HDA2_ARATH
ID HDA2_ARATH Reviewed; 387 AA.
AC Q944K3; Q3E940; Q8LRK7; Q9XH00;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-MAR-2007, sequence version 2.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Histone deacetylase 2;
DE EC=3.5.1.98;
GN Name=HDA2; OrderedLocusNames=At5g26040; ORFNames=T1N24.9;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 48-387 (ISOFORMS 1 AND 3), GENE FAMILY, AND
RP NOMENCLATURE.
RX PubMed=12466527; DOI=10.1093/nar/gkf660;
RA Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S.,
RA Richards E.J., Bender J., Mount D.W., Jorgensen R.A.;
RT "Analysis of histone acetyltransferase and histone deacetylase families of
RT Arabidopsis thaliana suggests functional diversification of chromatin
RT modification among multicellular eukaryotes.";
RL Nucleic Acids Res. 30:5036-5055(2002).
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone
CC deacetylation gives a tag for epigenetic repression and plays an
CC important role in transcriptional regulation, cell cycle progression
CC and developmental events. Histone deacetylases act via the formation of
CC large multiprotein complexes. {ECO:0000250|UniProtKB:O22446}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-
CC [histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA-
CC COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:61930; EC=3.5.1.98;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q8GXJ1};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q8GXJ1};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q944K3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q944K3-2; Sequence=VSP_023528, VSP_023529;
CC Name=3;
CC IsoId=Q944K3-3; Sequence=VSP_023527;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 3
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD40129.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF149413; AAD40129.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93516.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93517.1; -; Genomic_DNA.
DR EMBL; AF428336; AAL16266.1; -; mRNA.
DR EMBL; BT002252; AAN72263.1; -; mRNA.
DR EMBL; AF510671; AAM34784.1; -; mRNA.
DR EMBL; AF510165; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; NP_568480.2; NM_122505.4. [Q944K3-1]
DR RefSeq; NP_851078.1; NM_180747.2. [Q944K3-3]
DR AlphaFoldDB; Q944K3; -.
DR SMR; Q944K3; -.
DR STRING; 3702.AT5G26040.2; -.
DR PaxDb; Q944K3; -.
DR PRIDE; Q944K3; -.
DR ProteomicsDB; 230299; -. [Q944K3-1]
DR EnsemblPlants; AT5G26040.1; AT5G26040.1; AT5G26040. [Q944K3-3]
DR EnsemblPlants; AT5G26040.2; AT5G26040.2; AT5G26040. [Q944K3-1]
DR GeneID; 832673; -.
DR Gramene; AT5G26040.1; AT5G26040.1; AT5G26040. [Q944K3-3]
DR Gramene; AT5G26040.2; AT5G26040.2; AT5G26040. [Q944K3-1]
DR KEGG; ath:AT5G26040; -.
DR Araport; AT5G26040; -.
DR TAIR; locus:2180657; AT5G26040.
DR eggNOG; KOG1344; Eukaryota.
DR HOGENOM; CLU_007727_1_1_1; -.
DR InParanoid; Q944K3; -.
DR OMA; RVFTFSM; -.
DR PhylomeDB; Q944K3; -.
DR PRO; PR:Q944K3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q944K3; baseline and differential.
DR Genevisible; Q944K3; AT.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0004407; F:histone deacetylase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016575; P:histone deacetylation; IBA:GO_Central.
DR CDD; cd09993; HDAC_classIV; 1.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR044150; HDAC_classIV.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chromatin regulator; Hydrolase; Metal-binding;
KW Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..387
FT /note="Histone deacetylase 2"
FT /id="PRO_0000280083"
FT REGION 73..382
FT /note="Histone deacetylase"
FT ACT_SITE 201
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 238
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 240
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 318
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT SITE 361
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT VAR_SEQ 208..235
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:12466527"
FT /id="VSP_023527"
FT VAR_SEQ 253..261
FT /note="NRVYILDMY -> SMIKTLYIS (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_023528"
FT VAR_SEQ 262..387
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_023529"
SQ SEQUENCE 387 AA; 43804 MW; 4BC4C14D6F0C4808 CRC64;
MTHTRVISTW TELTRDLAIY LLFTFFAIKV FKFLFSCNRT SEISSFSMAT HPEALRRERI
LNSKLYFDVP LSKVSIIYSS SYDISFMGIE KLHPFDSSKW GRVCKFLVSD GFLEEKAIVE
PLEASKIDLL VVHSENYLNS LKSSATVARI TEVAPVAFFP NFLVQQKVLY PFRKQVGGTI
LAAKLATERG WAINIGGGFH HCTAERGGGF CAFADISLCI HFAFLRLRIS RVMIIDLDAH
QGNGHETDLG DDNRVYILDM YNPEIYPFDY RARRFIDQKV EVMSGTTTDE YLRKLDEALE
VASRNFQPEL VIYNAGTDIL DGDPLGLLKI SPDGITSRDE KVFRFAREKN IPLVMLTSGG
YMKSSARVIA DSIENLSRQG LIQTRPE
