8KAP | pdb_00008kap

Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free)

PDB DOI: https://doi.org/10.2210/pdb8KAP/pdb

Classification: HYDROLASE
Organism(s): Streptomyces griseus subsp. griseus NBRC 13350
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Kumakura, H., Motouchi, S., Nakai, H., Nakajima, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.257 (Depositor), 0.221 (DCC)
R-Value Work:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus.

Kumakura, H., Motouchi, S., Kobayashi, K., Inoue, M., Kariuda, N., Nakai, H., Nakajima, M.

(2025) Protein Sci 34: e70255-e70255

PubMed: 40838837 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70255
Primary Citation Related Structures:
8KAP, 9U98

PubMed Abstract:
β-Glucosidases, major enzymes that release glucose from various natural compounds, are phylogenetically classified into glycoside hydrolase (GH) families. GH1 is the largest of these families. No β-1,2-glucan-associated GH1 enzyme has been found, even though β-1,2-glucans are natural carbohydrates that are important for interaction between organisms and environmental adaptation. In this study, functional and structural analyses of a GH1 enzyme from Streptomyces griseus (SGR_2426 protein) were performed. SGR_2426 showed the highest hydrolytic activity toward p-nitrophenyl β-glucopyranoside among p-nitrophenyl sugars. This enzyme showed hydrolytic activity toward β-1,2-glucooligosaccharides specifically among β-linked glucooligosaccharides. A structure of the enzyme in complex with sophorose (β-1,2-glucodisaccharide) was obtained as a Michaelis complex. The six-membered ring of the glucose unit at the reducing end of sophorose is positioned in a hydrophobic environment between Trp291 and Met171, while only residue Gln229 forms a hydrogen bond directly. Trp291 and Gln229 are proposed as candidates for the residues important for substrate specificity based on comparison with structurally characterized GH1 homologs. Mutational analysis of Trp291 and Gln229 suggested that Trp291 is important for substrate recognition but not for substrate specificity and that Gln229 is involved in substrate specificity. SGR_2426 is the first identified β-1,2-glucan-associated β-glucosidase in the GH1 family.

Organizational Affiliation

Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan.

Macromolecule Content

Total Structure Weight: 184.74 kDa
Atom Count: 12,655
Modeled Residue Count: 1,574
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGR_2426	A, B, C, D	414	Streptomyces griseus subsp. griseus NBRC 13350	Mutation(s): 0 EC: 3.2.1.21
UniProt
Find proteins for B1W1N0 (Streptomyces griseus subsp. griseus (strain JCM 4626 / CBS 651.72 / NBRC 13350 / KCC S-0626 / ISP 5235)) Explore B1W1N0 Go to UniProtKB: B1W1N0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1W1N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth C], M [auth D]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth B] MOL2 format, chain L [auth D] MOL2 format, chain G [auth B] mmCIF format, chain L [auth D] mmCIF format, chain G [auth B]	G [auth B], L [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]