ID   HDA11_DICDI             Reviewed;         495 AA.
AC   Q55FN5;
DT   29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT   24-MAY-2005, sequence version 1.
DT   03-AUG-2022, entry version 103.
DE   RecName: Full=Type-1 histone deacetylase 1;
DE            Short=DdHdaA;
DE            EC=3.5.1.98;
GN   Name=hdaA; ORFNames=DDB_G0268024;
OS   Dictyostelium discoideum (Slime mold).
OC   Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC   Dictyosteliaceae; Dictyostelium.
OX   NCBI_TaxID=44689;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AX4;
RX   PubMed=15875012; DOI=10.1038/nature03481;
RA   Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA   Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA   Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA   Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA   Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA   Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA   Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA   Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA   Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA   Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA   Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA   Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA   Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA   Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA   Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA   Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA   Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT   "The genome of the social amoeba Dictyostelium discoideum.";
RL   Nature 435:43-57(2005).
RN   [2]
RP   DEVELOPMENTAL STAGE.
RX   PubMed=19576222; DOI=10.1016/j.jmb.2009.06.067;
RA   Sawarkar R., Visweswariah S.S., Nellen W., Nanjundiah V.;
RT   "Histone deacetylases regulate multicellular development in the social
RT   amoeba Dictyostelium discoideum.";
RL   J. Mol. Biol. 391:833-848(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 plays an important role in transcriptional regulation,
CC       cell cycle progression and developmental events. Histone deacetylases
CC       act via the formation of large multiprotein complexes (By similarity).
CC       {ECO:0000250}.
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   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm {ECO:0000250}.
CC   -!- DEVELOPMENTAL STAGE: Expressed throughout growth and development.
CC       {ECO:0000269|PubMed:19576222}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 1
CC       subfamily. {ECO:0000305}.
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DR   EMBL; AAFI02000003; EAL73465.1; -; Genomic_DNA.
DR   RefSeq; XP_647498.1; XM_642406.1.
DR   AlphaFoldDB; Q55FN5; -.
DR   SMR; Q55FN5; -.
DR   STRING; 44689.DDB0234190; -.
DR   PaxDb; Q55FN5; -.
DR   EnsemblProtists; EAL73465; EAL73465; DDB_G0268024.
DR   GeneID; 8616305; -.
DR   KEGG; ddi:DDB_G0268024; -.
DR   dictyBase; DDB_G0268024; hdaA.
DR   eggNOG; KOG1342; Eukaryota.
DR   HOGENOM; CLU_007727_7_12_1; -.
DR   InParanoid; Q55FN5; -.
DR   OMA; EIPMNEY; -.
DR   PhylomeDB; Q55FN5; -.
DR   Reactome; R-DDI-1538133; G0 and Early G1.
DR   Reactome; R-DDI-3214815; HDACs deacetylate histones.
DR   Reactome; R-DDI-4551638; SUMOylation of chromatin organization proteins.
DR   Reactome; R-DDI-9701898; STAT3 nuclear events downstream of ALK signaling.
DR   PRO; PR:Q55FN5; -.
DR   Proteomes; UP000002195; Chromosome 1.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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   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; Cytoplasm; Hydrolase; Metal-binding; Nucleus;
KW   Reference proteome; Repressor; Transcription; Transcription regulation.
FT   CHAIN           1..495
FT                   /note="Type-1 histone deacetylase 1"
FT                   /id="PRO_0000331369"
FT   REGION          372..495
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        399..426
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        427..481
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        136
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         94
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         144
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         171
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250"
FT   BINDING         173
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250"
FT   BINDING         259
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250"
FT   BINDING         298
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   495 AA;  56633 MW;  B325100AB480CD63 CRC64;
     MSTRKVSYFY DNEVGNHYYG PNHPMKPHRM RMTHDLVLNY GIYKKMQIFR PRKASELELT
     NFHSDDYINF LKLVTPDNMH DYSKQLVKFN VREDCPVFDG MYNFCQISSG GSIGCAVKVN
     SKESDVAINW AGGLHHAKKS EASGFCYTND IVLSILELLK HHERVLYIDI DIHHGDGVEE
     AFYTTDRVMT VSFHKYGDYF PGTGDVKDIG ADKGKYYSLN FPLKDGIDDE SYQSIFRPII
     RSVMDFYRPG AVVIQCGADS LTGDRLGCFN LTLRGHAQCI EFLKSFNVPL VVLGGGGYTI
     KNVARCWTYE TSILVDSELK DELPYNDYLE YYGPEYRLHI TPNNMENQNT KDYLEKLKIQ
     LLENLRNLNH APAAAHHDIP PDSFNYSDDE DDEDPDVRIS EADRDKKVHH QGELSDSDEE
     DGRRNYSNGL EATSTSRRNQ VSISAYDKER PSYNSRNNNN NNNNNNNNNN NNNNNSNNNN
     SHHHNEDADV DMDSG