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O22446

- HDA19_ARATH

UniProt

O22446 - HDA19_ARATH

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Protein
Histone deacetylase 19
Gene
HDA19, HD1, HDA1, RPD3A, At4g38130, F20D10.250
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 1491 By similarity

GO - Molecular functioni

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

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
Complete GO annotation...

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

GO - Cellular componenti

  1. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 501501Histone deacetylase 19
PRO_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.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni17 – 329313Histone deacetylase
Add
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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti69 – 691D → E in AAB66486. 1 Publication
Sequence conflicti69 – 691D → E in AAG28474. 1 Publication

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...

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 124 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

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