1GP6

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin (with 30 min exposure to O2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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

  • DOI: 10.1016/s0969-2126(01)00695-5
  • Primary Citation of Related Structures:  
    1GP4, 1GP5, 1GP6

  • 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 flavonoids ...

    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 (Camb) --: 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 D Biol Crystallogr 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCOANTHOCYANIDIN DIOXYGENASEA356Arabidopsis thalianaMutation(s): 0 
Gene Names: LDOXAt4g22880F7H19.60
EC: 1.14.11.19 (PDB Primary Data), 1.14.20.4 (UniProt)
UniProt
Find proteins for Q96323 (Arabidopsis thaliana)
Explore Q96323 
Go to UniProtKB:  Q96323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DH2
Query on DH2

Download Ideal Coordinates CCD File 
F [auth A](2S,3S)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE
C15 H12 O7
CXQWRCVTCMQVQX-CABCVRRESA-N
 Ligand Interaction
QUE
Query on QUE

Download Ideal Coordinates CCD File 
E [auth A]3,5,7,3',4'-PENTAHYDROXYFLAVONE
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SIN
Query on SIN

Download Ideal Coordinates CCD File 
B [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.258α = 90
b = 72.385β = 90
c = 87.054γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance