1GP5 | pdb_00001gp5

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin

• PDB DOI: https://doi.org/10.2210/pdb1GP5/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: 2.20 Å
• R-Value Free: 
  0.237 (Depositor) 
• R-Value Work: 
  0.204 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

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 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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.65 kDa 
• Atom Count: 2,998 
• Modeled Residue Count: 347 
• 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 (PDB Primary Data), 1.14.20.4 (UniProt)
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
DQH	E [auth A]	(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE C15 H12 O7 CXQWRCVTCMQVQX-LSDHHAIUSA-N
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
MES	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
AKG	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor) 
• R-Value Work:  0.204 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.033	α = 90
b = 74.362	β = 90
c = 88.109	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: Database references, Derived calculations, Refinement description, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description