HDAC2_ORYSJ
ID HDAC2_ORYSJ Reviewed; 509 AA.
AC Q6YV04; B9F497; Q0E2T7; Q7Y0Y7;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Histone deacetylase 2 {ECO:0000303|PubMed:12581311};
DE Short=OsHDAC2 {ECO:0000303|PubMed:12581311};
DE EC=3.5.1.98 {ECO:0000250|UniProtKB:O22446};
GN Name=HDAC2 {ECO:0000303|PubMed:12581311};
GN Synonyms=HDA710 {ECO:0000303|PubMed:19664599};
GN OrderedLocusNames=Os02g0215200 {ECO:0000312|EMBL:BAS77631.1},
GN LOC_Os02g12380 {ECO:0000305};
GN ORFNames=B1307A11.3-1 {ECO:0000312|EMBL:BAD17681.1},
GN OJ1006_D05.31-1 {ECO:0000312|EMBL:BAD25051.1},
GN OsJ_05884 {ECO:0000312|EMBL:EEE56554.1};
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] (ISOFORM 2), 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;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6YV04-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6YV04-2; Sequence=VSP_058972, VSP_058973;
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 semi-dwarf phenotype.
CC {ECO:0000269|PubMed:19664599}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD Type 1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF08201.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF513383; AAP47172.1; -; mRNA.
DR EMBL; AP005846; BAD17681.1; -; Genomic_DNA.
DR EMBL; AP004039; BAD25051.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF08201.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014958; BAS77631.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS77632.1; -; Genomic_DNA.
DR EMBL; CM000139; EEE56554.1; -; Genomic_DNA.
DR EMBL; AK103097; BAG95887.1; -; mRNA.
DR RefSeq; XP_015627743.1; XM_015772257.1. [Q6YV04-1]
DR AlphaFoldDB; Q6YV04; -.
DR SMR; Q6YV04; -.
DR STRING; 4530.OS02T0215200-02; -.
DR PaxDb; Q6YV04; -.
DR PRIDE; Q6YV04; -.
DR EnsemblPlants; Os02t0215200-01; Os02t0215200-01; Os02g0215200. [Q6YV04-2]
DR EnsemblPlants; Os02t0215200-02; Os02t0215200-02; Os02g0215200. [Q6YV04-1]
DR GeneID; 4328720; -.
DR Gramene; Os02t0215200-01; Os02t0215200-01; Os02g0215200. [Q6YV04-2]
DR Gramene; Os02t0215200-02; Os02t0215200-02; Os02g0215200. [Q6YV04-1]
DR KEGG; osa:4328720; -.
DR eggNOG; KOG1342; Eukaryota.
DR InParanoid; Q6YV04; -.
DR OMA; LAQHARF; -.
DR OrthoDB; 732770at2759; -.
DR BRENDA; 3.5.1.98; 8948.
DR PlantReactome; R-OSA-6787011; Jasmonic acid signaling.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; Q6YV04; 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 Alternative splicing; Chromatin regulator; Hydrolase; Metal-binding;
KW Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..509
FT /note="Histone deacetylase 2"
FT /id="PRO_0000440561"
FT REGION 24..338
FT /note="Histone deacetylase"
FT /evidence="ECO:0000305"
FT REGION 394..509
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 COMPBIAS 484..509
FT /note="Polar 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"
FT VAR_SEQ 487..498
FT /note="TADANSMAINAP -> VSRRLLYPSANP (in isoform 2)"
FT /id="VSP_058972"
FT VAR_SEQ 499..509
FT /note="Missing (in isoform 2)"
FT /id="VSP_058973"
FT CONFLICT 69
FT /note="Q -> E (in Ref. 5; EEE56554)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 509 AA; 56782 MW; E3F48D23EE3A2C41 CRC64;
MDPSSAGAGG NSLASASCGD AQKRRVCYFY DPEVGNYYYG QGHPMKPHRV RMTHALLAHY
GLLAPAKMQV LRPLPARDRD LCRFHSDDYV AFLRAVTPET QFDQIRSLRR FNVGEDCPVF
DGLYAYCQTY AGASVGAAVK LNHGTHDIAI NWSGGLHHAK KSEASGFCYV NDIVLAILEL
LKLHERVLYI DIDIHHGDGV EEAFYTTNRV MTVSFHKFGD YFPGTGDIRD IGYSEGKYYC
LNVPLDDGID DDSYQSIFKP IISKVMEMYR PGAVVLQCGA DSLSGDRLGC FNLSGKGHAE
CVKFMRSFNV PLLLLGGGGY TIRNVARCWC YETGVALGEE LREKLPYNEY YEYFGPEYSL
YVAASNMENR NTNKQLEEIK CNILDNLSKL QHAPSVQFEE RIPETKLPEP DEDQDDPDER
HDPDSDMLLD DHKPMGHSAR SLIHNIGVKR EITETETKDQ HGKRLTTEHK VPEPMADDLG
SSKQVPTADA NSMAINAPGN AKNEPGSSL
