HDA2_YEAST
ID HDA2_YEAST Reviewed; 674 AA.
AC Q06629; D6VSS4;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=HDA1 complex subunit 2;
DE AltName: Full=Histone deacetylase complex 1 subunit 2;
GN Name=HDA2; Synonyms=PLO2; OrderedLocusNames=YDR295C;
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=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(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 FUNCTION, AND IDENTIFICATION IN THE HDA1 HISTONE DEACETYLASE COMPLEX.
RX PubMed=8663039; DOI=10.1074/jbc.271.26.15837;
RA Carmen A.A., Rundlett S.E., Grunstein M.;
RT "HDA1 and HDA3 are components of a yeast histone deacetylase (HDA)
RT complex.";
RL J. Biol. Chem. 271:15837-15844(1996).
RN [4]
RP FUNCTION, AND INTERACTION WITH HDA1 AND HDA3.
RX PubMed=11287668; DOI=10.1073/pnas.081560698;
RA Wu J., Carmen A.A., Kobayashi R., Suka N., Grunstein M.;
RT "HDA2 and HDA3 are related proteins that interact with and are essential
RT for the activity of the yeast histone deacetylase HDA1.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4391-4396(2001).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
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: Required for activity of HDA1 histone deacetylase complex.
CC The HDA1 histone deacetylase complex is responsible for the
CC deacetylation of lysine residues on the N-terminal part of the core
CC histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for
CC epigenetic repression and plays an important role in transcriptional
CC regulation, cell cycle progression and developmental events.
CC {ECO:0000269|PubMed:11287668, ECO:0000269|PubMed:8663039}.
CC -!- SUBUNIT: Heterodimer with HDA3. Component of the HDA1 histone
CC deacetylase complex composed of at least one HDA1 homodimer and one
CC HDA2/HDA3 heterodimer. Interacts with HDA1 and HDA3.
CC {ECO:0000269|PubMed:11287668, ECO:0000269|PubMed:8663039}.
CC -!- INTERACTION:
CC Q06629; P53973: HDA1; NbExp=6; IntAct=EBI-32800, EBI-8206;
CC Q06629; Q06623: HDA3; NbExp=5; IntAct=EBI-32800, EBI-38663;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1500 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the HDA2/3 family. HDA2 subfamily.
CC {ECO:0000305}.
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DR EMBL; U28374; AAB64731.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12134.1; -; Genomic_DNA.
DR PIR; S61181; S61181.
DR RefSeq; NP_010581.3; NM_001180603.3.
DR PDB; 6Z6F; EM; 3.11 A; C=10-638.
DR PDB; 6Z6H; EM; 8.55 A; C/I=10-638.
DR PDB; 6Z6O; EM; 3.80 A; C/G/K/O=10-638.
DR PDB; 6Z6P; EM; 4.43 A; N=10-638.
DR PDBsum; 6Z6F; -.
DR PDBsum; 6Z6H; -.
DR PDBsum; 6Z6O; -.
DR PDBsum; 6Z6P; -.
DR AlphaFoldDB; Q06629; -.
DR SMR; Q06629; -.
DR BioGRID; 32347; 372.
DR ComplexPortal; CPX-1884; HDA1 histone deacetylase complex.
DR DIP; DIP-2988N; -.
DR IntAct; Q06629; 14.
DR MINT; Q06629; -.
DR STRING; 4932.YDR295C; -.
DR MaxQB; Q06629; -.
DR PaxDb; Q06629; -.
DR PRIDE; Q06629; -.
DR EnsemblFungi; YDR295C_mRNA; YDR295C; YDR295C.
DR GeneID; 851889; -.
DR KEGG; sce:YDR295C; -.
DR SGD; S000002703; HDA2.
DR VEuPathDB; FungiDB:YDR295C; -.
DR eggNOG; ENOG502QU6B; Eukaryota.
DR HOGENOM; CLU_409446_0_0_1; -.
DR InParanoid; Q06629; -.
DR OMA; DHYMPRQ; -.
DR BioCyc; YEAST:G3O-29857-MON; -.
DR PRO; PR:Q06629; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q06629; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0070823; C:HDA1 complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0003677; F:DNA binding; IDA:SGD.
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:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.40.50.12360; -; 1.
DR InterPro; IPR038609; HDA1_su2/3_sf.
DR InterPro; IPR021006; Hda2/3.
DR Pfam; PF11496; HDA2-3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Coiled coil; Nucleus;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..674
FT /note="HDA1 complex subunit 2"
FT /id="PRO_0000083930"
FT REGION 185..211
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 468..637
FT /evidence="ECO:0000255"
FT STRAND 11..16
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 20..41
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 70..85
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 88..91
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 100..103
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 106..110
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 140..147
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 148..157
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 222..226
FT /evidence="ECO:0007829|PDB:6Z6F"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 237..242
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 243..248
FT /evidence="ECO:0007829|PDB:6Z6F"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 259..266
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 273..281
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 288..296
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 299..306
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 327..340
FT /evidence="ECO:0007829|PDB:6Z6F"
FT TURN 341..343
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 354..362
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 390..392
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 414..436
FT /evidence="ECO:0007829|PDB:6Z6F"
FT TURN 437..439
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 440..510
FT /evidence="ECO:0007829|PDB:6Z6F"
FT HELIX 518..600
FT /evidence="ECO:0007829|PDB:6Z6F"
FT STRAND 629..632
FT /evidence="ECO:0007829|PDB:6Z6F"
SQ SEQUENCE 674 AA; 77059 MW; CE768CBCC84CCD97 CRC64;
MSRKNSKKLK VYYLPVTLTQ FQKDLSEILI SLHAKSFKAS IIGEPQADAV NKPSGLPAGP
ETHPYPTLSQ RQLTYIFDSN IRAIANHPSL LVDHYMPRQL LRMEPTESSI AGSHKFQVLN
QLINSICFRD REGSPNEVIK CAIIAHSIKE LDLLEGLILG KKFRTKRLSG TSLYNEKHKF
PNLPTVDSTI NKDGTPNSVS STSSNSNSTS YTGYSKDDYD YSVKRNLKKR KINTDDWLFL
ATTKHLKHDQ YLLANYDIDM IISFDPMLEV ELPALQVLRN NANKDIPIIK LLVQNSPDHY
LLDSEIKNSS VKSSHLSNNG HVDDSQEYEE IKSSLLYFLQ ARNAPVNNCE IDYIKLVKCC
LEGKDCNNIL PVLDLITLDE ASKDSSDSGF WQPQLTKLQY SSTELPLWDG PLDIKTYQTE
LMHRAVIRLR DIQDEYAKGT VPLYEKRLNE TQRQNQLDEI KNSVGLTFKK KQEVEKSIND
SEKRLKHAMT ESTKLQNKIN HLLKNRQELE NFNKLPSNTI SSENHLEEGS ALADKLKEYI
DKNATLFNKL KELQQANAEK SKLNDELRSK YQIESSKAAE SAQTLKILQE SMKSLENEVN
GPLTKFSTES LKKELERLQN DFQSLKARNK FLKNYITLMN RQYDLKNKNN VQVEKAAANG
TRFRSTRSNT PNYT
