8X18 | pdb_00008x18

Xanthomonas campestris pv. campestris OpgD mutant-D379N with beta-1,2-glucan

• PDB DOI: https://doi.org/10.2210/pdb8X18/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-11-06 Released: 2024-11-06 
• Deposition Author(s): Motouchi, S., Nakajima, M.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.176 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 

Starting Model: in silico

Literature

Discovery of Anomer-Inverting Transglycosylase: Cyclic Glucohexadecaose-Producing Enzyme from Xanthomonas , a Phytopathogen.

Motouchi, S., Komba, S., Nakai, H., Nakajima, M.

(2024) J Am Chem Soc 146: 17738-17746

• PubMed: 38957137 
• DOI: https://doi.org/10.1021/jacs.4c02579
• Primary Citation of Related Structures:  
  8X18


• PubMed Abstract: 
  

  Various Xanthomonas species cause well-known plant diseases. Among various pathogenic factors, the role of α-1,6-cyclized β-1,2-glucohexadecaose (CβG16α) produced by Xanthomonas campestris pv. campestris was previously shown to be vital for infecting model organisms, Arabidopsis thaliana and Nicotiana benthamiana . However, enzymes responsible for biosynthesizing CβG16α are essentially unknown, which limits the generation of agrichemicals that inhibit CβG16α synthesis. In this study, we discovered that OpgD from X. campestris pv. campestris converts linear β-1,2-glucan to CβG16α. Structural and functional analyses revealed OpgD from X. campestris pv. campestris possesses an anomer-inverting transglycosylation mechanism, which is unprecedented among glycoside hydrolase family enzymes.

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Organizational Affiliation: 
• Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
Division of Food Processing and Biomaterials Biomaterials Development Group, Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 129.56 kDa 
• Atom Count: 9,012 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,082 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucans biosynthesis protein D	A, B	541	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1  Gene Names: opgD
UniProt
Find proteins for Q8P3C6 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P3C6  Go to UniProtKB:  Q8P3C6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(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-(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-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	C	22		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	D	11		N/A

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	E	10		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.176 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.878	α = 90
b = 171.878	β = 90
c = 128.691	γ = 120

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: 2024-11-06 
Deposition Author(s): Motouchi, S., Nakajima, M.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJSP2151

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Database references
• Version 1.2: 2025-05-28
  Changes: Database references