Q96323 (LDOX_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Leucoanthocyanidin dioxygenase
Short name=LDOX
Short name=Leucocyanidin oxygenase
EC=1.14.11.19

Alternative name(s):
Anthocyanidin synthase
Short name=ANS
Leucoanthocyanidin hydroxylase
Protein TANNIN DEFICIENT SEED 4
Short name=TDS4
Protein TRANSPARENT TESTA 11
Short name=TT11
Protein TRANSPARENT TESTA 17
Short name=TT17
Protein TRANSPARENT TESTA 18
Short name=TT18

Gene names

Name:	LDOX
Ordered Locus Names:	At4g22880
ORF Names:	F7H19.60

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	356 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in anthocyanin and protoanthocyanidin biosynthesis by catalyzing the oxidation of leucoanthocyanidins into anthocyanidins. Possesses low flavonol synthase activity in vitro towards dihydrokaempferol and dihydroquercetin producing kaempferol and quercitin, respectively. Ref.6 Ref.7 Ref.9 Ref.11 Ref.14
Catalytic activity	Leucocyanidin + 2-oxoglutarate + O2 = cis- and trans-dihydroquercetins + succinate + CO2 + H2O. Ref.7
Cofactor	Binds 1 ascorbate molecule per subunit. Binds 1 Fe2+ ion per subunit.
Pathway	Pigment biosynthesis; anthocyanin biosynthesis.
Tissue specificity	Expressed in young seedlings (at protein level). Ref.5
Induction	By methyl jasmonate, 6-benzylaminopurine, light and sucrose. Ref.1 Ref.8 Ref.10
Disruption phenotype	No accumulation of anthocyanins, accumulation of protoanthocyanidin intermediates and presence of numerous small vacuoles in leaf epidermal cells. Ref.6 Ref.9 Ref.11
Sequence similarities	Belongs to the iron/ascorbate-dependent oxidoreductase family. Contains 1 Fe2OG dioxygenase domain.

Ontologies

Keywords
Biological process	Flavonoid biosynthesis
Ligand	Iron Metal-binding Vitamin C
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	anthocyanin-containing compound biosynthetic process Traceable author statement PubMed 16702218. Source: TAIR proanthocyanidin biosynthetic process Inferred from mutant phenotype Ref.6. Source: TAIR response to jasmonic acid stimulus Inferred from expression pattern PubMed 16021335. Source: TAIR response to wounding Inferred from expression pattern PubMed 16021335. Source: TAIR vacuole organization Inferred from mutant phenotype Ref.6. Source: TAIR
Molecular_function	L-ascorbic acid binding Inferred from electronic annotation. Source: UniProtKB-KW leucocyanidin oxygenase activity Inferred from sequence or structural similarity Ref.1. Source: TAIR metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 356

356

Leucoanthocyanidin dioxygenase

PRO_0000067299

Regions

Domain

208 – 307

100

Fe2OG dioxygenase

Region

215 – 217

3

2-oxoglutarate binding

Region

298 – 300

3

2-oxoglutarate binding

Sites

Metal binding

232

1

Iron; catalytic

Metal binding

234

1

Iron; catalytic

Metal binding

288

1

Iron; catalytic

Binding site

142

1

Substrate

Binding site

213

1

Substrate

Binding site

233

1

Substrate

Binding site

306

1

Substrate

Binding site

341

1

Substrate

Experimental info

Mutagenesis

78

1

G → E in tt11-2; no accumulation of anthocyanin. Ref.11

Mutagenesis

128

1

K → A: Retains two-third of the original activity. Ref.14

Mutagenesis

131

1

N → A or D: Retains two-third of the original activity. Ref.14

Mutagenesis

142

1

Y → H: Retains two-third of the original activity. Ref.14

Mutagenesis

220

1

C → Y in tt17; no accumulation of anthocyanin. Ref.11

Mutagenesis

228

1

G → D in tds4-1; no accumulation of anthocyanin. Ref.6 Ref.11

Mutagenesis

230

1

E → Q: Retains one half of the original activity. Ref.14

Mutagenesis

341

1

K → N: Retains two-third of the original activity. Ref.14

Secondary structure

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356

Helix Strand Turn

Details...

