O22446 (HDA19_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	501 AA.
Sequence status	Complete.
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.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 process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Chromatin regulator Hydrolase Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA mediated transformation Inferred from mutant phenotype PubMed 17827277. Source: TAIR histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC 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-dependent 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-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from direct assay Ref.9PubMed 16763149PubMed 22381007. Source: TAIR
Molecular_function	NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K18 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from electronic annotation. Source: EC histone deacetylase activity Inferred from direct assay Ref.11PubMed 22381007. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
At2g45640	O64644	2	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.14
Experimental info
	Sequence conflict	69	1	D → E in AAB66486. Ref.1
	Sequence conflict	69	1	D → E in AAG28474. 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] [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, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[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.
IPI	IPI00522349.
PIR	T05640.
RefSeq	NP_195526.1. NM_119974.3.
UniGene	At.25069.
3D structure databases
ProteinModelPortal	O22446.
SMR	O22446. Positions 16-381.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-33483N.
IntAct	O22446. 5 interactions.
Proteomic databases
PaxDb	O22446.
PRIDE	O22446.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G38130.1; AT4G38130.1; AT4G38130.
GeneID	829969.
KEGG	ath:AT4G38130.
Organism-specific databases
TAIR	At4g38130.
Phylogenomic databases
eggNOG	COG0123.
HOGENOM	HOG000225180.
InParanoid	O22446.
KO	K06067.
OMA	MEIFRPG.
PhylomeDB	O22446.
ProtClustDB	CLSN2685384.
Gene expression databases
ArrayExpress	O22446.
Genevestigator	O22446.
GermOnline	AT4G38130. Arabidopsis thaliana.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR003084. His_deacetylse_1. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 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:	May 1, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program