HDA1_YEAST
ID HDA1_YEAST Reviewed; 706 AA.
AC P53973; D6W1F8;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Histone deacetylase HDA1;
DE EC=3.5.1.98;
GN Name=HDA1; OrderedLocusNames=YNL021W; ORFNames=N2819;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP CHARACTERIZATION.
RX PubMed=8962081; DOI=10.1073/pnas.93.25.14503;
RA Rundlett S.E., Carmen A.A., Kobayashi R., Bavykin S., Turner B.M.,
RA Grunstein M.;
RT "HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes
RT that regulate silencing and transcription.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:14503-14508(1996).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
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.
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 -!- INTERACTION:
CC P53973; P53973: HDA1; NbExp=4; IntAct=EBI-8206, EBI-8206;
CC P53973; Q06629: HDA2; NbExp=6; IntAct=EBI-8206, EBI-32800;
CC P53973; Q06623: HDA3; NbExp=6; IntAct=EBI-8206, EBI-38663;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- MISCELLANEOUS: Present with 3050 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Z71297; CAA95883.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10524.1; -; Genomic_DNA.
DR PIR; S62933; S62933.
DR RefSeq; NP_014377.1; NM_001182860.1.
DR PDB; 5J8J; X-ray; 2.72 A; A=457-698.
DR PDBsum; 5J8J; -.
DR AlphaFoldDB; P53973; -.
DR SMR; P53973; -.
DR BioGRID; 35805; 743.
DR ComplexPortal; CPX-1884; HDA1 histone deacetylase complex.
DR DIP; DIP-1360N; -.
DR IntAct; P53973; 17.
DR MINT; P53973; -.
DR STRING; 4932.YNL021W; -.
DR ESTHER; yeast-hda1; Arb2_domain.
DR iPTMnet; P53973; -.
DR MaxQB; P53973; -.
DR PaxDb; P53973; -.
DR PRIDE; P53973; -.
DR EnsemblFungi; YNL021W_mRNA; YNL021W; YNL021W.
DR GeneID; 855710; -.
DR KEGG; sce:YNL021W; -.
DR SGD; S000004966; HDA1.
DR VEuPathDB; FungiDB:YNL021W; -.
DR eggNOG; KOG1343; Eukaryota.
DR GeneTree; ENSGT00940000159563; -.
DR HOGENOM; CLU_007727_4_0_1; -.
DR InParanoid; P53973; -.
DR OMA; FVSPACY; -.
DR BioCyc; YEAST:G3O-33059-MON; -.
DR BRENDA; 3.5.1.98; 984.
DR Reactome; R-SCE-3214815; HDACs deacetylate histones.
DR Reactome; R-SCE-3371511; HSF1 activation.
DR Reactome; R-SCE-4551638; SUMOylation of chromatin organization proteins.
DR Reactome; R-SCE-5617833; Cilium Assembly.
DR Reactome; R-SCE-9646399; Aggrephagy.
DR PRO; PR:P53973; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53973; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0070823; C:HDA1 complex; IDA:SGD.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0031047; P:gene silencing by RNA; IMP:SGD.
DR GO; GO:0016575; P:histone deacetylation; IDA:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:ComplexPortal.
DR GO; GO:0010621; P:negative regulation of transcription by transcription factor localization; IGI:SGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR019154; Arb2_domain.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR017321; Hist_deAcase_II_yeast.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR Pfam; PF09757; Arb2; 1.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037919; HDAC_II_yeast; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Hydrolase; Nucleus; Reference proteome;
KW Repressor; Transcription; Transcription regulation.
FT CHAIN 1..706
FT /note="Histone deacetylase HDA1"
FT /id="PRO_0000114738"
FT REGION 1..36
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 67..396
FT /note="Histone deacetylase"
FT COMPBIAS 1..34
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 206
FT /evidence="ECO:0000250"
FT HELIX 457..473
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 483..485
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 487..489
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 490..492
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 496..498
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 500..508
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 511..513
FT /evidence="ECO:0007829|PDB:5J8J"
FT TURN 518..520
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 525..527
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 529..531
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 535..542
FT /evidence="ECO:0007829|PDB:5J8J"
FT TURN 543..545
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 547..553
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 558..561
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 563..579
FT /evidence="ECO:0007829|PDB:5J8J"
FT TURN 580..583
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 590..595
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 596..598
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 599..608
FT /evidence="ECO:0007829|PDB:5J8J"
FT TURN 612..614
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 615..623
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 637..644
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 646..650
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 667..669
FT /evidence="ECO:0007829|PDB:5J8J"
FT STRAND 672..674
FT /evidence="ECO:0007829|PDB:5J8J"
FT HELIX 680..696
FT /evidence="ECO:0007829|PDB:5J8J"
SQ SEQUENCE 706 AA; 80070 MW; 4E7069E66D03264D CRC64;
MDSVMVKKEV LENPDHDLKR KLEENKEEEN SLSTTSKSKR QVIVPVCMPK IHYSPLKTGL
CYDVRMRYHA KIFTSYFEYI DPHPEDPRRI YRIYKILAEN GLINDPTLSG VDDLGDLMLK
IPVRAATSEE ILEVHTKEHL EFIESTEKMS REELLKETEK GDSVYFNNDS YASARLPCGG
AIEACKAVVE GRVKNSLAVV RPPGHHAEPQ AAGGFCLFSN VAVAAKNILK NYPESVRRIM
ILDWDIHHGN GTQKSFYQDD QVLYVSLHRF EMGKYYPGTI QGQYDQTGEG KGEGFNCNIT
WPVGGVGDAE YMWAFEQVVM PMGREFKPDL VIISSGFDAA DGDTIGQCHV TPSCYGHMTH
MLKSLARGNL CVVLEGGYNL DAIARSALSV AKVLIGEPPD ELPDPLSDPK PEVIEMIDKV
IRLQSKYWNC FRRRHANSGC NFNEPINDSI ISKNFPLQKA IRQQQQHYLS DEFNFVTLPL
VSMDLPDNTV LCTPNISESN TIIIVVHDTS DIWAKRNVIS GTIDLSSSVI IDNSLDFIKW
GLDRKYGIID VNIPLTLFEP DNYSGMITSQ EVLIYLWDNY IKYFPSVAKI AFIGIGDSYS
GIVHLLGHRD TRAVTKTVIN FLGDKQLKPL VPLVDETLSE WYFKNSLIFS NNSHQCWKEN
ESRKPRKKFG RVLRCDTDGL NNIIEERFEE ATDFILDSFE EWSDEE
