-18
Deposition Author(s): Kurauchi, I., Okura, K., Hosokawa, C., Ito, K., Miyahra, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of endo-beta-N-acetylglucosaminidase HS alpha.

Kurauchi, I., Okura, K., Hosokawa, C., Ito, K., Miyahara, I.

(2026) Acta Crystallogr F Struct Biol Commun 82: 94-100

PubMed: 41784007 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X26001214
Primary Citation Related Structures:
9X1I

PubMed Abstract:
The crystal structure of endo-β-N-acetylglucosaminidase HSα (Endo HSα) was determined at 1.8 Å resolution, revealing that the enzyme is composed of five distinct domains. Domains I to III adopt a fold that is conserved among GH85 enzymes, with catalytic residues Asn216, Glu218 and Tyr252 corresponding to conserved positions, while Tyr282 is newly implicated in catalysis based on the Endo HSα structure. A long loop unique to Endo HSα constricts the active site in domain I. Domain IV represents a novel structural element that is not observed in other GH85 enzymes. Its glycan-binding model and structural similarity to known sugar-binding domains play a role in substrate recognition. The minimal contacts with other domains allow it to remain flexible, accommodating bulky substrates at the active site. These features provide insights into the structural basis for substrate specificity and expand the structural diversity of the GH85 family.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.

Macromolecule Content

Total Structure Weight: 218.59 kDa
Atom Count: 17,463
Modeled Residue Count: 1,944
Deposited Residue Count: 1,962
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-N-acetylglucosaminidase HS	A, B	981	human oral metagenome	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]