HDT3_ARATH
ID HDT3_ARATH Reviewed; 294 AA.
AC Q9LZR5; Q9M4T4;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2005, sequence version 2.
DT 25-MAY-2022, entry version 129.
DE RecName: Full=Histone deacetylase HDT3;
DE AltName: Full=HD-tuins protein 3;
DE AltName: Full=Histone deacetylase 2c;
GN Name=HDT3; Synonyms=HD2C; OrderedLocusNames=At5g03740;
GN ORFNames=F17C15_160, MED24.1;
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], GENE FAMILY, AND NOMENCLATURE.
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 [2]
RP NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
RN [4]
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 [5]
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 [6]
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 [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 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 [9]
RP TISSUE SPECIFICITY, FUNCTION, AND INDUCTION.
RX PubMed=16553900; DOI=10.1111/j.1365-313x.2006.02678.x;
RA Sridha S., Wu K.;
RT "Identification of AtHD2C as a novel regulator of abscisic acid responses
RT in Arabidopsis.";
RL Plant J. 46:124-133(2006).
RN [10]
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 [11]
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. Involved in the modulation of abscisic acid
CC and stress-responsive genes. {ECO:0000269|PubMed:12694598,
CC ECO:0000269|PubMed:16553900}.
CC -!- SUBUNIT: Interacts with DNMT2. {ECO:0000269|PubMed:20331964}.
CC -!- INTERACTION:
CC Q9LZR5; Q17TI5: BRX; NbExp=3; IntAct=EBI-3387398, EBI-4426649;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:15144374}.
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:15144374, ECO:0000269|PubMed:16553900}.
CC -!- INDUCTION: Repressed by abscisic acid. {ECO:0000269|PubMed:16553900}.
CC -!- SIMILARITY: Belongs to the histone deacetylase HD2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB82939.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF255712; AAF70197.1; -; mRNA.
DR EMBL; AF510168; AAM49770.1; -; mRNA.
DR EMBL; AB005235; BAB08599.1; -; Genomic_DNA.
DR EMBL; AL162506; CAB82939.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90649.1; -; Genomic_DNA.
DR EMBL; AF372889; AAK49605.1; -; mRNA.
DR EMBL; AY142039; AAM98303.1; -; mRNA.
DR PIR; T48401; T48401.
DR RefSeq; NP_195994.3; NM_120455.4.
DR AlphaFoldDB; Q9LZR5; -.
DR SMR; Q9LZR5; -.
DR BioGRID; 17009; 12.
DR IntAct; Q9LZR5; 11.
DR STRING; 3702.AT5G03740.1; -.
DR iPTMnet; Q9LZR5; -.
DR PaxDb; Q9LZR5; -.
DR PRIDE; Q9LZR5; -.
DR ProteomicsDB; 230302; -.
DR EnsemblPlants; AT5G03740.1; AT5G03740.1; AT5G03740.
DR GeneID; 831733; -.
DR Gramene; AT5G03740.1; AT5G03740.1; AT5G03740.
DR KEGG; ath:AT5G03740; -.
DR Araport; AT5G03740; -.
DR TAIR; locus:2144623; AT5G03740.
DR eggNOG; ENOG502QVH6; Eukaryota.
DR HOGENOM; CLU_061903_0_0_1; -.
DR InParanoid; Q9LZR5; -.
DR OMA; GCKSCTR; -.
DR OrthoDB; 1260281at2759; -.
DR PhylomeDB; Q9LZR5; -.
DR PRO; PR:Q9LZR5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LZR5; baseline and differential.
DR Genevisible; Q9LZR5; AT.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:TAIR.
DR GO; GO:0009737; P:response to abscisic acid; IEP:TAIR.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR GO; GO:0009414; P:response to water deprivation; IMP:TAIR.
DR GO; GO:0010162; P:seed dormancy process; IBA:GO_Central.
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; Chromatin regulator; Developmental protein; Hydrolase;
KW Metal-binding; Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..294
FT /note="Histone deacetylase HDT3"
FT /id="PRO_0000195206"
FT ZN_FING 267..290
FT /note="C2H2-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 2..5
FT /note="Required to repress transcription"
FT /evidence="ECO:0000250"
FT REGION 124..269
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 143..189
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 204..219
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 239..269
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"
SQ SEQUENCE 294 AA; 31830 MW; 7B69F3BE8324C1D1 CRC64;
MEFWGVEVKN GKPLHLDPGL DRLVHISQVA LGESKNNVTE PIQLYVTVGS DKLLIGTLSH
EKFPQLSTEI VLERNFALSH TWKNGSVFFS GYKVDASDPE PEDLIDDQLE AAGFKAAPKS
AAKQVNFQLP NEDVKAKQDD DADGSEEDSS DDDDSENSGD EEEEKVTAES DSEEDDSSDD
EEDDSSEEET PKKPEEPKKR SAEPNSSKNP ASNKKAKFVT PQKTDSKKPH VHVATPHPSK
QAGKNSGGGS TGETSKQQQT PKSAGAFGCK SCTRTFTSEM GLQSHTKAKH SAAA
