3BXX

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: 2.90 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.292 

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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 D Biol Crystallogr D64: 883-891

  • DOI: 10.1107/S0907444908017769
  • Primary Citation of Related Structures:  
    3BXX, 3C1T

  • 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 tannins, two major classes of phenolic compounds that strongly influence the organoleptic properties of wine ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dihydroflavonol 4-reductase
A, B, C, D, E, F
A, B, C, D, E, F
337Vitis viniferaMutation(s): 0 
Gene Names: DFR1, DFR
EC: 1.1.1.219 (PDB Primary Data), 1.1.1.234 (UniProt)
UniProt
Find proteins for P51110 (Vitis vinifera)
Explore P51110 
Go to UniProtKB:  P51110
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51110
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
O [auth D],
R [auth E],
G [auth A],
I [auth B],
L [auth C],
O [auth D],
R [auth E],
S [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
QUE
Query on QUE
Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
T [auth F],
U [auth F]
3,5,7,3',4'-PENTAHYDROXYFLAVONE
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.292 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.943α = 90
b = 174.943β = 90
c = 290.167γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance