9UFI | pdb_00009ufi

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.202 (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 of Related Structures:  
    9UEI, 9UF7, 9UFI

  • PubMed Abstract: 

    Phenylethanoid glycosides (PhGs) are a group of important natural products found in a wide variety of medicinal plants, and are known to possess outstanding 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, via the formation of a (1→3) glycosidic bond. In this study, we report the crystal structure of UGT79G15 in its apo form, UDP-bound form and, most importantly, its ternary complex form containing UDP and a mimic acceptor, forsythiaside A, in its active site. Structural and comparative analyses revealed that UGT79G15 has a unique 'funnel-shaped' acceptor-binding pocket with a small accessory cave sufficient to accommodate the 4'-hydroxycinnamoyl group of PhG, explaining the enzyme's regiospecificity for the 3'-OH of PhG. Further structural analysis and site-directed mutagenesis explored a number of variants of the enzyme and identified key residues that recognize and stabilize UDP-rhamnose and the sugar acceptor. Meanwhile, I204W, a point variant obtained in the process, was found to possess increased catalytic efficiency for osmanthuside A conversion, up to 2.2 times the efficiency of the wild type. This study provides mechanistic insights into the donor specificity and acceptor regioselectivity of PhG 1,3-rhamnosyltransferase and enriches structural information on 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UGT79G15
A, B
455Rehmannia 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: 2.12 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.105α = 90
b = 73.244β = 97.52
c = 134.294γ = 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