Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with kaempferol

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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This is version 1.2 of the entry. See complete history


Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea

Hiromoto, T.Honjo, E.Noda, N.Tamada, T.Kazuma, K.Suzuki, M.Blaber, M.Kuroki, R.

(2015) Protein Sci 24: 395-407

  • DOI: https://doi.org/10.1002/pro.2630
  • Primary Citation of Related Structures:  
    4REL, 4REM, 4REN, 4WHM

  • PubMed Abstract: 

    UDP-glucose: anthocyanidin 3-O-glucosyltransferase (UGT78K6) from Clitoria ternatea catalyzes the transfer of glucose from UDP-glucose to anthocyanidins such as delphinidin. After the acylation of the 3-O-glucosyl residue, the 3'- and 5'-hydroxyl groups of the product are further glucosylated by a glucosyltransferase in the biosynthesis of ternatins, which are anthocyanin pigments. To understand the acceptor-recognition scheme of UGT78K6, the crystal structure of UGT78K6 and its complex forms with anthocyanidin delphinidin and petunidin, and flavonol kaempferol were determined to resolutions of 1.85 Å, 2.55 Å, 2.70 Å, and 1.75 Å, respectively. The enzyme recognition of unstable anthocyanidin aglycones was initially observed in this structural determination. The anthocyanidin- and flavonol-acceptor binding details are almost identical in each complex structure, although the glucosylation activities against each acceptor were significantly different. The 3-hydroxyl groups of the acceptor substrates were located at hydrogen-bonding distances to the Nε2 atom of the His17 catalytic residue, supporting a role for glucosyl transfer to the 3-hydroxyl groups of anthocyanidins and flavonols. However, the molecular orientations of these three acceptors are different from those of the known flavonoid glycosyltransferases, VvGT1 and UGT78G1. The acceptor substrates in UGT78K6 are reversely bound to its binding site by a 180° rotation about the O1-O3 axis of the flavonoid backbones observed in VvGT1 and UGT78G1; consequently, the 5- and 7-hydroxyl groups are protected from glucosylation. These substrate recognition schemes are useful to understand the unique reaction mechanism of UGT78K6 for the ternatin biosynthesis, and suggest the potential for controlled synthesis of natural pigments.

  • Organizational Affiliation

    Quantum Beam Science Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki, 319-1195, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glucose:anthocyanidin 3-O-glucosyltransferase446Clitoria ternateaMutation(s): 0 
Gene Names: Ct3GT-A
EC: (PDB Primary Data), 2.4.1 (UniProt)
Find proteins for A4F1R4 (Clitoria ternatea)
Explore A4F1R4 
Go to UniProtKB:  A4F1R4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4F1R4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.042α = 90
b = 55.137β = 104.92
c = 85.88γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description