HDT4_ARATH
ID HDT4_ARATH Reviewed; 203 AA.
AC Q9M4T3; Q0WN36; Q9ZUY5;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Histone deacetylase HDT4;
DE AltName: Full=HD-tuins protein 4;
DE AltName: Full=Histone deacetylase 2d;
GN Name=HDT4; Synonyms=HD2D, HDA13; OrderedLocusNames=At2g27840;
GN ORFNames=F15K20.6;
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].
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
RP TISSUE SPECIFICITY.
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 [8]
RP FUNCTION.
RX PubMed=16176989; DOI=10.1073/pnas.0503143102;
RA Xu C.-R., Liu C., Wang Y.-L., Li L.-C., Chen W.-Q., Xu Z.-H., Bai S.-N.;
RT "Histone acetylation affects expression of cellular patterning genes in the
RT Arabidopsis root epidermis.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:14469-14474(2005).
CC -!- FUNCTION: Probably mediates the deacetylation of lysine residues lysine
CC residues on the N-terminal part of the core histones (H2A, H2B, H3 and
CC H4). Histone deacetylation gives a tag for epigenetic repression and
CC plays an important role in transcriptional regulation, cell cycle
CC progression and developmental events. {ECO:0000269|PubMed:16176989}.
CC -!- INTERACTION:
CC Q9M4T3; Q17TI5: BRX; NbExp=3; IntAct=EBI-25518903, EBI-4426649;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000305}.
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=Q9M4T3-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Confined to stems and flowers with young siliques.
CC {ECO:0000269|PubMed:15144374}.
CC -!- MISCELLANEOUS: HDT4 is not required for the cellular patterning in the
CC root epidermis.
CC -!- SIMILARITY: Belongs to the histone deacetylase HD2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC73016.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF255713; AAF70198.1; -; mRNA.
DR EMBL; AC005824; AAC73016.2; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; ANM62648.1; -; Genomic_DNA.
DR EMBL; BT006162; AAP04146.1; -; mRNA.
DR EMBL; BT008535; AAP40362.1; -; mRNA.
DR EMBL; AK229619; BAF01464.1; -; mRNA.
DR PIR; F84677; F84677.
DR RefSeq; NP_565661.2; NM_128344.4. [Q9M4T3-1]
DR RefSeq; NP_850109.1; NM_179778.1.
DR AlphaFoldDB; Q9M4T3; -.
DR SMR; Q9M4T3; -.
DR BioGRID; 2681; 3.
DR IntAct; Q9M4T3; 1.
DR STRING; 3702.AT2G27840.1; -.
DR PaxDb; Q9M4T3; -.
DR PRIDE; Q9M4T3; -.
DR ProteomicsDB; 230316; -. [Q9M4T3-1]
DR EnsemblPlants; AT2G27840.3; AT2G27840.3; AT2G27840. [Q9M4T3-1]
DR GeneID; 817331; -.
DR Gramene; AT2G27840.3; AT2G27840.3; AT2G27840. [Q9M4T3-1]
DR KEGG; ath:AT2G27840; -.
DR Araport; AT2G27840; -.
DR TAIR; locus:2041990; AT2G27840.
DR HOGENOM; CLU_1311650_0_0_1; -.
DR InParanoid; Q9M4T3; -.
DR OMA; MDMFRSE; -.
DR OrthoDB; 1260281at2759; -.
DR PRO; PR:Q9M4T3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9M4T3; baseline and differential.
DR Genevisible; Q9M4T3; AT.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
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 Alternative splicing; Chromatin regulator; Developmental protein;
KW Hydrolase; Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..203
FT /note="Histone deacetylase HDT4"
FT /id="PRO_0000195207"
FT REGION 2..5
FT /note="Required to repress transcription"
FT /evidence="ECO:0000250"
FT REGION 121..203
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 128..155
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 203 AA; 22651 MW; 69A1DA5941D7A293 CRC64;
MEFWGIEIKP GKPFKVIQKD GFMVHASQVT LGDVEKVKKD ETFAVYVKIG DDENGFMIGN
LSQKFPQFSI DLYLGHEFEI SHNSTSSVYL IGYRTFDAFD ELDEEIDSDS ELDEYMEQQI
AALPQNEINP EEDDESDSDE MGLDEDDDSS DEEDVEAEAP LKVAPPSKKM PNGAFEIAKG
GKKNKSSGGK KRCPFPCGPS CKK
