2C1Z

Structure and activity of a flavonoid 3-O glucosyltransferase reveals the basis for plant natural product modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Flavonoid Glucosyltransferase Reveals the Basis for Plant Natural Product Modification.

Offen, W.Martinez-Fleites, C.Yang, M.Kiat-Lim, E.Davis, B.G.Tarling, C.A.Ford, C.M.Bowles, D.J.Davies, G.J.

(2006) Embo J. 25: 1396

  • DOI: 10.1038/sj.emboj.7600970
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosylation is a key mechanism for orchestrating the bioactivity, metabolism and location of small molecules in living cells. In plants, a large multigene family of glycosyltransferases is involved in these processes, conjugating hormones, secondar ...

    Glycosylation is a key mechanism for orchestrating the bioactivity, metabolism and location of small molecules in living cells. In plants, a large multigene family of glycosyltransferases is involved in these processes, conjugating hormones, secondary metabolites, biotic and abiotic environmental toxins, to impact directly on cellular homeostasis. The red grape enzyme UDP-glucose:flavonoid 3-O-glycosyltransferase (VvGT1) is responsible for the formation of anthocyanins, the health-promoting compounds which, in planta, function as colourants determining flower and fruit colour and are precursors for the formation of pigmented polymers in red wine. We show that VvGT1 is active, in vitro, on a range of flavonoids. VvGT1 is somewhat promiscuous with respect to donor sugar specificity as dissected through full kinetics on a panel of nine sugar donors. The three-dimensional structure of VvGT1 has also been determined, both in its 'Michaelis' complex with a UDP-glucose-derived donor and the acceptor kaempferol and in complex with UDP and quercetin. These structures, in tandem with kinetic dissection of activity, provide the foundation for understanding the mechanism of these enzymes in small molecule homeostasis.


    Organizational Affiliation

    Department of Chemistry, University of York, York, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-GLUCOSE FLAVONOID 3-O GLYCOSYLTRANSFERASE
A
456Vitis viniferaMutation(s): 0 
Gene Names: UFGT (AlUFGT1, AlUFGT2, FlUFGT1, FlUFGT2, ITUFGT1, ITUFGT2, RUUFGT1, RUUFGT2, VVGT1)
EC: 2.4.1.115
Find proteins for P51094 (Vitis vinifera)
Go to UniProtKB:  P51094
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U2F
Query on U2F

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
 Ligand Interaction
KMP
Query on KMP

Download SDF File 
Download CCD File 
A
3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE
KAEMPHEROL
C15 H10 O6
IYRMWMYZSQPJKC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.106α = 90.00
b = 93.531β = 90.00
c = 106.670γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance