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O22446

- HDA19_ARATH

UniProt

O22446 - HDA19_ARATH

Protein

Histone deacetylase 19

Gene

HDA19

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 125 (01 Oct 2014)
      Sequence version 2 (06 Jun 2002)
      Previous versions | rss
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    Functioni

    Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. HDA19 is involved in jasmonic acid and ethylene signaling of pathogen response.4 Publications

    Catalytic activityi

    Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei149 – 1491By similarity

    GO - Molecular functioni

    1. histone deacetylase activity Source: TAIR
    2. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
    3. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
    4. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
    5. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
    6. protein binding Source: UniProtKB

    GO - Biological processi

    1. DNA mediated transformation Source: TAIR
    2. histone acetylation Source: TAIR
    3. jasmonic acid and ethylene-dependent systemic resistance Source: TAIR
    4. negative regulation of transcription, DNA-templated Source: TAIR
    5. pathogenesis Source: TAIR
    6. regulation of multicellular organismal development Source: TAIR
    7. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciARA:AT4G38130-MONOMER.
    ARA:GQT-1431-MONOMER.
    ReactomeiREACT_187702. G0 and Early G1.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone deacetylase 19 (EC:3.5.1.98)
    Short name:
    AtHD1
    Short name:
    HD
    Gene namesi
    Name:HDA19
    Synonyms:HD1, HDA1, RPD3A
    Ordered Locus Names:At4g38130
    ORF Names:F20D10.250
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G38130.

    Subcellular locationi

    Nucleus 2 Publications
    Note: excluded from the nucleolus, but associated with the condensing chromatids.

    GO - Cellular componenti

    1. nucleus Source: TAIR

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 501501Histone deacetylase 19PRO_0000114721Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei416 – 4161Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiO22446.
    PRIDEiO22446.

    Expressioni

    Tissue specificityi

    Highly expressed in leaves, stems, flowers and young siliques.3 Publications

    Inductioni

    By jasmonic acid, ethylene, wounding and pathogen infection. Inhibited by sodium butyrate.2 Publications

    Gene expression databases

    GenevestigatoriO22446.

    Interactioni

    Subunit structurei

    Interacts with SIN3, SAP18 and TPR1. Interacts with CDKE-1, MED14 and LUG.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    At2g45640O646442EBI-593040,EBI-965964
    SCL1Q6DLS13EBI-593040,EBI-593035From a different organism.
    WRKY38Q8GWF12EBI-593040,EBI-1993263
    WRKY62Q9LZV64EBI-593040,EBI-1993243

    Protein-protein interaction databases

    BioGridi15249. 11 interactions.
    DIPiDIP-33483N.
    IntActiO22446. 6 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliO22446.
    SMRiO22446. Positions 16-384.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni17 – 329313Histone deacetylaseAdd
    BLAST

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0123.
    HOGENOMiHOG000225180.
    InParanoidiO22446.
    KOiK06067.
    OMAiVSIRAHD.
    PhylomeDBiO22446.

    Family and domain databases

    Gene3Di3.40.800.20. 1 hit.
    InterProiIPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view]
    PANTHERiPTHR10625. PTHR10625. 1 hit.
    PfamiPF00850. Hist_deacetyl. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSiPR01270. HDASUPER.
    PR01271. HISDACETLASE.

    Sequencei

    Sequence statusi: Complete.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: O22446-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MDTGGNSLAS GPDGVKRKVC YFYDPEVGNY YYGQGHPMKP HRIRMTHALL    50
    AHYGLLQHMQ VLKPFPARDR DLCRFHADDY VSFLRSITPE TQQDQIRQLK 100
    RFNVGEDCPV FDGLYSFCQT YAGGSVGGSV KLNHGLCDIA INWAGGLHHA 150
    KKCEASGFCY VNDIVLAILE LLKQHERVLY VDIDIHHGDG VEEAFYATDR 200
    VMTVSFHKFG DYFPGTGHIQ DIGYGSGKYY SLNVPLDDGI DDESYHLLFK 250
    PIMGKVMEIF RPGAVVLQCG ADSLSGDRLG CFNLSIKGHA ECVKFMRSFN 300
    VPLLLLGGGG YTIRNVARCW CYETGVALGV EVEDKMPEHE YYEYFGPDYT 350
    LHVAPSNMEN KNSRQMLEEI RNDLLHNLSK LQHAPSVPFQ ERPPDTETPE 400
    VDEDQEDGDK RWDPDSDMDV DDDRKPIPSR VKREAVEPDT KDKDGLKGIM 450
    ERGKGCEVEV DESGSTKVTG VNPVGVEEAS VKMEEEGTNK GGAEQAFPPK 500
    T 501
    Length:501
    Mass (Da):56,023
    Last modified:June 6, 2002 - v2
    Checksum:i857D2E3D16B7CC1F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti69 – 691D → E in AAB66486. 1 PublicationCurated
    Sequence conflicti69 – 691D → E in AAG28474. (PubMed:11117260)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF014824 mRNA. Translation: AAB66486.1.
    AF195547 mRNA. Translation: AAG28474.1.
    AL035538 Genomic DNA. Translation: CAB37553.1.
    AL161593 Genomic DNA. Translation: CAB80478.1.
    CP002687 Genomic DNA. Translation: AEE86881.1.
    AY093153 mRNA. Translation: AAM13152.1.
    BT008873 mRNA. Translation: AAP68312.1.
    AK226389 mRNA. Translation: BAE98535.1.
    PIRiT05640.
    RefSeqiNP_195526.1. NM_119974.3. [O22446-1]
    UniGeneiAt.25069.

