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Q96323

- LDOX_ARATH

UniProt

Q96323 - LDOX_ARATH

Protein

Leucoanthocyanidin dioxygenase

Gene

LDOX

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    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

    Binds 1 ascorbate molecule per subunit.
    Binds 1 Fe2+ ion per subunit.

    Pathwayi

    Sites

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

    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

    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

    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 – 126
    Helixi20 – 223
    Helixi26 – 294
    Helixi35 – 406
    Beta strandi49 – 513
    Turni53 – 564
    Helixi60 – 7617
    Beta strandi78 – 847
    Helixi89 – 10315
    Helixi107 – 1104
    Helixi111 – 1133
    Helixi117 – 1193
    Beta strandi123 – 1264
    Beta strandi132 – 1343
    Beta strandi141 – 1499
    Helixi150 – 1523
    Helixi155 – 1573
    Helixi165 – 19026
    Helixi197 – 2015
    Helixi204 – 2074
    Beta strandi209 – 2179
    Turni223 – 2253
    Beta strandi228 – 2325
    Beta strandi236 – 2438
    Beta strandi249 – 2535
    Beta strandi256 – 2594
    Beta strandi267 – 2715
    Helixi273 – 2786
    Turni279 – 2813
    Beta strandi288 – 2903
    Beta strandi298 – 3069
    Turni309 – 3113
    Helixi318 – 3203
    Beta strandi323 – 3253
    Helixi334 – 34916

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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 binding
    Regioni298 – 30032-oxoglutarate binding

    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

    MVAVERVESL AKSGIISIPK EYIRPKEELE SINDVFLEEK KEDGPQVPTI    50
    DLKNIESDDE KIRENCIEEL KKASLDWGVM HLINHGIPAD LMERVKKAGE 100
    EFFSLSVEEK EKYANDQATG KIQGYGSKLA NNASGQLEWE DYFFHLAYPE 150
    EKRDLSIWPK TPSDYIEATS EYAKCLRLLA TKVFKALSVG LGLEPDRLEK 200
    EVGGLEELLL QMKINYYPKC PQPELALGVE AHTDVSALTF ILHNMVPGLQ 250
    LFYEGKWVTA KCVPDSIVMH IGDTLEILSN GKYKSILHRG LVNKEKVRIS 300
    WAVFCEPPKD KIVLKPLPEM VSVESPAKFP PRTFAQHIEH KLFGKEQEEL 350
    VSEKND 356
    Length:356
    Mass (Da):40,396
    Last modified:February 1, 1997 - v1
    Checksum:i1B74AE3A54056201
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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

    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

    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: October 1, 2014
    This is version 120 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