ID J3MSC3_ORYBR Unreviewed; 458 AA.
AC J3MSC3;
DT 03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 03-OCT-2012, sequence version 1.
DT 27-MAR-2024, entry version 65.
DE RecName: Full=Histone deacetylase {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037913};
DE EC=3.5.1.98 {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037913};
GN Name=102711553 {ECO:0000313|EnsemblPlants:OB08G20020.1};
OS Oryza brachyantha (malo sina).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza.
OX NCBI_TaxID=4533 {ECO:0000313|EnsemblPlants:OB08G20020.1};
RN [1] {ECO:0000313|EnsemblPlants:OB08G20020.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IRGC 101232 {ECO:0000313|EnsemblPlants:OB08G20020.1};
RX PubMed=23481403;
RA Chen J., Huang Q., Gao D., Wang J., Lang Y., Liu T., Li B., Bai Z.,
RA Luis Goicoechea J., Liang C., Chen C., Zhang W., Sun S., Liao Y., Zhang X.,
RA Yang L., Song C., Wang M., Shi J., Liu G., Liu J., Zhou H., Zhou W., Yu Q.,
RA An N., Chen Y., Cai Q., Wang B., Liu B., Min J., Huang Y., Wu H., Li Z.,
RA Zhang Y., Yin Y., Song W., Jiang J., Jackson S.A., Wing R.A., Wang J.,
RA Chen M.;
RT "Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying
RT Oryza genome evolution.";
RL Nat. Commun. 4:1595-1595(2013).
RN [2] {ECO:0000313|EnsemblPlants:OB08G20020.1}
RP IDENTIFICATION.
RG EnsemblPlants;
RL Submitted (APR-2013) to UniProtKB.
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:0000256|ARBA:ARBA00001028,
CC ECO:0000256|PIRNR:PIRNR037913};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|ARBA:ARBA00001947};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|PIRNR:PIRNR037913}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD Type 1
CC subfamily. {ECO:0000256|PIRNR:PIRNR037913}.
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DR RefSeq; XP_006659341.1; XM_006659278.2.
DR AlphaFoldDB; J3MSC3; -.
DR STRING; 4533.J3MSC3; -.
DR EnsemblPlants; OB08G20020.1; OB08G20020.1; OB08G20020.
DR GeneID; 102711553; -.
DR Gramene; OB08G20020.1; OB08G20020.1; OB08G20020.
DR KEGG; obr:102711553; -.
DR eggNOG; KOG1342; Eukaryota.
DR HOGENOM; CLU_007727_7_4_1; -.
DR OMA; GKIMEWY; -.
DR OrthoDB; 1327607at2759; -.
DR Proteomes; UP000006038; Chromosome 8.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd09991; HDAC_classI; 1.
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:SF14; HISTONE DEACETYLASE 6; 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 3: Inferred from homology;
KW Chromatin regulator {ECO:0000256|ARBA:ARBA00022853,
KW ECO:0000256|PIRNR:PIRNR037913}; Hydrolase {ECO:0000256|PIRNR:PIRNR037913};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRSR:PIRSR037913-3}; Nucleus {ECO:0000256|PIRNR:PIRNR037913};
KW Reference proteome {ECO:0000313|Proteomes:UP000006038};
KW Transcription {ECO:0000256|PIRNR:PIRNR037913};
KW Transcription regulation {ECO:0000256|PIRNR:PIRNR037913}.
FT DOMAIN 41..330
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 389..458
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 393..417
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 440..458
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 154
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-1"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 189
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 191
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 277
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 316
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
SQ SEQUENCE 458 AA; 50986 MW; F032815D9690111E CRC64;
MAASGEGASL PSQGGGEDAR RRRVSYFYEP SIGDYYYGQG HPMKPHRIRM AHSLVVHYGL
HRLLELSRPY PASEADIRRF HSDDYVAFLA SATGNPALLD ARAVKRFNVG EDCPVFDGLF
PFCQASAGGS IGAAVKLNRG DADITVNWAG GLHHAKKGEA SGFCYVNDIV LAILELLKFH
RRVLYVDIDV HHGDGVEEAF FTTNRVMTCS FHKYGDFFPG TGHISDIGIG EGKHYALNVP
LSDGIDDDTF RDLFQCIIKK VMEVYQPDVV VLQCGADSLA GDRLGCFNLS VKGHADCLRY
LRSFNIPMMV LGGGGYTIRN VARCWCYETA VAVGVEPDNK LPYNDYYEYF GPDYNLHIQP
RSVENLNTTK ELENMKTMIL EHLSQIEHVP STQFHDRPSD PEAPQEEEED MDKRPPQRSR
LWSGGAYESD TEDPDNMKTE TNDLSASSVM KDESNGDS
//