Q944K3 (HDA2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase 2
EC=3.5.1.98

Gene names

Name:	HDA2
Ordered Locus Names:	At5g26040
ORF Names:	T1N24.9

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	387 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript 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 By similarity.
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the histone deacetylase family. HD type 3 subfamily.
Sequence caution	The sequence AAD40129.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q944K3-1)

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.

Isoform 2 (identifier: Q944K3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     253-261: NRVYILDMY → SMIKTLYIS
     262-387: Missing.

Note: May be due to intron retention. No experimental confirmation available.

Isoform 3 (identifier: Q944K3-3)

The sequence of this isoform differs from the canonical sequence as follows:
     208-235: Missing.

Note: Derived from EST data. May be due to a competing acceptor splice site. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 387	387	Histone deacetylase 2		PRO_0000280083
Regions
	Region	73 – 382	310	Histone deacetylase
Sites
	Active site	201	1	By similarity
Natural variations
	Alternative sequence	208 – 235	28	Missing in isoform 3.		VSP_023527
	Alternative sequence	253 – 261	9	NRVYILDMY → SMIKTLYIS in isoform 2.		VSP_023528
	Alternative sequence	262 – 387	126	Missing in isoform 2.		VSP_023529

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 6, 2007. Version 2. Checksum: 4BC4C14D6F0C4808	FASTA	387	43,804
	10 20 30 40 50 60 MTHTRVISTW TELTRDLAIY LLFTFFAIKV FKFLFSCNRT SEISSFSMAT HPEALRRERI 70 80 90 100 110 120 LNSKLYFDVP LSKVSIIYSS SYDISFMGIE KLHPFDSSKW GRVCKFLVSD GFLEEKAIVE 130 140 150 160 170 180 PLEASKIDLL VVHSENYLNS LKSSATVARI TEVAPVAFFP NFLVQQKVLY PFRKQVGGTI 190 200 210 220 230 240 LAAKLATERG WAINIGGGFH HCTAERGGGF CAFADISLCI HFAFLRLRIS RVMIIDLDAH 250 260 270 280 290 300 QGNGHETDLG DDNRVYILDM YNPEIYPFDY RARRFIDQKV EVMSGTTTDE YLRKLDEALE 310 320 330 340 350 360 VASRNFQPEL VIYNAGTDIL DGDPLGLLKI SPDGITSRDE KVFRFAREKN IPLVMLTSGG 370 380 YMKSSARVIA DSIENLSRQG LIQTRPE
	Isoform 2 [UniParc]. Checksum: 0452A8B9401EC669	FASTA	261	29,407
	10 20 30 40 50 60 MTHTRVISTW TELTRDLAIY LLFTFFAIKV FKFLFSCNRT SEISSFSMAT HPEALRRERI 70 80 90 100 110 120 LNSKLYFDVP LSKVSIIYSS SYDISFMGIE KLHPFDSSKW GRVCKFLVSD GFLEEKAIVE 130 140 150 160 170 180 PLEASKIDLL VVHSENYLNS LKSSATVARI TEVAPVAFFP NFLVQQKVLY PFRKQVGGTI 190 200 210 220 230 240 LAAKLATERG WAINIGGGFH HCTAERGGGF CAFADISLCI HFAFLRLRIS RVMIIDLDAH 250 260 QGNGHETDLG DDSMIKTLYI S
	Isoform 3 [UniParc]. Checksum: 24993D8597EDD144	FASTA	359	40,651
	10 20 30 40 50 60 MTHTRVISTW TELTRDLAIY LLFTFFAIKV FKFLFSCNRT SEISSFSMAT HPEALRRERI 70 80 90 100 110 120 LNSKLYFDVP LSKVSIIYSS SYDISFMGIE KLHPFDSSKW GRVCKFLVSD GFLEEKAIVE 130 140 150 160 170 180 PLEASKIDLL VVHSENYLNS LKSSATVARI TEVAPVAFFP NFLVQQKVLY PFRKQVGGTI 190 200 210 220 230 240 LAAKLATERG WAINIGGGFH HCTAERGDLD AHQGNGHETD LGDDNRVYIL DMYNPEIYPF 250 260 270 280 290 300 DYRARRFIDQ KVEVMSGTTT DEYLRKLDEA LEVASRNFQP ELVIYNAGTD ILDGDPLGLL 310 320 330 340 350 KISPDGITSR DEKVFRFARE KNIPLVMLTS GGYMKSSARV IADSIENLSR QGLIQTRPE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana." Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F. Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"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] (ISOFORM 2). Strain: cv. Columbia.
[4]	"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: NUCLEOTIDE SEQUENCE [MRNA] OF 48-387 (ISOFORMS 1 AND 3), GENE FAMILY, NOMENCLATURE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF149413 Genomic DNA. Translation: AAD40129.1. Sequence problems. CP002688 Genomic DNA. Translation: AED93516.1. CP002688 Genomic DNA. Translation: AED93517.1. AF428336 mRNA. Translation: AAL16266.1. BT002252 mRNA. Translation: AAN72263.1. AF510671 mRNA. Translation: AAM34784.1. AF510165 mRNA. No translation available.
IPI	IPI00535394. IPI00539406. IPI00837463.
RefSeq	NP_568480.2. NM_122505.3. NP_851078.1. NM_180747.2.
UniGene	At.58. At.70191.
3D structure databases
HSSP	HSSP built from PDB template 1T67 based on UniProtKB Q9BY41.
ProteinModelPortal	Q944K3.
SMR	Q944K3. Positions 93-367.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT5G26040.2-P.
Proteomic databases
PaxDb	Q944K3.
PRIDE	Q944K3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G26040.2; AT5G26040.2; AT5G26040.
GeneID	832673.
KEGG	ath:AT5G26040.
Organism-specific databases
TAIR	At5g26040.
Phylogenomic databases
eggNOG	COG0123.
HOGENOM	HOG000280018.
InParanoid	Q944K3.
KO	K11418.
OMA	DRGWAIN.
PhylomeDB	Q944K3.
ProtClustDB	CLSN2680263.
Gene expression databases
Genevestigator	Q944K3.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PRINTS	PR01270. HDASUPER.
ProtoNet	Search...

Entry information

Entry name

HDA2_ARATH

Accession

Primary (citable) accession number: Q944K3
Secondary accession number(s): Q3E940, Q8LRK7, Q9XH00

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	March 6, 2007
Last modified:	May 1, 2013
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program