ID   HDAC3_ORYSJ             Reviewed;         510 AA.
AC   Q7Y0Y6;
DT   07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   27-MAR-2024, entry version 150.
DE   RecName: Full=Histone deacetylase 3 {ECO:0000303|PubMed:12581311};
DE            Short=OsHDAC3 {ECO:0000303|PubMed:12581311};
DE            EC=3.5.1.98 {ECO:0000250|UniProtKB:O22446};
GN   Name=HDAC3 {ECO:0000303|PubMed:12581311};
GN   Synonyms=HDA703 {ECO:0000303|PubMed:19664599};
GN   OrderedLocusNames=Os02g0214900 {ECO:0000312|EMBL:BAF08198.1},
GN   LOC_Os02g12350 {ECO:0000305};
GN   ORFNames=OJ1006_D05.27-1 {ECO:0000312|EMBL:BAD25048.1};
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX   PubMed=12581311; DOI=10.1046/j.1365-313x.2003.01650.x;
RA   Jang I.C., Pahk Y.M., Song S.I., Kwon H.J., Nahm B.H., Kim J.K.;
RT   "Structure and expression of the rice class-I type histone deacetylase
RT   genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to
RT   increased growth rate and altered architecture.";
RL   Plant J. 33:531-541(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare; TISSUE=Callus {ECO:0000312|EMBL:AAP47173.1};
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   INDUCTION.
RX   PubMed=19664599; DOI=10.1016/j.bbrc.2009.07.162;
RA   Hu Y., Qin F., Huang L., Sun Q., Li C., Zhao Y., Zhou D.X.;
RT   "Rice histone deacetylase genes display specific expression patterns and
RT   developmental functions.";
RL   Biochem. Biophys. Res. Commun. 388:266-271(2009).
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         Evidence={ECO:0000250|UniProtKB:O22446};
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   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O22446}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots. {ECO:0000269|PubMed:12581311}.
CC   -!- INDUCTION: Induced by drought and salt stresses.
CC       {ECO:0000269|PubMed:19664599}.
CC   -!- MISCELLANEOUS: Plants silencing HDAC3 exhibit reduced peduncle
CC       elongation and fertility. {ECO:0000269|PubMed:19664599}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD Type 1
CC       subfamily. {ECO:0000305}.
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DR   EMBL; AF513384; AAP47173.1; -; mRNA.
DR   EMBL; AP004039; BAD25048.1; -; Genomic_DNA.
DR   EMBL; AP008208; BAF08198.1; -; Genomic_DNA.
DR   EMBL; AP014958; BAS77624.1; -; Genomic_DNA.
DR   RefSeq; XP_015623652.1; XM_015768166.1.
DR   AlphaFoldDB; Q7Y0Y6; -.
DR   SMR; Q7Y0Y6; -.
DR   STRING; 39947.Q7Y0Y6; -.
DR   PaxDb; 39947-Q7Y0Y6; -.
DR   EnsemblPlants; Os02t0214900-01; Os02t0214900-01; Os02g0214900.
DR   GeneID; 4328717; -.
DR   Gramene; Os02t0214900-01; Os02t0214900-01; Os02g0214900.
DR   KEGG; osa:4328717; -.
DR   eggNOG; KOG1342; Eukaryota.
DR   HOGENOM; CLU_007727_7_12_1; -.
DR   InParanoid; Q7Y0Y6; -.
DR   OMA; ENMEQYQ; -.
DR   OrthoDB; 1327607at2759; -.
DR   PlantReactome; R-OSA-6787011; Jasmonic acid signaling.
DR   Proteomes; UP000000763; Chromosome 2.
DR   Proteomes; UP000059680; Chromosome 2.
DR   ExpressionAtlas; Q7Y0Y6; baseline and differential.
DR   GO; GO:1902494; C:catalytic complex; IEA:UniProt.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004407; F:histone deacetylase activity; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   Gene3D; 3.40.800.20; Histone deacetylase domain; 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   PANTHER; PTHR10625:SF25; HISTONE DEACETYLASE 3; 1.
DR   PANTHER; PTHR10625; HISTONE DEACETYLASE HDAC1-RELATED; 1.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   PRINTS; PR01271; HISDACETLASE.
DR   SUPFAM; SSF52768; Arginase/deacetylase; 1.
PE   2: Evidence at transcript level;
KW   Chromatin regulator; Hydrolase; Metal-binding; Nucleus; Reference proteome;
KW   Repressor; Transcription; Transcription regulation; Zinc.
FT   CHAIN           1..510
FT                   /note="Histone deacetylase 3"
FT                   /id="PRO_0000440562"
FT   REGION          24..338
FT                   /note="Histone deacetylase"
FT                   /evidence="ECO:0000305"
FT   REGION          394..510
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        421..438
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        447..476
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        158
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         193
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         195
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         281
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   SITE            320
FT                   /note="Polarizes the scissile carbonyl of the substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
SQ   SEQUENCE   510 AA;  56504 MW;  664090CF78C12535 CRC64;
     MDPSSAGAGG NSLASASCGD AQKRRVCYFY DPEVGNYYYG QGHPMKPHRV RMTHALLAHY
     GLLAPAKMEV LRPLPARGID LCRFHSDDYV AFLRAVTPET QLGQVRALRR FNIGPDCPVF
     DGLYAYCQTY AGASVGAAVK LNHGTHDIAI NWSGGLHHAK KSEASGFCYV NDIVLAILEL
     LKLHERVLYI DIDIHHGDGV EEAFYTTNRV MTVSFHKFGD YFPGTGDIRD IGYSEGKYYC
     LNVPLDDGID DDSYQSIFKP IISKVMEMYR PGAVVLQCGA DSLSGDRLGC FNLSGKGHAE
     CVKFMRSFNV PLLLLGGGGY TIRNVARCWC YETGVALGEE LQEKLPYNEY YEYFGPEYSL
     YVAASNMENR NTNKQLEEIK CNILDNLSKL QHAPSVQFQE RIPETKLPEP DEDQEDPDER
     HDPDSDMVLD DHKPTGHSAR SLIHNIGVKR EITETETKDQ HGKRLTTEHK GPEPMAEDLG
     SSKQAPTADA NAVAVNAPGN ARNEPGSSPK
//