HDT2_ARATH
ID HDT2_ARATH Reviewed; 306 AA.
AC Q56WH4; O49209; Q9FNJ6;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2005, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Histone deacetylase HDT2;
DE AltName: Full=HD-tuins protein 2;
DE AltName: Full=Histone deacetylase 2b;
GN Name=HDT2; Synonyms=HD2, HD2B, HDA4; OrderedLocusNames=At5g22650;
GN ORFNames=MDJ22.7;
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 [MRNA] (ISOFORM 2), AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10792817; DOI=10.1046/j.1365-313x.2000.00711.x;
RA Wu K., Tian L., Malik K., Brown D., Miki B.;
RT "Functional analysis of HD2 histone deacetylase homologues in Arabidopsis
RT thaliana.";
RL Plant J. 22:19-27(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=11469594; DOI=10.1007/s004250000506;
RA Dangl M., Brosch G., Haas H., Loidl P., Lusser A.;
RT "Comparative analysis of HD2 type histone deacetylases in higher plants.";
RL Planta 213:280-285(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 207-306 (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP GENE FAMILY, AND 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).
RN [8]
RP FUNCTION.
RX PubMed=12694598; DOI=10.1046/j.1365-313x.2003.01714.x;
RA Wu K., Tian L., Zhou C., Brown D., Miki B.;
RT "Repression of gene expression by Arabidopsis HD2 histone deacetylases.";
RL Plant J. 34:241-247(2003).
RN [9]
RP TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=15144374; DOI=10.1111/j.1365-313x.2004.02083.x;
RA Zhou C., Labbe H., Sridha S., Wang L., Tian L., Latoszek-Green M., Yang Z.,
RA Brown D., Miki B., Wu K.;
RT "Expression and function of HD2-type histone deacetylases in Arabidopsis
RT development.";
RL Plant J. 38:715-724(2004).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-259 AND SER-266, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [13]
RP INTERACTION WITH DNMT2, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=20331964; DOI=10.1016/j.bbrc.2010.03.119;
RA Song Y., Wu K., Dhaubhadel S., An L., Tian L.;
RT "Arabidopsis DNA methyltransferase AtDNMT2 associates with histone
RT deacetylase AtHD2s activity.";
RL Biochem. Biophys. Res. Commun. 396:187-192(2010).
RN [14]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Probably mediates 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. {ECO:0000269|PubMed:12694598}.
CC -!- SUBUNIT: Interacts with DNMT2. {ECO:0000269|PubMed:20331964}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:15144374}.
CC Nucleus {ECO:0000269|PubMed:20331964}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q56WH4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q56WH4-2; Sequence=VSP_015551;
CC -!- TISSUE SPECIFICITY: Expressed in leaves, roots, stems, young plantlets,
CC flowers and siliques. Highest levels in ovules, embryos, shoot apical
CC meristems and first leaves. Also expressed in somatic embryos.
CC {ECO:0000269|PubMed:10792817, ECO:0000269|PubMed:15144374}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the histone deacetylase HD2 family.
CC {ECO:0000305}.
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DR EMBL; AF195546; AAG28473.1; -; mRNA.
DR EMBL; AF044914; AAC02539.1; -; mRNA.
DR EMBL; AB006699; BAB11671.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93058.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93059.1; -; Genomic_DNA.
DR EMBL; AY059893; AAL24375.1; -; mRNA.
DR EMBL; AY079014; AAL84970.1; -; mRNA.
DR EMBL; AY122890; AAM67423.1; -; mRNA.
DR EMBL; AK222066; BAD94880.1; -; mRNA.
DR PIR; T52287; T52287.
DR RefSeq; NP_197657.3; NM_122171.3. [Q56WH4-2]
DR RefSeq; NP_851056.1; NM_180725.3. [Q56WH4-1]
DR AlphaFoldDB; Q56WH4; -.
DR SMR; Q56WH4; -.
DR BioGRID; 17603; 5.
DR STRING; 3702.AT5G22650.1; -.
DR iPTMnet; Q56WH4; -.
DR PaxDb; Q56WH4; -.
DR PRIDE; Q56WH4; -.
DR ProteomicsDB; 230301; -. [Q56WH4-1]
DR EnsemblPlants; AT5G22650.1; AT5G22650.1; AT5G22650. [Q56WH4-1]
DR EnsemblPlants; AT5G22650.2; AT5G22650.2; AT5G22650. [Q56WH4-2]
DR GeneID; 832328; -.
DR Gramene; AT5G22650.1; AT5G22650.1; AT5G22650. [Q56WH4-1]
DR Gramene; AT5G22650.2; AT5G22650.2; AT5G22650. [Q56WH4-2]
DR KEGG; ath:AT5G22650; -.
DR Araport; AT5G22650; -.
DR TAIR; locus:2162479; AT5G22650.
DR eggNOG; ENOG502S7T2; Eukaryota.
DR InParanoid; Q56WH4; -.
DR OMA; AGSHHCK; -.
DR OrthoDB; 1260281at2759; -.
DR PhylomeDB; Q56WH4; -.
DR BRENDA; 3.5.1.98; 399.
DR PRO; PR:Q56WH4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q56WH4; baseline and differential.
DR Genevisible; Q56WH4; AT.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0009505; C:plant-type cell wall; HDA:TAIR.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0004407; F:histone deacetylase activity; IMP:TAIR.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:TAIR.
DR GO; GO:0009944; P:polarity specification of adaxial/abaxial axis; IMP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR GO; GO:0010162; P:seed dormancy process; IEP:TAIR.
DR InterPro; IPR041232; NPL.
DR Pfam; PF17800; NPL; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Chromatin regulator;
KW Developmental protein; Hydrolase; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..306
FT /note="Histone deacetylase HDT2"
FT /id="PRO_0000195205"
FT REGION 2..5
FT /note="Required to repress transcription"
FT /evidence="ECO:0000250"
FT REGION 97..306
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 151..199
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 259..299
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES 259
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 266
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19376835"
FT VAR_SEQ 239
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:10792817,
FT ECO:0000303|PubMed:11469594"
FT /id="VSP_015551"
SQ SEQUENCE 306 AA; 32348 MW; A19274D43BDD142C CRC64;
MEFWGVAVTP KNATKVTPEE DSLVHISQAS LDCTVKSGES VVLSVTVGGA KLVIGTLSQD
KFPQISFDLV FDKEFELSHS GTKANVHFIG YKSPNIEQDD FTSSDDEDVP EAVPAPAPTA
VTANGNAGAA VVKADTKPKA KPAEVKPAEE KPESDEEDES DDEDESEEDD DSEKGMDVDE
DDSDDDEEED SEDEEEEETP KKPEPINKKR PNESVSKTPV SGKKAKPAAA PASTPQKTEE
KKKGGHTATP HPAKKGGKSP VNANQSPKSG GQSSGGNNNK KPFNSGKQFG GSNNKGSNKG
KGKGRA
