8XUK | pdb_00008xuk

Structure of beta-1,2-glucanase from Photobacterium gaetbulicola (PgSGL3, ligand-free)

• PDB DOI: https://doi.org/10.2210/pdb8XUK/pdb

• Classification: HYDROLASE
• Organism(s): Photobacterium gaetbulicola Gung47
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-13 Released: 2025-01-22 
• Deposition Author(s): Nakajima, M., Motouchi, S., Nakai, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.201 (DCC) 

Literature

New glycoside hydrolase families of beta-1,2-glucanases.

Nakajima, M., Tanaka, N., Motouchi, S., Kobayashi, K., Shimizu, H., Abe, K., Hosoyamada, N., Abara, N., Morimoto, N., Hiramoto, N., Nakata, R., Takashima, A., Hosoki, M., Suzuki, S., Shikano, K., Fujimaru, T., Imagawa, S., Kawadai, Y., Wang, Z., Kitano, Y., Nihira, T., Nakai, H., Taguchi, H.

(2025) Protein Sci 34: e70147-e70147

• PubMed: 40411428 
• DOI: https://doi.org/10.1002/pro.70147
• Primary Citation Related Structures: 
  8XUJ, 8XUK, 8XUL


• PubMed Abstract: 
  

  β-1,2-Glucans are natural glucose polymers produced by bacteria and play important physiological roles, including as symbiotic or pathogenic factors and in osmoregulation. Glycoside hydrolase (GH) families related to β-1,2-glucan metabolism (GH144, GH162, and GH189) have recently been created by identification of two β-1,2-glucanases and a β-1,2-glucanotransferase, respectively. In this study, we further found four phylogenetically new groups with unknown functions (Groups 1-4) by sequence database analysis using enzymes from GH144 and GH162 as queries. Biochemical analysis of representative proteins in these groups revealed that the proteins in Groups 1-3 showed hydrolytic activity specific to β-1,2-glucan, while no substrate was found for the Group 4 protein. The kinetic parameters of the enzymes of Groups 1-3 were similar to GH144 and GH162 β-1,2-glucanases, indicating that these enzymes were β-1,2-glucanases. Optical rotation analysis revealed that the β-1,2-glucanases followed an anomer-inverting mechanism. Structural analysis of the proteins in Groups 1-4 revealed that they possess (α/α) ₆ -barrel folds similar to those of GH144, GH162, and GH189 enzymes. Comparison of spatial positions of predicted acidic catalytic residues suggested that Groups 1-3 and GH144 had the same reaction mechanism. Overall, phylogenetic, biochemical, and structural analyses revealed that Groups 1-3 are new GH families, GH192, GH193, and GH194, respectively, and that the three families belong to clan GH-S (clan GH, classification based on structural similarity) as GH144 and GH162.

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Organizational Affiliation: 
• Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Faculty of Agriculture, Niigata University, Niigata, Niigata, Japan.
Faculty of Engineering, Niigata Institute of Technology, Kashiwazaki, Niigata, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.06 kDa 
• Atom Count: 3,819 
• Modeled Residue Count: 420 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H744_1c0222	A	428	Photobacterium gaetbulicola Gung47	Mutation(s): 0  Gene Names: H744_1c0222
UniProt
Find proteins for A0A0C5WDX4 (Photobacterium gaetbulicola Gung47) Explore A0A0C5WDX4  Go to UniProtKB:  A0A0C5WDX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.201 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.284	α = 90
b = 76.595	β = 90
c = 94.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Nakajima, M., Motouchi, S., Nakai, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23K05041

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-08-06
  Changes: Database references