3C1T

Binding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.252 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols

Trabelsi, N.Petit, P.Manigand, C.Langlois d'Estaintot, B.Granier, T.Chaudiere, J.Gallois, B.

(2008) Acta Crystallogr.,Sect.D D64: 883-891

  • DOI: 10.1107/S0907444908017769
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. The latter are the precursors of anthocyans and condensed ta ...

    Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. The latter are the precursors of anthocyans and condensed tannins, two major classes of phenolic compounds that strongly influence the organoleptic properties of wine. DFR has been investigated in many plant species, but little was known about its structural properties until the three-dimensional structure of the Vitis vinifera enzyme complexed with NADP(+) and its natural substrate dihydroquercetin (DHQ) was described. In the course of the study of substrate specificity, crystals of DFR-NADP(+)-flavonol (myricetin and quercetin) complexes were obtained. Their structures exhibit major changes with respect to that of the abortive DFR-NADP(+)-DHQ complex. Two flavonol molecules bind to the catalytic site in a stacking arrangement and alter its geometry, which becomes incompatible with enzymatic activity. The X-ray structures of both DFR-NADP(+)-myricetin and DFR-NADP(+)-quercetin are reported together with preliminary spectroscopic data. The results suggest that flavonols could be inhibitors of the activity of DFR towards dihydroflavonols.


    Organizational Affiliation

    CBMN, UMR CNRS 5248, Bâtiment B8, Avenue des Facultés, Université Bordeaux 1, 33405 Talence CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dihydroflavonol 4-reductase
A, B, C, D
337Vitis viniferaMutation(s): 0 
Gene Names: DFR
EC: 1.1.1.219
Find proteins for P51110 (Vitis vinifera)
Go to UniProtKB:  P51110
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MYC
Query on MYC

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Download CCD File 
A, B, C, D
3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE
2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE; 3,3',4',5,5',7-HEXAHYDROXYFLAVONE; MYRICETIN; CANNABISCETIN
C15 H10 O8
IKMDFBPHZNJCSN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.252 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.231α = 90.00
b = 177.958β = 104.77
c = 92.597γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance