HDT1_ARATH
ID HDT1_ARATH Reviewed; 245 AA.
AC Q9FVE6; O22238;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Histone deacetylase HDT1 {ECO:0000303|PubMed:12466527};
DE AltName: Full=HD-tuins protein 1 {ECO:0000303|PubMed:12466527};
DE AltName: Full=Histone deacetylase 2a {ECO:0000303|PubMed:10792817, ECO:0000303|PubMed:12694598};
DE Short=AtHD2A {ECO:0000303|PubMed:12694598};
GN Name=HDT1 {ECO:0000303|PubMed:12466527};
GN Synonyms=HD2A {ECO:0000303|PubMed:10792817, ECO:0000303|PubMed:12694598},
GN HDA3; OrderedLocusNames=At3g44750 {ECO:0000312|Araport:AT3G44750};
GN ORFNames=T32N15.8 {ECO:0000312|EMBL:AAB70032.1};
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], FUNCTION, 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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
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 [6]
RP SUBCELLULAR LOCATION.
RX PubMed=14505352; DOI=10.1002/jcb.10624;
RA Calikowski T.T., Meulia T., Meier I.;
RT "A proteomic study of the Arabidopsis nuclear matrix.";
RL J. Cell. Biochem. 90:361-378(2003).
RN [7]
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 [8]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=14992728; DOI=10.1016/s1097-2765(04)00064-4;
RA Lawrence R.J., Earley K., Pontes O., Silva M., Chen Z.J., Neves N.,
RA Viegas W., Pikaard C.S.;
RT "A concerted DNA methylation/histone methylation switch regulates rRNA gene
RT dosage control and nucleolar dominance.";
RL Mol. Cell 13:599-609(2004).
RN [9]
RP FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP 2-GLU--GLY-5; HIS-25 AND ASP-69.
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. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [11]
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 [12]
RP INTERACTION WITH DNMT2.
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 [13]
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).
RN [14]
RP INTERACTION WITH DEK3, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=cv. Columbia;
RX PubMed=25387881; DOI=10.1105/tpc.114.129254;
RA Waidmann S., Kusenda B., Mayerhofer J., Mechtler K., Jonak C.;
RT "A DEK domain-containing protein modulates chromatin structure and function
RT in Arabidopsis.";
RL Plant Cell 26:4328-4344(2014).
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. Required for histone H3 'Lys-9'
CC deacetylation. Involved in rRNA gene silencing in nucleolar dominance.
CC Seems to be implicated in the regulation of genes involved in seeds
CC development. {ECO:0000269|PubMed:10792817, ECO:0000269|PubMed:12694598,
CC ECO:0000269|PubMed:14992728, ECO:0000269|PubMed:15144374}.
CC -!- SUBUNIT: Interacts with DNMT2 (PubMed:20331964). Interacts with DEK3
CC (PubMed:25387881). {ECO:0000269|PubMed:20331964,
CC ECO:0000269|PubMed:25387881}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14505352,
CC ECO:0000269|PubMed:14992728, ECO:0000269|PubMed:15144374}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9FVE6-1; Sequence=Displayed;
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: Loss-of-function mutant (antisense inhibition) induces
CC increased methylation of histone H3 'Lys-4' and hypomethylation of DNA
CC at rDNA repeats.
CC -!- SIMILARITY: Belongs to the histone deacetylase HD2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB70032.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF195545; AAG28472.1; -; mRNA.
DR EMBL; AC002534; AAB70032.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE77944.1; -; Genomic_DNA.
DR EMBL; AY065396; AAL38837.1; -; mRNA.
DR EMBL; AY096729; AAM20363.1; -; mRNA.
DR RefSeq; NP_566872.1; NM_114344.4. [Q9FVE6-1]
DR AlphaFoldDB; Q9FVE6; -.
DR SMR; Q9FVE6; -.
DR BioGRID; 8925; 3.
DR IntAct; Q9FVE6; 3.
DR STRING; 3702.AT3G44750.1; -.
DR iPTMnet; Q9FVE6; -.
DR PaxDb; Q9FVE6; -.
DR PRIDE; Q9FVE6; -.
DR ProteomicsDB; 230300; -. [Q9FVE6-1]
DR EnsemblPlants; AT3G44750.1; AT3G44750.1; AT3G44750. [Q9FVE6-1]
DR GeneID; 823605; -.
DR Gramene; AT3G44750.1; AT3G44750.1; AT3G44750. [Q9FVE6-1]
DR KEGG; ath:AT3G44750; -.
DR Araport; AT3G44750; -.
DR TAIR; locus:2101655; AT3G44750.
DR eggNOG; ENOG502QVH6; Eukaryota.
DR HOGENOM; CLU_061903_0_0_1; -.
DR InParanoid; Q9FVE6; -.
DR OMA; YLHMSQA; -.
DR OrthoDB; 1260281at2759; -.
DR PhylomeDB; Q9FVE6; -.
DR BRENDA; 3.5.1.98; 399.
DR PRO; PR:Q9FVE6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9FVE6; baseline and differential.
DR Genevisible; Q9FVE6; AT.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0004407; F:histone deacetylase activity; IMP:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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; IBA:GO_Central.
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 InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF17800; NPL; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Chromatin regulator;
KW Developmental protein; Hydrolase; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; Transcription; Transcription regulation;
KW Zinc; Zinc-finger.
FT CHAIN 1..245
FT /note="Histone deacetylase HDT1"
FT /id="PRO_0000195204"
FT ZN_FING 218..241
FT /note="C2H2-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 2..5
FT /note="Required to repress transcription"
FT /evidence="ECO:0000269|PubMed:15144374"
FT REGION 99..245
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 101..162
FT /note="Required to repress transcription"
FT COMPBIAS 136..159
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 160..174
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 193..207
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 209..235
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 211
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q56WH4"
FT MUTAGEN 2..5
FT /note="Missing: Loss of transcriptional repression
FT activity."
FT /evidence="ECO:0000269|PubMed:15144374"
FT MUTAGEN 25
FT /note="H->A: Decrease of transcriptional repression
FT activity."
FT /evidence="ECO:0000269|PubMed:15144374"
FT MUTAGEN 69
FT /note="D->A: No effect on transcriptional repression
FT activity."
FT /evidence="ECO:0000269|PubMed:15144374"
SQ SEQUENCE 245 AA; 26372 MW; E8E4F7E0A0D24F28 CRC64;
MEFWGIEVKS GKPVTVTPEE GILIHVSQAS LGECKNKKGE FVPLHVKVGN QNLVLGTLST
ENIPQLFCDL VFDKEFELSH TWGKGSVYFV GYKTPNIEPQ GYSEEEEEEE EEVPAGNAAK
AVAKPKAKPA EVKPAVDDEE DESDSDGMDE DDSDGEDSEE EEPTPKKPAS SKKRANETTP
KAPVSAKKAK VAVTPQKTDE KKKGGKAANQ SPKSASQVSC GSCKKTFNSG NALESHNKAK
HAAAK
