ID W1NGP3_AMBTC Unreviewed; 506 AA.
AC W1NGP3;
DT 19-MAR-2014, integrated into UniProtKB/TrEMBL.
DT 19-MAR-2014, sequence version 1.
DT 27-MAR-2024, entry version 55.
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 ORFNames=AMTR_s00009p00217140 {ECO:0000313|EMBL:ERM94967.1};
OS Amborella trichopoda.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Amborellales; Amborellaceae; Amborella.
OX NCBI_TaxID=13333 {ECO:0000313|EMBL:ERM94967.1, ECO:0000313|Proteomes:UP000017836};
RN [1] {ECO:0000313|Proteomes:UP000017836}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=24357323;
RG Amborella Genome Project;
RT "The Amborella genome and the evolution of flowering plants.";
RL Science 342:1241089-1241089(2013).
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 EMBL; KI397501; ERM94967.1; -; Genomic_DNA.
DR RefSeq; XP_006827551.1; XM_006827488.2.
DR AlphaFoldDB; W1NGP3; -.
DR STRING; 13333.W1NGP3; -.
DR EnsemblPlants; ERM94967; ERM94967; AMTR_s00009p00217140.
DR GeneID; 18422837; -.
DR Gramene; ERM94967; ERM94967; AMTR_s00009p00217140.
DR KEGG; atr:18422837; -.
DR eggNOG; KOG1342; Eukaryota.
DR HOGENOM; CLU_007727_7_12_1; -.
DR OMA; RCHTDEY; -.
DR OrthoDB; 1327607at2759; -.
DR Proteomes; UP000017836; Unassembled WGS sequence.
DR GO; GO:0000118; C:histone deacetylase complex; IEA:EnsemblPlants.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004407; F:histone deacetylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042742; P:defense response to bacterium; IEA:EnsemblPlants.
DR GO; GO:0009294; P:DNA-mediated transformation; IEA:EnsemblPlants.
DR GO; GO:0009861; P:jasmonic acid and ethylene-dependent systemic resistance; IEA:EnsemblPlants.
DR GO; GO:0045892; P:negative regulation of DNA-templated transcription; IEA:EnsemblPlants.
DR GO; GO:1901001; P:negative regulation of response to salt stress; IEA:EnsemblPlants.
DR GO; GO:1902459; P:positive regulation of stem cell population maintenance; IEA:EnsemblPlants.
DR GO; GO:2000026; P:regulation of multicellular organismal development; IEA:EnsemblPlants.
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:SF11; HISTONE DEACETYLASE 19; 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|PIRSR:PIRSR037913-3};
KW Nucleus {ECO:0000256|PIRNR:PIRNR037913};
KW Reference proteome {ECO:0000313|Proteomes:UP000017836};
KW Transcription {ECO:0000256|PIRNR:PIRNR037913};
KW Transcription regulation {ECO:0000256|PIRNR:PIRNR037913}.
FT DOMAIN 36..324
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 383..410
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 480..506
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 485..506
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 149
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-1"
FT BINDING 107
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 184
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 186
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 272
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
SQ SEQUENCE 506 AA; 57312 MW; 21C55100CE2D7F85 CRC64;
MDTGGSSLPS GPDGVKRKVS YFYDPEVGNY YYGQGHPMKP HRIRMTHALL AHYGLLHQMQ
VLKPFPSRDR DLCKFHADDY VAFLRGITPE TQQDHMKALK RFNVGEDCPV FDGLYSFCQT
YAGGSVGGAV KLNHRLCDIA INWAGGLHHA KKCEASGFCY VNDIVLAILE LLKQHERVLY
VDIDIHHGDG VEEAFYTTDR VMTVSFHKFG DYFPGTGDIR DIGYGKGKYY SLNVPLDDGI
DDDSYQFLFK PIMAKVMEVF QPGAVVLQCG ADSLSGDRLG CFNLSIKGHA ECVRFMRSFN
VPLLLLGGGG YTIRNVARCW CYETGVAIGV EVDDKMPQHE YYEYFGPDYT LHVAPSNMEN
KNSRQLVENI KVKSLQNLSR LPHAPSVPFY ERPPDTELPE EDDDYDRKEE RLESDHLNLD
TEMGELKHSN EVIWYPDRKS IPSIQNIRPK KAIGEAELKD ENQDDRKEVV ENVRCMDIET
EENLGSKSSE PVLVETDQPR SNITEP
//
