8ZNK | pdb_00008znk

chromone glycosyltransferase (UGT93BB1,SdUGT2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: integrative
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This is version 1.1 of the entry. See complete history


Literature

Complete biosynthetic pathway of furochromones in Saposhnikovia divaricata and its evolutionary mechanism in Apiaceae plants.

Zou, J.L.Li, H.Y.Nie, B.Wang, Z.L.Zhao, C.X.Tian, Y.G.Lin, L.Q.Xu, W.Z.Hou, Z.W.Sun, W.K.Han, X.X.Zhang, M.Wang, H.T.Li, Q.Y.Wang, L.Ye, M.

(2025) Nat Commun 16: 3109-3109

  • DOI: https://doi.org/10.1038/s41467-025-58498-8
  • Primary Citation of Related Structures:  
    8ZNK

  • PubMed Abstract: 

    Furochromones are specific bioactive secondary metabolites of many Apiaceae plants. Their biosynthesis remains largely unexplored. In this work, we dissect the complete biosynthetic pathway of major furochromones in the medicinal plant Saposhnikovia divaricata by characterizing prenyltransferase, peucenin cyclase, methyltransferase, hydroxylase, and glycosyltransferases. De novo biosynthesis of prim-O-glucosylcimifugin and 5-O-methylvisamminoside is realized in Nicotiana benthamiana leaves. Through comparative genomic and transcriptomic analyses, we further find that proximal duplication and high expression of a pentaketide chromone synthase gene SdPCS, together with the presence of a lineage-specific peucenin cyclase gene SdPC, lead to the predominant accumulation of furochromones in the roots of S. divaricata among surveyed Apiaceae plants. This study paves the way for metabolic engineering production of furochromones, and sheds light into evolutionary mechanisms of furochromone biosynthesis among Apiaceae plants.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
chromone glycosyltransferase (UGT93BB1)
A, B
473Saposhnikovia divaricataMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for A0A164WR66 (Daucus carota subsp. sativus)
Explore A0A164WR66 
Go to UniProtKB:  A0A164WR66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A164WR66
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.56α = 90
b = 67.61β = 99.4
c = 93.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2023YFA0914100

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references