1GP5

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 11796114 Search on PubMed
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.

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

Macromolecule Content

Total Structure Weight: 41.65 kDa
Atom Count: 2,998
Modelled Residue Count: 347
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DH2 Query on DH2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DQH Query on DQH Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.204
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-02-21

Deposition Author(s):

Revision History (Full details and data files)

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