2C1X

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: 0.226 
  • R-Value Work: 0.185 

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
B3P
Query on B3P
Download SDF File 
Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP
Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.014α = 90.00
b = 93.394β = 90.00
c = 106.464γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

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View more in-depth experimental data

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