9UF7 | pdb_00009uf7

Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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Literature

Structural insights into the catalytic mechanism of the phenylethanoid glycoside rhamnosyltransferase UGT79G15 from Rehmannia glutinosa.

Ma, R.Wei, H.Zhuang, Y.Wu, Y.Li, Z.Chen, Y.Huang, J.Yan, X.Liu, W.Liu, T.

(2025) Plant Commun 6: 101539-101539

  • DOI: https://doi.org/10.1016/j.xplc.2025.101539
  • Primary Citation Related Structures: 
    9UEI, 9UF7, 9UFI

  • PubMed Abstract: 

    Phenylethanoid glycosides (PhGs) are a group of important natural products widely distributed in medicinal plants and known for their remarkable pharmacological properties. Uridine diphosphate (UDP) glycosyltransferase 79G15 (UGT79G15) from Rehmannia glutinosa catalyzes the conversion of osmanthuside A to osmanthuside B, a key intermediate in the PhG biosynthetic pathway, through the formation of a (1→3) glycosidic bond. In this study, we present the crystal structures of UGT79G15 in its apo form, UDP-bound form, and, notably, its ternary complex containing UDP and a mimic acceptor, forsythiaside A, within its active site. Structural and comparative analyses revealed that UGT79G15 possesses a distinctive funnel-shaped acceptor-binding pocket with a small auxiliary cavity capable of accommodating the 4'-hydroxycinnamoyl group of PhGs, explaining the enzyme's regiospecificity toward the 3'-OH of the acceptor. Additional structural examination and site-directed mutagenesis identified key residues that recognize and stabilize UDP-rhamnose and the sugar acceptor. Among the variants generated, I204W exhibits enhanced catalytic efficiency for osmanthuside A conversion, reaching up to 2.2-fold higher activity than the wild type. This study provides mechanistic insight into the donor specificity and acceptor regioselectivity of PhG 1,3-rhamnosyltransferase and expands the structural understanding of plant UGTs.


  • Organizational Affiliation
    • National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.

Macromolecule Content 

  • Total Structure Weight: 101.37 kDa 
  • Atom Count: 7,283 
  • Modeled Residue Count: 900 
  • Deposited Residue Count: 900 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UGT79G15
A, B
450Rehmannia glutinosaMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for A0A2G9HDX9 (Handroanthus impetiginosus)
Explore A0A2G9HDX9 
Go to UniProtKB:  A0A2G9HDX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2G9HDX9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.254α = 90
b = 72.059β = 97.83
c = 134.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references