HDAC1_ORYSJ
ID HDAC1_ORYSJ Reviewed; 518 AA.
AC Q7Y0Y8; Q5VP94;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Histone deacetylase 1 {ECO:0000303|PubMed:12581311};
DE Short=OsHDAC1 {ECO:0000303|PubMed:12581311};
DE EC=3.5.1.98 {ECO:0000250|UniProtKB:O22446};
GN Name=HDAC1 {ECO:0000303|PubMed:12581311};
GN Synonyms=HDA702 {ECO:0000303|PubMed:19664599};
GN OrderedLocusNames=Os06g0583400 {ECO:0000312|EMBL:BAF19857.1},
GN LOC_Os06g38470 {ECO:0000305};
GN ORFNames=P0498C03.28-1 {ECO:0000312|EMBL:BAD68730.1};
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], FUNCTION, 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 MRNA] (ISOFORMS 1 AND 2).
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 [6]
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).
RN [7]
RP FUNCTION.
RX PubMed=19453457; DOI=10.1111/j.1365-313x.2009.03908.x;
RA Chung P.J., Kim Y.S., Jeong J.S., Park S.H., Nahm B.H., Kim J.K.;
RT "The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene
RT that controls seedling root growth in rice.";
RL Plant J. 59:764-776(2009).
RN [8]
RP FUNCTION, AND INTERACTION WITH TPR3.
RX PubMed=27468891; DOI=10.1105/tpc.16.00171;
RA Tang N., Ma S., Zong W., Yang N., Lv Y., Yan C., Guo Z., Li J., Li X.,
RA Xiang Y., Song H., Xiao J., Li X., Xiong L.;
RT "MODD mediates deactivation and degradation of OsbZIP46 to negatively
RT regulate ABA signaling and drought resistance in rice.";
RL Plant Cell 28:2161-2177(2016).
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 (Probable). Regulates negatively the
CC expression of the NAC48/NAC6 gene that controls root growth in
CC seedlings. Epigenetically represses the expression of NAC48/NAC6 by
CC deacetylating 'Lys-9' (H3K9ac), 'Lys-14' (H3K14ac) and 'Lys-18'
CC (H3K18ac) of histone H3, and 'Lys-5' (H4K5ac), 'Lys-12' (H4K12ac) and
CC 'Lys-16' (H4K16ac) of histone H4 (PubMed:19453457). Functions in the
CC regulation of gene expression in the whole genome (PubMed:12581311).
CC Acts as chromatin remodeling regulator to promote the formation of a
CC repressive chromatin state. Functions with MODD via its interaction
CC with TPR3, to down-regulates the histone acetylation level at BZIP46
CC target genes. BZIP46 is a positive regulator of abscisic acid (ABA)
CC signaling and drought stress tolerance (PubMed:27468891).
CC {ECO:0000269|PubMed:12581311, ECO:0000269|PubMed:19453457,
CC ECO:0000269|PubMed:27468891, ECO:0000305|PubMed:19453457}.
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 -!- SUBUNIT: Interacts with TPR3. {ECO:0000269|PubMed:27468891}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O22446}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q7Y0Y8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q7Y0Y8-2; Sequence=VSP_058970, VSP_058971;
CC -!- TISSUE SPECIFICITY: Expressed in roots and leaves.
CC {ECO:0000269|PubMed:12581311}.
CC -!- INDUCTION: Down-regulated by drought and salt stresses.
CC {ECO:0000269|PubMed:19664599}.
CC -!- MISCELLANEOUS: Plants over-expressing HDAC1 exhibit increased growth
CC rate and altered plant architecture (PubMed:12581311). Plants silencing
CC HDAC1 exhibit narrow leaves, reduced diameter of stems and reduced
CC plant height (PubMed:19664599). {ECO:0000269|PubMed:12581311,
CC 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; AF513382; AAP47171.1; -; mRNA.
DR EMBL; AP003724; BAD68730.1; -; Genomic_DNA.
DR EMBL; AP003724; BAD68731.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF19857.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS98377.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS98378.1; -; Genomic_DNA.
DR EMBL; AK068051; BAG90733.1; -; mRNA.
DR EMBL; AK068682; BAG91027.1; -; mRNA.
DR RefSeq; XP_015643781.1; XM_015788295.1. [Q7Y0Y8-1]
DR AlphaFoldDB; Q7Y0Y8; -.
DR SMR; Q7Y0Y8; -.
DR STRING; 4530.OS06T0583400-01; -.
DR iPTMnet; Q7Y0Y8; -.
DR PaxDb; Q7Y0Y8; -.
DR PRIDE; Q7Y0Y8; -.
DR EnsemblPlants; Os06t0583400-01; Os06t0583400-01; Os06g0583400. [Q7Y0Y8-1]
DR EnsemblPlants; Os06t0583400-02; Os06t0583400-02; Os06g0583400. [Q7Y0Y8-2]
DR GeneID; 4341387; -.
DR Gramene; Os06t0583400-01; Os06t0583400-01; Os06g0583400. [Q7Y0Y8-1]
DR Gramene; Os06t0583400-02; Os06t0583400-02; Os06g0583400. [Q7Y0Y8-2]
DR KEGG; osa:4341387; -.
DR eggNOG; KOG1342; Eukaryota.
DR InParanoid; Q7Y0Y8; -.
DR OMA; WAIHTAT; -.
DR OrthoDB; 732770at2759; -.
DR BRENDA; 3.5.1.98; 8948.
DR PlantReactome; R-OSA-6787011; Jasmonic acid signaling.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
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 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Hydrolase; Metal-binding;
KW Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..518
FT /note="Histone deacetylase 1"
FT /id="PRO_0000440560"
FT REGION 22..333
FT /note="Histone deacetylase"
FT /evidence="ECO:0000305"
FT REGION 387..518
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 410..454
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 502..518
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 153
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 188
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 276
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT SITE 315
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT VAR_SEQ 457..460
FT /note="DGNR -> VFFY (in isoform 2)"
FT /id="VSP_058970"
FT VAR_SEQ 461..518
FT /note="Missing (in isoform 2)"
FT /id="VSP_058971"
SQ SEQUENCE 518 AA; 57506 MW; 2179EA9ED8D09EA4 CRC64;
MDASAGGGGN SLPTAGADGA KRRVCYFYDA EVGNYYYGQG HPMKPHRIRM THALLAHYGL
LDQMQVLKPH PARDRDLCRF HADDYVAFLR SVTPETQQDQ IRALKRFNVG EDCPVFDGLY
SFCQTYAGGS VGGAVKLNHG HDIAINWAGG LHHAKKCEAS GFCYVNDIVL AILELLKYHQ
RVLYVDIDIH HGDGVEEAFY TTDRVMTVSF HKFGDYFPGT GDIRDIGHSK GKYYSLNVPL
DDGIDDESYQ SLFKPIMGKV MEVFRPGAVV LQCGADSLSG DRLGCFNLSI RGHAECVRFM
RSFNVPLLLL GGGGYTIRNV ARCWCYETGV ALGHELTDKM PPNEYFEYFG PDYTLHVAPS
NMENKNTRQQ LDDIRSRLLD NLSKLRHAPS VQFQERPPEA ELPEQDEDQE DPDERHHADS
DVEMDDVKPL DDSGRRSSIQ NVRVKRESAE TDAADQDGNR VAAENTKGTE PAADGVGSSK
QTVPTDASAM AIDEPGSLKV EPDNSNKLQD QPSVHQKT
