1GP5 | pdb_00001gp5

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1gp5a_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Penicillin synthase-like	Anthocyanidin synthase	MOUSE-EAR CRESS (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Clavaminate synthase-like	8036128	3001848	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DIOX_N	e1gp5A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: DIOX_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.330	Mainly Beta	Sandwich	Jelly Rolls	B-lactam Antibiotic, Isopenicillin N Synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03171	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reactio ...	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.	Domain
A	PF14226	non-haem dioxygenase in morphine synthesis N-terminal (DIOX_N)	non-haem dioxygenase in morphine synthesis N-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LEUCOANTHOCYANIDIN DIOXYGENASE	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen leucocyanidin oxygenase activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen leucocyanidin oxygenase activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding cation binding metal ion binding	phenylpropanoid metabolic process biosynthetic process secondary metabolite biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process proanthocyanidin biosynthetic process metabolic process cellular process phenylpropanoid biosynthetic process secondary metabolic process response to stimulus response to stress response to wounding anthocyanin-containing compound biosynthetic process phenylpropanoid metabolic process biosynthetic process secondary metabolite biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process proanthocyanidin biosynthetic process metabolic process cellular process phenylpropanoid biosynthetic process secondary metabolic process response to stimulus response to stress response to wounding anthocyanin-containing compound biosynthetic process pigment metabolic process flavonoid metabolic process anthocyanin-containing compound metabolic process flavonoid biosynthetic process pigment biosynthetic process response to lipid response to jasmonic acid response to hormone response to fatty acid response to chemical response to endogenous stimulus response to oxygen-containing compound cellular component organization organelle organization vacuole organization cellular component organization or biogenesis	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050295	Plant 2-oxoglutarate-dependent oxidoreductases	Family
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A	IPR027443	Isopenicillin N synthase-like superfamily	Homologous Superfamily
A	IPR044861	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	Domain
A	IPR026992	Non-haem dioxygenase N-terminal domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	anthocyanidin synthase M-CSA #685	The 2-oxoglutarate dependent enzyme anthocyanidin synthase is able to catalyse the synthesis of anthocyanidin from quercetin, a vital step in the synthesis of flavoids and flavones in plant cells. The reaction is coupled to the decarboxylation of 2-oxoglutarate to form succinate. It is part of the family of 2OG dependent non-haem iron oxygenases, which use 2-oxoglutarate as a cosubstrate and Iron (II) as a cofactor in their reaction mechanisms. The enzyme is of particular interest to geneticists as a mutated form is responsible for the original tall/dwarf dimorphism observed in peas by Mendel.	Defined by 4 residues: LYS:A-213HIS:A-232ASP:A-234HIS:A-288 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.14.11.19 (PDB Primary Data) Search M-CSA Motif + EC 1.14.11.19 EC: 1.14.20.4 (UniProt) Search M-CSA Motif + EC 1.14.20.4

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.