8K09

Pq3-O-UGT2 with 20(S)-Ginsenoside F2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 
    0.332 (Depositor), 0.331 (DCC) 
  • R-Value Work: 
    0.296 (Depositor), 0.296 (DCC) 
  • R-Value Observed: 
    0.298 (Depositor) 

Starting Model: experimental
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Literature

Structural Insights into the Substrate Recognition of Ginsenoside Glycosyltransferase Pq3-O-UGT2.

Ji, Q.Liu, Y.Zhang, H.Gao, Y.Ding, Y.Ding, Y.Xie, J.Zhang, J.Jin, X.Lai, B.Chen, C.Wang, J.Gao, W.Mei, K.

(2025) Adv Sci (Weinh) : e2413185-e2413185

  • DOI: https://doi.org/10.1002/advs.202413185
  • Primary Citation of Related Structures:  
    8JZQ, 8K08, 8K09

  • PubMed Abstract: 

    Ginsenosides are a group of tetracyclic triterpenoids with promising health benefits, consisting of ginseng aglycone attached to various glycans. Pq3-O-UGT2, an important UDP-dependent glycosyltransferase (UGT), catalyzes the production of Ginsenoside Rg3 and Rd by extending the glycan chain of Ginsenoside Rh2 and F2, respectively, with higher selectivity for F2. However, the mechanism underlying its substrate recognition remains unclear. In this study, the crystal structures of Pq3-O-UGT2 in complex with its acceptor substrates are solved. The structures revealed a Nα5-oriented acceptor binding pocket in Pq3-O-UGT2, shaped by the unique conformation of the Nα5-Nα6 linker. Hydrophobic interactions play a pivotal role in the recognition of both Rh2 and F2, while hydrogen bonds specifically aid in F2 recognition due to its additional glucose moiety. The hydrophobic nature of the acceptor binding pocket also enables Pq3-O-UGT2 to recognize flavonoids. Overall, this study provides novel insights into the substrate recognition mechanisms of ginsenoside UGTs, advancing the understanding of their function and specificity.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, 300072, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlycosyltransferaseA [auth C],
B [auth A]
455Panax quinquefoliusMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for A0A0M4ME80 (Panax quinquefolius)
Explore A0A0M4ME80 
Go to UniProtKB:  A0A0M4ME80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4ME80
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VEI (Subject of Investigation/LOI)
Query on VEI

Download Ideal Coordinates CCD File 
C,
D [auth A]
(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(3~{S},5~{R},8~{R},9~{R},10~{R},12~{R},13~{R},14~{R},17~{S})-17-[(2~{S})-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-methyl-hept-5-en-2-yl]-4,4,8,10,14-pentamethyl-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol
C42 H72 O13
SWIROVJVGRGSPO-JBVRGBGGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free:  0.332 (Depositor), 0.331 (DCC) 
  • R-Value Work:  0.296 (Depositor), 0.296 (DCC) 
  • R-Value Observed: 0.298 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.27α = 90
b = 88.18β = 90
c = 164.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
Cootmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references