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   27-MAR-2024, entry version 127.
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.Q944K3; -.
DR   PaxDb; 3702-AT5G26040-2; -.
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; AT5G26040; HDA2.
DR   eggNOG; KOG1344; Eukaryota.
DR   HOGENOM; CLU_007727_1_1_1; -.
DR   InParanoid; Q944K3; -.
DR   OMA; GTHHAHY; -.
DR   OrthoDB; 239005at2759; -.
DR   PhylomeDB; Q944K3; -.
DR   PRO; PR:Q944K3; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q944K3; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   CDD; cd09993; HDAC_classIV; 1.
DR   Gene3D; 3.40.800.20; Histone deacetylase domain; 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   PANTHER; PTHR10625:SF33; HISTONE DEACETYLASE 11; 1.
DR   PANTHER; PTHR10625; HISTONE DEACETYLASE HDAC1-RELATED; 1.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   SUPFAM; SSF52768; Arginase/deacetylase; 1.
DR   Genevisible; Q944K3; AT.
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
//