Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

O22446 (HDA19_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone deacetylase 19

Short name=AtHD1
Short name=HD
EC=3.5.1.98
Gene names
Name:HDA19
Synonyms:HD1, HDA1, RPD3A
Ordered Locus Names:At4g38130
ORF Names:F20D10.250
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length501 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.7 Ref.9 Ref.11

Catalytic activity

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

Subunit structure

Interacts with SIN3, SAP18 and TPR1. Interacts with CDKE-1, MED14 and LUG. Ref.10 Ref.12 Ref.13 Ref.15

Subcellular location

Nucleus. Note: excluded from the nucleolus, but associated with the condensing chromatids. Ref.9 Ref.11

Tissue specificity

Highly expressed in leaves, stems, flowers and young siliques. Ref.2 Ref.7 Ref.11

Induction

By jasmonic acid, ethylene, wounding and pathogen infection. Inhibited by sodium butyrate. Ref.9 Ref.11

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.

Sequence similarities

Belongs to the histone deacetylase family. HD type 1 subfamily.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   Molecular functionChromatin regulator
Hydrolase
Repressor
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA mediated transformation

Inferred from mutant phenotype PubMed 17827277. Source: TAIR

histone acetylation

Inferred from direct assay PubMed 17085686. Source: TAIR

jasmonic acid and ethylene-dependent systemic resistance

Inferred from mutant phenotype Ref.9. Source: TAIR

negative regulation of transcription, DNA-templated

Inferred from direct assay Ref.10. Source: TAIR

pathogenesis

Inferred from mutant phenotype PubMed 22381007. Source: TAIR

regulation of multicellular organismal development

Inferred from mutant phenotype Ref.7. Source: TAIR

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.9PubMed 16763149PubMed 22381007. Source: TAIR

   Molecular_functionNAD-dependent histone deacetylase activity (H3-K14 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K18 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K9 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H4-K16 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

histone deacetylase activity

Inferred from direct assay Ref.11PubMed 22381007. Source: TAIR

protein binding

Inferred from physical interaction Ref.13. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

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

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: O22446-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 501501Histone deacetylase 19
PRO_0000114721

Regions

Region17 – 329313Histone deacetylase

Sites

Active site1491 By similarity

Amino acid modifications

Modified residue4161Phosphoserine Ref.14

Experimental info

Sequence conflict691D → E in AAB66486. Ref.1
Sequence conflict691D → E in AAG28474. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 6, 2002. Version 2.
Checksum: 857D2E3D16B7CC1F

FASTA50156,023
        10         20         30         40         50         60 
MDTGGNSLAS GPDGVKRKVC YFYDPEVGNY YYGQGHPMKP HRIRMTHALL AHYGLLQHMQ 

        70         80         90        100        110        120 
VLKPFPARDR DLCRFHADDY VSFLRSITPE TQQDQIRQLK RFNVGEDCPV FDGLYSFCQT 

       130        140        150        160        170        180 
YAGGSVGGSV KLNHGLCDIA INWAGGLHHA KKCEASGFCY VNDIVLAILE LLKQHERVLY 

       190        200        210        220        230        240 
VDIDIHHGDG VEEAFYATDR VMTVSFHKFG DYFPGTGHIQ DIGYGSGKYY SLNVPLDDGI 

       250        260        270        280        290        300 
DDESYHLLFK PIMGKVMEIF RPGAVVLQCG ADSLSGDRLG CFNLSIKGHA ECVKFMRSFN 

       310        320        330        340        350        360 
VPLLLLGGGG YTIRNVARCW CYETGVALGV EVEDKMPEHE YYEYFGPDYT LHVAPSNMEN 

       370        380        390        400        410        420 
KNSRQMLEEI RNDLLHNLSK LQHAPSVPFQ ERPPDTETPE VDEDQEDGDK RWDPDSDMDV 

       430        440        450        460        470        480 
DDDRKPIPSR VKREAVEPDT KDKDGLKGIM ERGKGCEVEV DESGSTKVTG VNPVGVEEAS 

       490        500 
VKMEEEGTNK GGAEQAFPPK T 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT05640.
RefSeqNP_195526.1. NM_119974.3. [O22446-1]
UniGeneAt.25069.

3D structure databases

ProteinModelPortalO22446.
SMRO22446. Positions 16-384.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid15249. 11 interactions.
DIPDIP-33483N.
IntActO22446. 6 interactions.

Proteomic databases

PaxDbO22446.
PRIDEO22446.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G38130.1; AT4G38130.1; AT4G38130. [O22446-1]
GeneID829969.
KEGGath:AT4G38130.

Organism-specific databases

TAIRAT4G38130.

Phylogenomic databases

eggNOGCOG0123.
HOGENOMHOG000225180.
InParanoidO22446.
KOK06067.
OMAVSIRAHD.
PhylomeDBO22446.

Enzyme and pathway databases

BioCycARA:AT4G38130-MONOMER.
ARA:GQT-1431-MONOMER.

Gene expression databases

GenevestigatorO22446.

Family and domain databases

Gene3D3.40.800.20. 1 hit.
InterProIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERPTHR10625. PTHR10625. 1 hit.
PfamPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSPR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNetSearch...

Entry information

Entry nameHDA19_ARATH
AccessionPrimary (citable) accession number: O22446
Secondary accession number(s): Q0WWG3, Q9SZL3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: June 6, 2002
Last modified: June 11, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names