HDAC3_ORYSJ
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 03-AUG-2022, entry version 142.
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; 4530.OS02T0214900-01; -.
DR PaxDb; Q7Y0Y6; -.
DR PRIDE; 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; 732770at2759; -.
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:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016575; P:histone deacetylation; IEA:InterPro.
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 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
