1GP6

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

• PDB DOI: https://doi.org/10.2210/pdb1GP6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-10-30 Released: 2002-02-21 
• Deposition Author(s): Wilmouth, R.C., Turnbull, J.J., Welford, R.W.D., Clifton, I.J., Prescott, A.G., Schofield, C.J.

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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 

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

• PubMed: 11796114 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

The Dyson Perrins Laboratory, Oxford Centre for Molecular Sciences, South Parks Road, Oxford OX1 3QY, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 41.62 kDa 
• Atom Count: 3,186 
• Modelled Residue Count: 350 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUCOANTHOCYANIDIN DIOXYGENASE	A	356	Arabidopsis thaliana	Mutation(s): 0  EC: 1.14.11.19
UniProt
Find proteins for Q96323 (Arabidopsis thaliana) Explore Q96323  Go to UniProtKB:  Q96323

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DH2	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
QUE	E [auth A]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C15 H10 O7 REFJWTPEDVJJIY-UHFFFAOYSA-N
MES	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SIN	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
FE2	G [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

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 = 61.258	α = 90
b = 72.385	β = 90
c = 87.054	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-21 
Deposition Author(s): Wilmouth, R.C., Turnbull, J.J., Welford, R.W.D., Clifton, I.J., Prescott, A.G., Schofield, C.J.

Revision History  

• 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
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description