HDA12_DICDI
ID HDA12_DICDI Reviewed; 422 AA.
AC Q55BW2;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Histone deacetylase B;
DE Short=DdHdaB;
DE AltName: Full=Type-1 histone deacetylase 2;
DE EC=3.5.1.98 {ECO:0000305|PubMed:19576222};
GN Name=hdaB; ORFNames=DDB_G0270338;
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 FUNCTION, ACTIVITY REGULATION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE,
RP AND SUBCELLULAR LOCATION.
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 May play a role in the regulation of the timing of gene expression
CC during the development and in the definition aspects of the phenotype
CC that mediate social behavior in genetically heterogeneous groups.
CC {ECO:0000250, ECO:0000269|PubMed:19576222}.
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:0000305|PubMed:19576222};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:58197;
CC Evidence={ECO:0000305|PubMed:19576222};
CC -!- ACTIVITY REGULATION: Its activity is inhibited by trichostatin A (TSA),
CC a well known histone deacetylase inhibitor. Cytosolic activity is
CC refractory to inhibition by TSA, while the nuclear activity is
CC inhibited completely. {ECO:0000269|PubMed:19576222}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19576222}. Cytoplasm
CC {ECO:0000269|PubMed:19576222}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout growth and development.
CC {ECO:0000269|PubMed:19576222}.
CC -!- DISRUPTION PHENOTYPE: Develop normally but when mixed with wild type
CC cells they sporulate less efficiently than the wild type. Do not show
CC major alterations in gross histone acetylation levels.
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; AAFI02000005; EAL72519.1; -; Genomic_DNA.
DR RefSeq; XP_646719.1; XM_641627.1.
DR AlphaFoldDB; Q55BW2; -.
DR SMR; Q55BW2; -.
DR STRING; 44689.DDB0237652; -.
DR PaxDb; Q55BW2; -.
DR PRIDE; Q55BW2; -.
DR EnsemblProtists; EAL72519; EAL72519; DDB_G0270338.
DR GeneID; 8617692; -.
DR KEGG; ddi:DDB_G0270338; -.
DR dictyBase; DDB_G0270338; hdaB.
DR eggNOG; KOG1342; Eukaryota.
DR HOGENOM; CLU_007727_7_4_1; -.
DR InParanoid; Q55BW2; -.
DR OMA; WAIHTAT; -.
DR PhylomeDB; Q55BW2; -.
DR Reactome; R-DDI-9701898; STAT3 nuclear events downstream of ALK signaling.
DR PRO; PR:Q55BW2; -.
DR Proteomes; UP000002195; Chromosome 1.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:dictyBase.
DR GO; GO:0004407; F:histone deacetylase activity; IMP:dictyBase.
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; IMP:dictyBase.
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..422
FT /note="Histone deacetylase B"
FT /id="PRO_0000331370"
FT REGION 399..422
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 144
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 102
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 179
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 181
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 268
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 422 AA; 48641 MW; 732B1FFDAF4F21DC CRC64;
MEYNTILNNT SKTRVCYFFD QDVGNYFYGP YHPMKPHRLC LTNNLVLNYG LHKKMHLYKA
RPADAEDMLK FHSEDYVDFL ERVTPENINE WKDVKRFHIG EDCPVFPGLY DYCSIYSGGS
IEGALKLNHR MYDIAINWSG GLHHARKDEA SGFCYVNDIV LAILELLKFH ARVLYIDIDV
HHGDGVQEAF YLTDRVMTVS FHKFGGDFFP GTGDIDEIGA KTGKLYSVNV PLADGIDDKN
YLNIFKPVIQ GVMDYYRPSV IVLQCGADSL RFDRLGCFNL TIKGHAECVR FVKSFNIPTL
VLGGGGYTVR NVARCWTYET SVCVDTEVNN ELPYNDYIQF YSPDFQLIPD YTGLPFKYEN
ANTKSYLESL RIKILENLRI LQWAPSVQIQ DVPPDIMPID FDRDEDSKEN MDKRKKKHND
FS
