8OUG | pdb_00008oug

Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus

PDB DOI: https://doi.org/10.2210/pdb8OUG/pdb

Classification: HYDROLASE
Organism(s): Thermococcus chitonophagus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-22 Released: 2024-05-01
Deposition Author(s): Rypniewski, W., Biniek-Antosiak, K., Bejger, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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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

Crystal structure, thermostability and temperature-dependent enzymatic activity of an exo-beta-d-glucosaminidase from Pyrococcus chitonophagus.

Biniek-Antosiak, K., Baranowski, D., Sliwiak, J., Milik, M., Bejger, M., Rypniewski, W.

(2026) J Struct Biol : 108327-108327

PubMed: 42177926 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2026.108327
Primary Citation Related Structures:
8OUG

PubMed Abstract:
Pch-GlmA is a hyperthermophilic GH35 exo-β-d-glucosaminidase whose structure closely resembles its archaeal homologs, yet its functional behavior differs markedly. Calorimetric and fluorimetric temperature scans consistently reveal a complex thermodynamic profile of the enzyme, characterized by distinct thermal transitions. The freshly purified protein appears to be monomeric and required thermal annealing to attain its biologically relevant dimeric state. Catalytic activity is observed only above 75 °C, where the enzyme specifically hydrolyses the glycosidic bond of GlcN-GlcNAc. These findings support a sequential role for Pch-GlmA alongside Pch-Dac in the processing of chitin-derived carbohydrates. Comparison with related GlmA proteins demonstrates that substantial structural similarity does not necessarily translate into equivalent enzymatic properties and that hyperthermophilic enzymes may operate within narrow temperature ranges. Overall, this work underscores the importance of experimental validation when interpreting or predicting the activity of enzymes derived from extremophiles.

Organizational Affiliation

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland.

Macromolecule Content

Total Structure Weight: 92.92 kDa
Atom Count: 6,769
Modeled Residue Count: 780
Deposited Residue Count: 781
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	781	Thermococcus chitonophagus	Mutation(s): 0 Gene Names: A3L04_10820 EC: 3.2.1.23
UniProt
Find proteins for A0A160VTD9 (Thermococcus chitonophagus) Explore A0A160VTD9 Go to UniProtKB: A0A160VTD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A160VTD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain V [auth A] SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain CA [auth A] SDF format, chain B [auth A] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain B [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain V [auth A] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain B [auth A] mmCIF format, chain AA [auth A]	AA [auth A] B [auth A] BA [auth A] C [auth A] CA [auth A] AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] 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] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] 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] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]