Helix

7 – 12

6

Helix

20 – 22

3

Helix

26 – 29

4

Helix

35 – 40

6

Beta strand

49 – 51

3

Turn

53 – 56

4

Helix

60 – 76

17

Beta strand

78 – 84

7

Helix

89 – 103

15

Helix

107 – 110

4

Helix

111 – 113

3

Helix

117 – 119

3

Beta strand

123 – 126

4

Beta strand

132 – 134

3

Beta strand

141 – 149

9

Helix

150 – 152

3

Helix

155 – 157

3

Helix

165 – 190

26

Helix

197 – 201

5

Helix

204 – 207

4

Beta strand

209 – 217

9

Turn

223 – 225

3

Beta strand

228 – 232

5

Beta strand

236 – 243

8

Beta strand

249 – 253

5

Beta strand

256 – 259

4

Beta strand

267 – 271

5

Helix

273 – 278

6

Turn

279 – 281

3

Beta strand

288 – 290

3

Beta strand

298 – 306

9

Turn

309 – 311

3

Helix

318 – 320

3

Beta strand

323 – 325

3

Helix

334 – 349

16

Sequences

	Sequence		Length	Mass (Da)
	Q96323 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 1B74AE3A54056201	FASTA	356	40,396
	10 20 30 40 50 60 MVAVERVESL AKSGIISIPK EYIRPKEELE SINDVFLEEK KEDGPQVPTI DLKNIESDDE 70 80 90 100 110 120 KIRENCIEEL KKASLDWGVM HLINHGIPAD LMERVKKAGE EFFSLSVEEK EKYANDQATG 130 140 150 160 170 180 KIQGYGSKLA NNASGQLEWE DYFFHLAYPE EKRDLSIWPK TPSDYIEATS EYAKCLRLLA 190 200 210 220 230 240 TKVFKALSVG LGLEPDRLEK EVGGLEELLL QMKINYYPKC PQPELALGVE AHTDVSALTF 250 260 270 280 290 300 ILHNMVPGLQ LFYEGKWVTA KCVPDSIVMH IGDTLEILSN GKYKSILHRG LVNKEKVRIS 310 320 330 340 350 WAVFCEPPKD KIVLKPLPEM VSVESPAKFP PRTFAQHIEH KLFGKEQEEL VSEKND

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of flavonol synthase and leucoanthocyanidin dioxygenase genes in Arabidopsis. Further evidence for differential regulation of 'early' and 'late' genes." Pelletier M.K., Murrell J.R., Shirley B.W. Plant Physiol. 113:1437-1445(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY LIGHT. Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana." Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B. , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R. Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]	"Disruption of specific flavonoid genes enhances the accumulation of flavonoid enzymes and end-products in Arabidopsis seedlings." Pelletier M.K., Burbulis I.E., Winkel-Shirley B. Plant Mol. Biol. 40:45-54(1999) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[6]	"The Arabidopsis TDS4 gene encodes leucoanthocyanidin dioxygenase (LDOX) and is essential for proanthocyanidin synthesis and vacuole development." Abrahams S., Lee E., Walker A.R., Tanner G.J., Larkin P.J., Ashton A.R. Plant J. 35:624-636(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLY-228. Strain: cv. Wassilewskija-4.
[7]	"Incorporation of oxygen into the succinate co-product of iron(II) and 2-oxoglutarate dependent oxygenases from bacteria, plants and humans." Welford R.W., Kirkpatrick J.M., McNeill L.A., Puri M., Oldham N.J., Schofield C.J. FEBS Lett. 579:5170-5174(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY.
[8]	"Sucrose-specific induction of the anthocyanin biosynthetic pathway in Arabidopsis." Solfanelli C., Poggi A., Loreti E., Alpi A., Perata P. Plant Physiol. 140:637-646(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION BY SUCROSE.
[9]	"Arabidopsis thaliana expresses a second functional flavonol synthase." Preuss A., Stracke R., Weisshaar B., Hillebrecht A., Matern U., Martens S. FEBS Lett. 583:1981-1986(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[10]	"Molecular mechanism for jasmonate-induction of anthocyanin accumulation in Arabidopsis." Shan X., Zhang Y., Peng W., Wang Z., Xie D. J. Exp. Bot. 60:3849-3860(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[11]	"Leucoanthocyanidin dioxygenase in Arabidopsis thaliana: characterization of mutant alleles and regulation by MYB-BHLH-TTG1 transcription factor complexes." Appelhagen I., Jahns O., Bartelniewoehner L., Sagasser M., Weisshaar B., Stracke R. Gene 484:61-68(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLY-78; CYS-220 AND GLY-228. Strain: cv. Est-1, cv. Landsberg erecta and cv. Wassilewskija-4.
[12]	"The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity." Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M., Tohge T., Fernie A.R. Plant Physiol. Biochem. 0:0-0(2013) Cited for: REVIEW, NOMENCLATURE.
[13]	"Structure and mechanism of anthocyanidin synthase from Arabidopsis thaliana." Wilmouth R.C., Turnbull J.J., Welford R.W., Clifton I.J., Prescott A.G., Schofield C.J. Structure 10:93-103(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH DIHYDROQUERCETIN; 2-OXOGLUTARATE AND IRON ION.
[14]	"Structural and mechanistic studies on anthocyanidin synthase catalysed oxidation of flavanone substrates: the effect of C-2 stereochemistry on product selectivity and mechanism." Welford R.W., Clifton I.J., Turnbull J.J., Wilson S.C., Schofield C.J. Org. Biomol. Chem. 3:3117-3126(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 2-356 IN COMPLEX WITH NARINGENIN; 2-OXOGLUTARATE AND IRON ION, FUNCTION, MUTAGENESIS OF LYS-128; ASN-131; TYR-142; GLU-230 AND LYS-341.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U70478 mRNA. Translation: AAB09572.1.
AL031018 Genomic DNA. Translation: CAA19803.1.
AL161558 Genomic DNA. Translation: CAB79243.1.
CP002687 Genomic DNA. Translation: AEE84672.1.
CP002687 Genomic DNA. Translation: AEE84673.1.
AY088203 mRNA. Translation: AAM65745.1.

IPI

IPI00525167.

PIR

T05119.

RefSeq

NP_001031700.1. NM_001036623.1.
NP_194019.1. NM_118417.1.

UniGene

At.2369.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GP4	X-ray	2.10	A	1-356	[»]
1GP5	X-ray	2.20	A	1-356	[»]
1GP6	X-ray	1.75	A	1-356	[»]
2BRT	X-ray	2.20	A	2-356	[»]

ProteinModelPortal

Q96323.

SMR

Q96323. Positions 2-350.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT4G22880.1-P.

Proteomic databases

PaxDb

Q96323.

PRIDE

Q96323.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT4G22880.1; AT4G22880.1; AT4G22880.
AT4G22880.2; AT4G22880.2; AT4G22880.

GeneID

828387.

KEGG

ath:AT4G22880.

Organism-specific databases

TAIR

At4g22880.

Phylogenomic databases

eggNOG

COG3491.

HOGENOM

HOG000276735.

InParanoid

Q96323.

KO

K05277.

OMA

RTHANDH.

PhylomeDB

Q96323.

ProtClustDB

PLN03178.

Enzyme and pathway databases

UniPathway

UPA00009.

Gene expression databases

ArrayExpress

Q96323.

Genevestigator

Q96323.

GermOnline

AT4G22880. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR026992. DIOX_N.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
[Graphical view]

Pfam

PF03171. 2OG-FeII_Oxy. 1 hit.
PF14226. DIOX_N. 1 hit.
[Graphical view]

PROSITE

PS51471. FE2OG_OXY. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q96323.

Entry information

Entry name

LDOX_ARATH

Accession

Primary (citable) accession number: Q96323

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 23, 2003
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program