8H25 | pdb_00008h25

Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

PDB DOI: https://doi.org/10.2210/pdb8H25/pdb

Classification: HYDROLASE
Organism(s): Lacticaseibacillus casei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-04 Released: 2023-08-16
Deposition Author(s): Saburi, W., Ota, T., Kato, K., Tagami, T., Yamashita, K., Yao, M., Mori, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.232 (Depositor), 0.210 (DCC)
R-Value Work:
0.195 (Depositor), 0.179 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Function and Structure of Lacticaseibacillus casei GH35 beta-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N -biose I and Galacto- N -biose.

Saburi, W., Ota, T., Kato, K., Tagami, T., Yamashita, K., Yao, M., Mori, H.

(2023) J Appl Glycosci (1999) 70: 43-52

PubMed: 37599861 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.5458/jag.jag.JAG-2022_0014
Primary Citation Related Structures:
8H25

PubMed Abstract:
β-Galactosidase (EC 3.2.1.23) hydrolyzes β-D-galactosidic linkages at the non-reducing end of substrates to produce β-D-galactose. Lacticaseibacillus casei is one of the most widely utilized probiotic species of lactobacilli. It possesses a putative β-galactosidase belonging to glycoside hydrolase family 35 (GH35). This enzyme is encoded by the gene included in the gene cluster for utilization of lacto- N -biose I (LNB; Galβ1-3GlcNAc) and galacto- N -biose (GNB; Galβ1-3GalNAc) via the phosphoenolpyruvate: sugar phosphotransferase system. The GH35 protein (GnbG) from L. casei BL23 is predicted to be 6-phospho-β-galactosidase (EC 3.2.1.85). However, its 6-phospho-β-galactosidase activity has not yet been examined, whereas its hydrolytic activity against LNB and GNB has been demonstrated. In this study, L. casei JCM1134 LBCZ_0230, homologous to GnbG, was characterized enzymatically and structurally. A recombinant LBCZ_0230, produced in Escherichia coli , exhibited high hydrolytic activity toward o -nitrophenyl β-D-galactopyranoside, p -nitrophenyl β-D-galactopyranoside, LNB, and GNB, but not toward o -nitrophenyl 6-phospho-β-D-galactopyranoside. Crystal structure analysis indicates that the structure of subsite -1 of LBCZ_0230 is very similar to that of Streptococcus pneumoniae β-galactosidase BgaC and not suitable for binding to 6-phospho-β-D-galactopyranoside. These biochemical and structural analyses indicate that LBCZ_0230 is a β-galactosidase. According to the prediction of LNB's binding mode, aromatic residues, Trp190, Trp240, Trp243, Phe244, and Tyr458, form hydrophobic interactions with N -acetyl-D-glucosamine residue of LNB at subsite +1.

Organizational Affiliation

1 Research Faculty of Agriculture, Hokkaido University.

Macromolecule Content

Total Structure Weight: 277.08 kDa
Atom Count: 19,500
Modeled Residue Count: 2,368
Deposited Residue Count: 2,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	604	Lacticaseibacillus casei	Mutation(s): 0 Gene Names: FEI12_08385

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C], M [auth C], O [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain K [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth C] E [auth A], F [auth A], G [auth A], H [auth A], K [auth C], N [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]