Reviewed, UniProtKB/Swiss-Prot O22446 (HDA19_ARATH)

Names and origin

Protein names

Recommended name:
    Histone deacetylase 19
      Short name=HD
      Short name=AtHD1
    EC=3.5.1.98

Gene names

Name:	HDA19
Synonyms:	HD1, HDA1, RPD3A
Ordered Locus Names:	At4g38130
ORF Names:	F20D10.250

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	501 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence 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.6 Ref.8 Ref.10
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subunit structure	Interacts with SIN3 and SAP18. Ref.9 Ref.11
Subcellular location	Nucleus. Note: excluded from the nucleolus, but associated with the condensing chromatids. Ref.8 Ref.10
Tissue specificity	Highly expressed in leaves, stems, flowers and young siliques. Ref.2 Ref.6 Ref.10
Induction	By jasmonic acid, ethylene, wounding and pathogen infection. Inhibited by sodium butyrate. Ref.8 Ref.10
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. Type 1 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Chromatin regulator Hydrolase Repressor
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA mediated transformation Inferred from mutant phenotype. Source: TAIR histone acetylation Inferred from direct assay. Source: TAIR histone deacetylation Inferred from electronic annotation. Source: InterPro jasmonic acid and ethylene-dependent systemic resistance Ref.8 Inferred from mutant phenotype. Source: TAIR negative regulation of transcription Ref.9 Inferred from direct assay. Source: TAIR transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Ref.8 Inferred from direct assay. Source: TAIR
Molecular function	basal transcription repressor activity Ref.11 Traceable author statement. Source: TAIR histone deacetylase activity Ref.6 Ref.10 Inferred from direct assay. Source: TAIR protein binding Ref.11 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
At2g45640	O64644	1	EBI-593040,EBI-965964
SCL1	Q6DLS1	3	EBI-593040,EBI-593035	From a different organism.
WRKY38	Q8GWF1	2	EBI-593040,EBI-1993263
WRKY62	Q9LZV6	4	EBI-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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 501	501	Histone deacetylase 19		PRO_0000114721
Regions
	Region	17 – 329	313	Histone deacetylase
Sites
	Active site	149	1	By similarity
Amino acid modifications
	Modified residue	416	1	Phosphoserine Ref.12
Experimental info
	Sequence conflict	69	1	D → E Ref.1
	Sequence conflict	69	1	D → E Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 6, 2002. Version 2. Checksum: 857D2E3D16B7CC1F	FASTA	501	56,023
	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

References

	« Hide 'large scale' referencesShow '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: 11117260] [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: 10617198] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	"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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"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.
[6]	"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: 11134508] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[7]	"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: 12466527] [Abstract] Cited for: GENE FAMILY, NOMENCLATURE.
[8]	"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: 15749761] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION.
[9]	"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: 15994908] [Abstract] Cited for: INTERACTION WITH SIN3.
[10]	"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: 16699543] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
[11]	"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: 16429262] [Abstract] Cited for: INTERACTION WITH SAP18.
[12]	"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: 19376835] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-416, MASS SPECTROMETRY. Tissue: Seedling.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF014824 mRNA. Translation: AAB66486.1. AF195547 mRNA. Translation: AAG28474.1. AL035538 Genomic DNA. Translation: CAB37553.1. AL161593 Genomic DNA. Translation: CAB80478.1. AY093153 mRNA. Translation: AAM13152.1. BT008873 mRNA. Translation: AAP68312.1. AK226389 mRNA. Translation: BAE98535.1.
IPI	IPI00522349.
PIR	T05640.
RefSeq	NP_195526.1.
UniGene	At.25069
3D structure databases
HSSP	HSSP built from PDB template 1C3P based on UniProtKB O67135.
ModBase	Search...
Protein-protein interaction databases
IntAct	O22446. 5 interactions.
STRING	O22446.
Proteomic databases
PRIDE	O22446.
Genome annotation databases
GeneID	829969.
GenomeReviews	Gene locus AT4G38130 in contig CT486007_GR.
NMPDR	fig|3702.1.peg.21927.
Organism-specific databases
TAIR	At4g38130.
Phylogenomic databases
OMA	DASIPNE.
Gene expression databases
ArrayExpress	O22446.
Genevestigator	O22446.
GermOnline	AT4G38130. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR000286. His_deacetylse. IPR003084. His_deacetylse_1. [Graphical view]
Gene3D	G3DSA:3.40.800.20. His_deacetylse. 1 hit.
PANTHER	PTHR10625. His_deacetylse. 1 hit. PTHR10625:SF28. His_deacetylse_1. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PIRSF	PIRSF037913. His_deacetylse_1. 1 hit.
PRINTS	PR01270. HDASUPER. PR01271. HISDACETLASE.
ProtoNet	Search...

Entry information

Entry name

HDA19_ARATH

Accession

Primary (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:	November 3, 2009
This is version 80 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)