1GP5

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Mechanism of Anthocyanidin Synthase from Arabidopsis Thaliana.

Wilmouth, R.C.Turnbull, J.J.Welford, R.W.D.Clifton, I.J.Prescott, A.G.Schofield, C.J.

(2002) Structure 10: 93

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavonoids are common colorants in plants and have long-established biomedicinal properties. Anthocyanidin synthase (ANS), a 2-oxoglutarate iron-dependent oxygenase, catalyzes the penultimate step in the biosynthesis of the anthocyanin class of flavo ...

    Flavonoids are common colorants in plants and have long-established biomedicinal properties. Anthocyanidin synthase (ANS), a 2-oxoglutarate iron-dependent oxygenase, catalyzes the penultimate step in the biosynthesis of the anthocyanin class of flavonoids. The crystal structure of ANS reveals a multicomponent active site containing metal, cosubstrate, and two molecules of a substrate analog (dihydroquercetin). An additional structure obtained after 30 min exposure to dioxygen is consistent with the oxidation of the dihydroquercetin to quercetin and the concomitant decarboxylation of 2-oxoglutarate to succinate. Together with in vitro studies, the crystal structures suggest a mechanism for ANS-catalyzed anthocyanidin formation from the natural leucoanthocyanidin substrates involving stereoselective C-3 hydroxylation. The structure of ANS provides a template for the ubiquitous family of plant nonhaem oxygenases for future engineering and inhibition studies.


    Related Citations: 
    • Are Anthocyanidins the Immediate Products of Anthocyanidin Synthase?
      Turnbull, J.J.,Sobey, W.J.,Aplin, R.T.,Hassan, A.,Firmin, J.L.,Schofield, C.J.,Prescott, A.G.
      (2000) Chem. Commun. --: 2473
    • Purification, Crystallization and Preliminary X-Ray Diffraction of Anthocyanidin Synthase from Arabidopsis Thaliana
      Turnbull, J.J.,Prescott, A.G.,Schofield, C.J.,Wilmouth, R.C.
      (2001) Acta Crystallogr.,Sect.D D57: 425
    • Direct Evidence for Anthocyanidin Synthase as a 2-Oxoglutarate-Dependent Oxygenase: Molecular Cloning and Functional Expression of Cdna from a Red Forma of Perilla Frutescens
      Saito, K.,Kobayashi, M.,Gong, Z.,Tanaka, Y.,Yamazaki, M.
      (1999) Plant J. 17: 181


    Organizational Affiliation

    The Dyson Perrins Laboratory, Oxford Centre for Molecular Sciences, South Parks Road, Oxford OX1 3QY, United Kingdom. rupert.wilmouth@new.ox.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCOANTHOCYANIDIN DIOXYGENASE
A
356Arabidopsis thalianaMutation(s): 0 
Gene Names: LDOX
EC: 1.14.20.4
Find proteins for Q96323 (Arabidopsis thaliana)
Go to UniProtKB:  Q96323
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DH2
Query on DH2

Download SDF File 
Download CCD File 
A
(2S,3S)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
(2S,3S)-TRANS-DIHYDROQUERCETIN
C15 H12 O7
CXQWRCVTCMQVQX-CABCVRRESA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
DQH
Query on DQH

Download SDF File 
Download CCD File 
A
(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
(2R,3R)-TRANS-DIHYDROQUERCETIN
C15 H12 O7
CXQWRCVTCMQVQX-LSDHHAIUSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.033α = 90.00
b = 74.362β = 90.00
c = 88.109γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references, Derived calculations, Refinement description, Version format compliance