8INH | pdb_00008inh

ZjOGT3, flavonoid 7,4'-di-O-glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb8INH/pdb

• Classification: PLANT PROTEIN
• Organism(s): Ziziphus jujuba var. spinosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-09 Released: 2023-04-19 
• Deposition Author(s): Wang, Z.L., Wang, H.D., Li, F.D., Ye, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Functional characterization, structural basis, and regio-selectivity control of a promiscuous flavonoid 7,4'-di- O -glycosyltransferase from Ziziphus jujuba var. spinosa.

Wang, Z.L., Wei, W., Wang, H.D., Zhou, J.J., Wang, H.T., Chen, K., Wang, R.S., Li, F.D., Qiao, X., Zhou, H., Liang, Y., Ye, M.

(2023) Chem Sci 14: 4418-4425

• PubMed: 37123177 
• DOI: https://doi.org/10.1039/d2sc06504e
• Primary Citation Related Structures: 
  8INH


• PubMed Abstract: 
  

  A highly efficient and promiscuous 7,4'-di- O -glycosyltransferase ZjOGT3 was discovered from the medicinal plant Ziziphus jujuba var. spinosa . ZjOGT3 could sequentially catalyse 4'- and 7- O -glycosylation of flavones to produce 7,4'-di- O -glycosides with obvious regio-selectivity. For 7,4'-dihydroxyl flavanones and 3- O -glycosylated 7,4'-dihydroxyl flavones, ZjOGT3 selectively catalyses 7- O -glycosylation. The crystal structure of ZjOGT3 was solved. Structural analysis, DFT calculations, MD simulations, and site-directed mutagenesis reveal that the regio-selectivity is mainly controlled by the enzyme microenvironment for 7,4'-dihydroxyl flavones and 3- O -glycosylated 7,4'-dihydroxyl flavones. For 7,4'-dihydroxyl flavanones, the selectivity is mainly controlled by intrinsic reactivity. ZjOGT3 is the first plant flavonoid 7,4'-di- O -glycosyltransferase with a crystal structure. This work could help understand the catalytic mechanisms of multi-site glycosyltransferases and provides an efficient approach to synthesise O -glycosides with medicinal potential.

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Organizational Affiliation: 
• State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University 38 Xueyuan Road Beijing 100191 China [e-mail].
State Key Laboratory of Food Science and Technology, Jiangnan University Wuxi 214122 China.
Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China Hefei 230036 China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences 239 Zhangheng Road, Pudong District Shanghai 201204 China [e-mail].
State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.04 kDa 
• Atom Count: 7,211 
• Modeled Residue Count: 908 
• Deposited Residue Count: 958 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A [auth B], B [auth A]	479	Ziziphus jujuba var. spinosa	Mutation(s): 0  Gene Names: FEM48_Zijuj09G0128800 EC: 2.4.1
UniProt
Find proteins for A0A978UT44 (Ziziphus jujuba var. spinosa) Explore A0A978UT44  Go to UniProtKB:  A0A978UT44

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth B], D [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.73	α = 90
b = 84.81	β = 93.33
c = 103.63	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Wang, Z.L., Wang, H.D., Li, F.D., Ye, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81725023

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary