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Q96323

- LDOX_ARATH

UniProt

Q96323 - LDOX_ARATH

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Protein

Leucoanthocyanidin dioxygenase

Gene

LDOX

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.5 Publications

Catalytic activityi

Leucocyanidin + 2-oxoglutarate + O2 = cis- and trans-dihydroquercetins + succinate + CO2 + H2O.1 Publication

Cofactori

Protein has several cofactor binding sites:

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei142 – 1421Substrate2 Publications
Binding sitei213 – 2131Substrate2 Publications
Metal bindingi232 – 2321Iron; catalytic2 Publications
Binding sitei233 – 2331Substrate2 Publications
Metal bindingi234 – 2341Iron; catalytic2 Publications
Metal bindingi288 – 2881Iron; catalytic2 Publications
Binding sitei306 – 3061Substrate2 Publications
Binding sitei341 – 3411Substrate2 Publications

GO - Molecular functioni

  1. L-ascorbic acid binding Source: UniProtKB-KW
  2. leucocyanidin oxygenase activity Source: TAIR
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. anthocyanin-containing compound biosynthetic process Source: TAIR
  2. proanthocyanidin biosynthetic process Source: TAIR
  3. response to jasmonic acid Source: TAIR
  4. response to wounding Source: TAIR
  5. vacuole organization Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Flavonoid biosynthesis

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

BioCyciARA:AT4G22880-MONOMER.
ARA:GQT-1369-MONOMER.
UniPathwayiUPA00009.

Names & Taxonomyi

Protein namesi
Recommended name:
Leucoanthocyanidin dioxygenase (EC:1.14.11.19)
Short name:
LDOX
Short name:
Leucocyanidin oxygenase
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 namesi
Name:LDOX
Ordered Locus Names:At4g22880
ORF Names:F7H19.60
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 4

Organism-specific databases

TAIRiAT4G22880.

Pathology & Biotechi

Disruption phenotypei

No accumulation of anthocyanins, accumulation of protoanthocyanidin intermediates and presence of numerous small vacuoles in leaf epidermal cells.3 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi78 – 781G → E in tt11-2; no accumulation of anthocyanin. 1 Publication
Mutagenesisi128 – 1281K → A: Retains two-third of the original activity. 1 Publication
Mutagenesisi131 – 1311N → A or D: Retains two-third of the original activity. 1 Publication
Mutagenesisi142 – 1421Y → H: Retains two-third of the original activity. 1 Publication
Mutagenesisi220 – 2201C → Y in tt17; no accumulation of anthocyanin. 1 Publication
Mutagenesisi228 – 2281G → D in tds4-1; no accumulation of anthocyanin. 2 Publications
Mutagenesisi230 – 2301E → Q: Retains one half of the original activity. 1 Publication
Mutagenesisi341 – 3411K → N: Retains two-third of the original activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 356356Leucoanthocyanidin dioxygenasePRO_0000067299Add
BLAST

Proteomic databases

PaxDbiQ96323.
PRIDEiQ96323.

Expressioni

Tissue specificityi

Expressed in young seedlings (at protein level).1 Publication

Inductioni

By methyl jasmonate, 6-benzylaminopurine, light and sucrose.3 Publications

Gene expression databases

ExpressionAtlasiQ96323. baseline and differential.
GenevestigatoriQ96323.

Interactioni

Protein-protein interaction databases

STRINGi3702.AT4G22880.1-P.

Structurei

Secondary structure

1
356
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 126Combined sources
Helixi20 – 223Combined sources
Helixi26 – 294Combined sources
Helixi35 – 406Combined sources
Beta strandi49 – 513Combined sources
Turni53 – 564Combined sources
Helixi60 – 7617Combined sources
Beta strandi78 – 847Combined sources
Helixi89 – 10315Combined sources
Helixi107 – 1104Combined sources
Helixi111 – 1133Combined sources
Helixi117 – 1193Combined sources
Beta strandi123 – 1264Combined sources
Beta strandi132 – 1343Combined sources
Beta strandi141 – 1499Combined sources
Helixi150 – 1523Combined sources
Helixi155 – 1573Combined sources
Helixi165 – 19026Combined sources
Helixi197 – 2015Combined sources
Helixi204 – 2074Combined sources
Beta strandi209 – 2179Combined sources
Turni223 – 2253Combined sources
Beta strandi228 – 2325Combined sources
Beta strandi236 – 2438Combined sources
Beta strandi249 – 2535Combined sources
Beta strandi256 – 2594Combined sources
Beta strandi267 – 2715Combined sources
Helixi273 – 2786Combined sources
Turni279 – 2813Combined sources
Beta strandi288 – 2903Combined sources
Beta strandi298 – 3069Combined sources
Turni309 – 3113Combined sources
Helixi318 – 3203Combined sources
Beta strandi323 – 3253Combined sources
Helixi334 – 34916Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GP4X-ray2.10A1-356[»]
1GP5X-ray2.20A1-356[»]
1GP6X-ray1.75A1-356[»]
2BRTX-ray2.20A2-356[»]
ProteinModelPortaliQ96323.
SMRiQ96323. Positions 2-350.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96323.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini208 – 307100Fe2OG dioxygenasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni215 – 21732-oxoglutarate binding2 Publications
Regioni298 – 30032-oxoglutarate binding2 Publications

Sequence similaritiesi

Contains 1 Fe2OG dioxygenase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG3491.
HOGENOMiHOG000276735.
InParanoidiQ96323.
KOiK05277.
OMAiKCVPDSI.
PhylomeDBiQ96323.

Family and domain databases

Gene3Di2.60.120.330. 1 hit.
InterProiIPR026992. DIOX_N.
IPR027443. IPNS-like.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
[Graphical view]
PfamiPF03171. 2OG-FeII_Oxy. 1 hit.
PF14226. DIOX_N. 1 hit.
[Graphical view]
PROSITEiPS51471. FE2OG_OXY. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q96323-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVAVERVESL AKSGIISIPK EYIRPKEELE SINDVFLEEK KEDGPQVPTI
60 70 80 90 100
DLKNIESDDE KIRENCIEEL KKASLDWGVM HLINHGIPAD LMERVKKAGE
110 120 130 140 150
EFFSLSVEEK EKYANDQATG KIQGYGSKLA NNASGQLEWE DYFFHLAYPE
160 170 180 190 200
EKRDLSIWPK TPSDYIEATS EYAKCLRLLA TKVFKALSVG LGLEPDRLEK
210 220 230 240 250
EVGGLEELLL QMKINYYPKC PQPELALGVE AHTDVSALTF ILHNMVPGLQ
260 270 280 290 300
LFYEGKWVTA KCVPDSIVMH IGDTLEILSN GKYKSILHRG LVNKEKVRIS
310 320 330 340 350
WAVFCEPPKD KIVLKPLPEM VSVESPAKFP PRTFAQHIEH KLFGKEQEEL

VSEKND
Length:356
Mass (Da):40,396
Last modified:February 1, 1997 - v1
Checksum:i1B74AE3A54056201
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiT05119.
RefSeqiNP_001031700.1. NM_001036623.1.
NP_194019.1. NM_118417.1.
UniGeneiAt.2369.

Genome annotation databases

EnsemblPlantsiAT4G22880.1; AT4G22880.1; AT4G22880.
AT4G22880.2; AT4G22880.2; AT4G22880.
GeneIDi828387.
KEGGiath:AT4G22880.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi T05119.
RefSeqi NP_001031700.1. NM_001036623.1.
NP_194019.1. NM_118417.1.
UniGenei At.2369.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
ProteinModelPortali Q96323.
SMRi Q96323. Positions 2-350.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 3702.AT4G22880.1-P.

Proteomic databases

PaxDbi Q96323.
PRIDEi Q96323.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT4G22880.1 ; AT4G22880.1 ; AT4G22880 .
AT4G22880.2 ; AT4G22880.2 ; AT4G22880 .
GeneIDi 828387.
KEGGi ath:AT4G22880.

Organism-specific databases

TAIRi AT4G22880.

Phylogenomic databases

eggNOGi COG3491.
HOGENOMi HOG000276735.
InParanoidi Q96323.
KOi K05277.
OMAi KCVPDSI.
PhylomeDBi Q96323.

Enzyme and pathway databases

UniPathwayi UPA00009 .
BioCyci ARA:AT4G22880-MONOMER.
ARA:GQT-1369-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q96323.

Gene expression databases

ExpressionAtlasi Q96323. baseline and differential.
Genevestigatori Q96323.

Family and domain databases

Gene3Di 2.60.120.330. 1 hit.
InterProi IPR026992. DIOX_N.
IPR027443. IPNS-like.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
[Graphical view ]
Pfami PF03171. 2OG-FeII_Oxy. 1 hit.
PF14226. DIOX_N. 1 hit.
[Graphical view ]
PROSITEi PS51471. FE2OG_OXY. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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 THE SUBSTRATE ANALOG DIHYDROQUERCETIN; 2-OXOGLUTARATE AND IRON ION, COFACTOR.
  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 THE SUBSTRATE ANALOG NARINGENIN; 2-OXOGLUTARATE AND IRON ION, FUNCTION, COFACTOR, MUTAGENESIS OF LYS-128; ASN-131; TYR-142; GLU-230 AND LYS-341.

Entry informationi

Entry nameiLDOX_ARATH
AccessioniPrimary (citable) accession number: Q96323
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: February 1, 1997
Last modified: November 26, 2014
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3