    Genome annotation databases

    EnsemblPlantsiAT4G38130.1; AT4G38130.1; AT4G38130. [O22446-1]
    GeneIDi829969.
    KEGGiath:AT4G38130.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF014824 mRNA. Translation: AAB66486.1 .
    AF195547 mRNA. Translation: AAG28474.1 .
    AL035538 Genomic DNA. Translation: CAB37553.1 .
    AL161593 Genomic DNA. Translation: CAB80478.1 .
    CP002687 Genomic DNA. Translation: AEE86881.1 .
    AY093153 mRNA. Translation: AAM13152.1 .
    BT008873 mRNA. Translation: AAP68312.1 .
    AK226389 mRNA. Translation: BAE98535.1 .
    PIRi T05640.
    RefSeqi NP_195526.1. NM_119974.3. [O22446-1 ]
    UniGenei At.25069.

    3D structure databases

    ProteinModelPortali O22446.
    SMRi O22446. Positions 16-384.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 15249. 11 interactions.
    DIPi DIP-33483N.
    IntActi O22446. 6 interactions.

    Proteomic databases

    PaxDbi O22446.
    PRIDEi O22446.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G38130.1 ; AT4G38130.1 ; AT4G38130 . [O22446-1 ]
    GeneIDi 829969.
    KEGGi ath:AT4G38130.

    Organism-specific databases

    TAIRi AT4G38130.

    Phylogenomic databases

    eggNOGi COG0123.
    HOGENOMi HOG000225180.
    InParanoidi O22446.
    KOi K06067.
    OMAi VSIRAHD.
    PhylomeDBi O22446.

    Enzyme and pathway databases

    BioCyci ARA:AT4G38130-MONOMER.
    ARA:GQT-1431-MONOMER.
    Reactomei REACT_187702. G0 and Early G1.

    Gene expression databases

    Genevestigatori O22446.

    Family and domain databases

    Gene3Di 3.40.800.20. 1 hit.
    InterProi IPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view ]
    PANTHERi PTHR10625. PTHR10625. 1 hit.
    Pfami PF00850. Hist_deacetyl. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSi PR01270. HDASUPER.
    PR01271. HISDACETLASE.
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of a histone deacetylase (EST G11C3T7) in Arabidopsis thaliana."
      Tomihama T., Shoji K., Hanyu H., Okano T.
      Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Columbia.
    2. "Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana."
      Wu K., Malik K., Tian L., Brown D., Miki B.
      Plant Mol. Biol. 44:167-176(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
      Strain: cv. Columbia.
    3. "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.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    7. "Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development."
      Tian L., Chen Z.J.
      Proc. Natl. Acad. Sci. U.S.A. 98:200-205(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.
    8. "Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes."
      Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A.
      Nucleic Acids Res. 30:5036-5055(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE.
    9. "HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis."
      Zhou C., Zhang L., Duan J., Miki B., Wu K.
      Plant Cell 17:1196-1204(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION.
    10. "Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses."
      Song C.-P., Agarwal M., Ohta M., Guo Y., Halfter U., Wang P., Zhu J.-K.
      Plant Cell 17:2384-2396(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SIN3.
    11. "Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro."
      Fong P.M., Tian L., Chen Z.J.
      Cell Res. 16:479-488(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
    12. "AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis."
      Song C.-P., Galbraith D.W.
      Plant Mol. Biol. 60:241-257(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SAP18.
    13. "The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription."
      Gonzalez D., Bowen A.J., Carroll T.S., Conlan R.S.
      Mol. Cell. Biol. 27:5306-5315(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH MED14; LUG AND CDKE-1.
    14. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-416, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Arabidopsis resistance protein SNC1 activates immune responses through association with a transcriptional corepressor."
      Zhu Z., Xu F., Zhang Y., Cheng Y.T., Wiermer M., Li X., Zhang Y.
      Proc. Natl. Acad. Sci. U.S.A. 107:13960-13965(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TPR1.

    Entry informationi

    Entry nameiHDA19_ARATH
    AccessioniPrimary (citable) accession number: O22446
    Secondary accession number(s): Q0WWG3, Q9SZL3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: June 6, 2002
    Last modified: October 1, 2014
    This is version 125 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Loss-of-function mutant (antisense inhibition) has an increased level of tetraacetylated histone H4 and shows late flowering, developmental pleiotropy and increased symptoms when infected by a pathogen.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3