9KSR | pdb_00009ksr

Complex structure of CaApiGT/UDP/Quercetin 3-O-glucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Insights into the Mechanisms of Sugar Acceptor Selectivity of Plant Flavonoid Apiosyltransferases.

Wang, H.T.Wang, Z.L.Chen, N.H.Huang, W.Zou, J.L.Tian, Y.G.Ye, G.Huang, J.Wu, R.Ye, M.

(2025) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.5c03771
  • Primary Citation of Related Structures:  
    9KSM, 9KSO, 9KSR, 9KSS, 9KSV, 9KSW, 9KSX, 9KSY, 9KSZ, 9KT0

  • PubMed Abstract: 

    Flavonoid apiosides are widely distributed in cereals, fruits, vegetables, and medicinal herbs and play critical roles in human health. Their facile and efficient synthesis has been a hot but challenging topic in the fields of both organic chemistry and biosynthesis. However, very few apiosyltransferases (ApiGTs) have been reported thus far. Here, we report the first flavonoid apiosyltransferase (CaApiGT) capable of catalyzing the 2″- O -apiosylation of flavonoid 3- O -glycosides in chickpea ( Cicer arietinum ). Moreover, we identify PcApiGT from parsley ( Petroselinum crispum ), which catalyzes the 2″- O -apiosylation of flavonoid 7-/4'- O -glycosides. To dissect the mechanisms underlying their different sugar acceptor selectivity, we obtain 10 complex crystal structures of CaApiGT and PcApiGT with resolutions ranging from 1.55 to 2.65 Å, including CaApiGT/UDP, 6 ternary structures of CaApiGT/UDP/sugar acceptors, PcApiGT/UDP, and 2 ternary structures of PcApiGT/UDP/sugar acceptors. Structural analyses, theoretical calculations, and site-directed mutagenesis indicate that flavonoid 3- O -glycosides and 7- O -glycosides exhibit a T-shape and streamline shape, respectively, and fit the active pockets of CaApiGT and PcApiGT. Moreover, the sugar acceptor selectivity of these two apiosyltransferases is determined by a key α-helix. In CaApiGT, this α-helix contains multiple polar amino acids, particularly a threonine residue at its end. Using this α-helix motif as a marker, we further characterize four apiosyltransferases from Leguminosae plants that exhibit functional similarity to CaApiGT. This work unravels detailed sugar acceptor selectivity mechanisms of plant apiosyltransferases and provides efficient biocatalysts for the synthesis of flavonoid apiosides.


  • 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
UDP-glycosyltransferase 79B30-like454Cicer arietinumMutation(s): 0 
Gene Names: LOC101505166
UniProt
Find proteins for A0A1S2XDD2 (Cicer arietinum)
Explore A0A1S2XDD2 
Go to UniProtKB:  A0A1S2XDD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S2XDD2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.91α = 90
b = 119.51β = 90
c = 47.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2025-06-25
    Type: Initial release