HDA9_ARATH
ID HDA9_ARATH Reviewed; 426 AA.
AC Q8H0W2; Q9M1N6;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Histone deacetylase 9;
DE Short=AtHDAC9 {ECO:0000303|PubMed:28663238};
DE EC=3.5.1.98;
GN Name=HDA9; Synonyms=HDAC9 {ECO:0000303|PubMed:28663238};
GN OrderedLocusNames=At3g44680 {ECO:0000312|Araport:AT3G44680};
GN ORFNames=T18B22.80 {ECO:0000312|EMBL:CAB72470.1};
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 [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 [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].
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 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 [5]
RP INTERACTION WITH AHL22.
RC STRAIN=cv. Columbia;
RX PubMed=22442143; DOI=10.1074/jbc.m111.318477;
RA Yun J., Kim Y.S., Jung J.H., Seo P.J., Park C.M.;
RT "The AT-hook motif-containing protein AHL22 regulates flowering initiation
RT by modifying FLOWERING LOCUS T chromatin in Arabidopsis.";
RL J. Biol. Chem. 287:15307-15316(2012).
RN [6]
RP INTERACTION WITH ASG2, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=28663238; DOI=10.1534/genetics.116.198382;
RA Ducos E., Verges V., Duge de Bernonville T., Blanc N.,
RA Giglioli-Guivarc'h N., Dutilleul C.;
RT "Remarkable evolutionary conservation of antiobesity ADIPOSE/WDTC1 homologs
RT in animals and plants.";
RL Genetics 207:153-162(2017).
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 -!- SUBUNIT: Interacts with AHL22 (PubMed:22442143). Binds to farnesylated
CC ASG2 in the cytosol (PubMed:28663238). {ECO:0000269|PubMed:22442143,
CC ECO:0000269|PubMed:28663238}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm, cytosol
CC {ECO:0000269|PubMed:28663238}. Note=Localized to the cytosol when in
CC complex with farnesylated ASG2. {ECO:0000269|PubMed:28663238}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB72470.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL138652; CAB72470.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE77930.1; -; Genomic_DNA.
DR EMBL; BT002003; AAN72014.1; -; mRNA.
DR EMBL; BT006576; AAP31920.1; -; mRNA.
DR PIR; T47443; T47443.
DR RefSeq; NP_190054.2; NM_114336.4.
DR AlphaFoldDB; Q8H0W2; -.
DR SMR; Q8H0W2; -.
DR BioGRID; 8914; 5.
DR STRING; 3702.AT3G44680.1; -.
DR PaxDb; Q8H0W2; -.
DR PRIDE; Q8H0W2; -.
DR ProteomicsDB; 247170; -.
DR EnsemblPlants; AT3G44680.1; AT3G44680.1; AT3G44680.
DR GeneID; 823594; -.
DR Gramene; AT3G44680.1; AT3G44680.1; AT3G44680.
DR KEGG; ath:AT3G44680; -.
DR Araport; AT3G44680; -.
DR TAIR; locus:2098115; AT3G44680.
DR eggNOG; KOG1342; Eukaryota.
DR HOGENOM; CLU_007727_7_4_1; -.
DR InParanoid; Q8H0W2; -.
DR OMA; GWLRAFH; -.
DR OrthoDB; 732770at2759; -.
DR PhylomeDB; Q8H0W2; -.
DR BRENDA; 3.5.1.98; 399.
DR PRO; PR:Q8H0W2; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8H0W2; baseline and differential.
DR Genevisible; Q8H0W2; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:1990619; P:histone H3-K9 deacetylation; IMP:TAIR.
DR GO; GO:0010187; P:negative regulation of seed germination; IMP:TAIR.
DR GO; GO:1900055; P:regulation of leaf senescence; IMP:TAIR.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR003084; His_deacetylse_1.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR PRINTS; PR01270; HDASUPER.
DR PRINTS; PR01271; HISDACETLASE.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Cytoplasm; Hydrolase; Metal-binding; Nucleus;
KW Reference proteome; Repressor; Transcription; Transcription regulation;
KW Zinc.
FT CHAIN 1..426
FT /note="Histone deacetylase 9"
FT /id="PRO_0000280088"
FT REGION 6..318
FT /note="Histone deacetylase"
FT REGION 383..426
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 393..416
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 137
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 172
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 174
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 261
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT SITE 300
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
SQ SEQUENCE 426 AA; 48688 MW; B7B4B9D7432C6DBD CRC64;
MRSKDKISYF YDGDVGSVYF GPNHPMKPHR LCMTHHLILA YGLHSKMEVY RPHKAYPIEM
AQFHSPDYVE FLQRINPENQ NLFPNEMARY NLGEDCPVFE DLFEFCQLYA GGTIDAARRL
NNKLCDIAIN WAGGLHHAKK CDASGFCYIN DLVLGILELL KHHPRVLYID IDVHHGDGVE
EAFYFTDRVM TVSFHKFGDK FFPGTGDVKE IGEREGKFYA INVPLKDGID DSSFNRLFRT
IISKVVEIYQ PGAIVLQCGA DSLARDRLGC FNLSIDGHAE CVKFVKKFNL PLLVTGGGGY
TKENVARCWT VETGILLDTE LPNEIPENDY IKYFAPDFSL KIPGGHIENL NTKSYISSIK
VQILENLRYI QHAPSVQMQE VPPDFYIPDF DEDEQNPDVR ADQRSRDKQI QRDDEYFDGD
NDNDAS
