8XUL | pdb_00008xul

Structure of beta-1,2-glucanase from Xanthomonas campestris pv. campestris (beta-1,2-glucoheptasaccharide complex)-E239Q mutant

• PDB DOI: https://doi.org/10.2210/pdb8XUL/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.50 Å
• R-Value Free: 
  0.365 (Depositor), 0.368 (DCC) 
• R-Value Work: 
  0.338 (Depositor), 0.342 (DCC) 

Starting Model: in silico

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 (software)

Macromolecule Content 

• Total Structure Weight: 62.86 kDa 
• Atom Count: 3,720 
• Modeled Residue Count: 442 
• Deposited Residue Count: 539 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XCC2207	A	539	Xanthomonas campestris pv. campestris	Mutation(s): 2  Gene Names: D0A39_03385
UniProt
Find proteins for Q8P8N3 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P8N3  Go to UniProtKB:  Q8P8N3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan: G19333TK GlyCosmos: G19333TK GlyGen: G19333TK

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.365 (Depositor), 0.368 (DCC) 
• R-Value Work:  0.338 (Depositor), 0.342 (DCC) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.178	α = 90
b = 220.178	β = 90
c = 220.178	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	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