ID   A8MSD0_ARATH            Unreviewed;       469 AA.
AC   A8MSD0;
DT   04-DEC-2007, integrated into UniProtKB/TrEMBL.
DT   04-DEC-2007, sequence version 1.
DT   02-SEP-2026, entry version 120.
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   Name=HD1 {ECO:0000313|EMBL:AEE86882.1, ECO:0000313|TAIR:AT4G38130};
GN   Synonyms=ATHD1 {ECO:0000313|EMBL:AEE86882.1}, ATHDA19
GN   {ECO:0000313|EMBL:AEE86882.1}, ATRPD3A {ECO:0000313|EMBL:AEE86882.1},
GN   HDA1 {ECO:0000313|EMBL:AEE86882.1}, HDA19
GN   {ECO:0000313|EMBL:AEE86882.1}, HISTONE DEACETYLASE
GN   {ECO:0000313|EMBL:AEE86882.1}, histone deacetylase 1
GN   {ECO:0000313|EMBL:AEE86882.1}, HISTONE DEACETYLASE 19
GN   {ECO:0000313|EMBL:AEE86882.1}, HISTONE DEACETYLASE19
GN   {ECO:0000313|EMBL:AEE86882.1}, RPD3A {ECO:0000313|EMBL:AEE86882.1};
GN   OrderedLocusNames=At4g38130 {ECO:0000313|Araport:AT4G38130,
GN   ECO:0000313|EMBL:AEE86882.1};
GN   ORFNames=F20D10.250 {ECO:0000313|EMBL:AEE86882.1}, F20D10_250
GN   {ECO:0000313|EMBL:AEE86882.1};
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702 {ECO:0000313|EMBL:AEE86882.1, ECO:0000313|Proteomes:UP000006548};
RN   [1] {ECO:0000313|EMBL:AEE86882.1, ECO:0000313|Proteomes:UP000006548}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia {ECO:0000313|Proteomes:UP000006548};
RX   PubMed=10617198; DOI=10.1038/47134;
RG   EU;
RG   CSHL and WU Arabidopsis Sequencing Project;
RA   Mayer K., Schuller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA   Dusterhoft A., Stiekema W., Entian K.D., Terryn N., Harris B., Ansorge W.,
RA   Brandt P., Grivell L., Rieger M., Weichselgartner M., de Simone V.,
RA   Obermaier B., Mache R., Muller M., Kreis M., Delseny M., Puigdomenech P.,
RA   Watson M., Schmidtheini T., Reichert B., Portatelle D., Perez-Alonso M.,
RA   Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H.,
RA   Ridley P., Langham S.A., McCullagh B., Bilham L., Robben J.,
RA   Van der Schueren J., Grymonprez B., Chuang Y.J., Vandenbussche F.,
RA   Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
RA   Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E.,
RA   Brandt A., Peters S., van Staveren M., Dirske W., Mooijman P.,
RA   Klein Lankhorst R., Rose M., Hauf J., Kotter P., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA   Gielen J., Villarroel R., De Clercq R., Van Montagu M., Rogers J.,
RA   Cronin A., Quail M., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M.,
RA   Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M.,
RA   Benes V., Rechmann S., Borkova D., Blocker H., Scharfe M., Grimm M.,
RA   Lohnert T.H., Dose S., de Haan M., Maarse A., Schafer M., Muller-Auer S.,
RA   Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
RA   Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O.,
RA   Quigley F., Clabauld G., Mundlein A., Felber R., Schnabl S., Hiller R.,
RA   Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C.,
RA   Montfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA   Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA   Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA   Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA   Mewes H.W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA   de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA   Huang E., Spiegel L., Sehkon M., Murray J., Sheet P., Cordes M.,
RA   Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA   Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA   Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA   Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L., Nelson J.,
RA   Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J.,
RA   Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA   Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA   Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA   O'Shaughnessy A., Rodriguez M., Hoffmann J., Till S., Granat S., Shohdy N.,
RA   Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.,
RA   Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL   Nature 402:769-777(1999).
RN   [2] {ECO:0007829|PubMed:19376835}
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19376835; DOI=10.1104/pp.109.138677;
RA   Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA   Grossmann J., Gruissem W., Baginsky S.;
RT   "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT   chloroplast kinase substrates and phosphorylation networks.";
RL   Plant Physiol. 150:889-903(2009).
RN   [3] {ECO:0000313|Proteomes:UP000006548}
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia {ECO:0000313|Proteomes:UP000006548};
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] +
CC         acetate; 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:ARBA00048287,
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|ARBA:ARBA00004123,
CC       ECO:0000256|PIRNR:PIRNR037913}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD Type 1
CC       subfamily. {ECO:0000256|ARBA:ARBA00061569,
CC       ECO:0000256|PIRNR:PIRNR037913}.
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DR   EMBL; CP002687; AEE86882.1; -; Genomic_DNA.
DR   RefSeq; NP_001078511.1; NM_001085042.1.
DR   AlphaFoldDB; A8MSD0; -.
DR   SMR; A8MSD0; -.
DR   iPTMnet; A8MSD0; -.
DR   ProteomicsDB; 195821; -.
DR   GeneID; 829969; -.
DR   Araport; AT4G38130; -.
DR   TAIR; AT4G38130; HD1.
DR   HOGENOM; CLU_007727_7_12_1; -.
DR   OMA; RCHTDEY; -.
DR   OrthoDB; 1918432at2759; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; A8MSD0; baseline and differential.
DR   GO; GO:0000785; C:chromatin; IEA:UniProtKB-ARBA.
DR   GO; GO:0000118; C:histone deacetylase complex; IEA:UniProtKB-ARBA.
DR   GO; GO:0000228; C:nuclear chromosome; IEA:UniProtKB-ARBA.
DR   GO; GO:0141221; F:histone deacetylase activity, hydrolytic mechanism; IEA:UniProtKB-EC.
DR   FunFam; 3.40.800.20:FF:000001; Histone deacetylase; 1.
DR   Gene3D; 3.40.800.20; Histone deacetylase domain; 1.
DR   InterPro; IPR003084; HDAC_I/II.
DR   InterPro; IPR000286; HDACs.
DR   InterPro; IPR023801; His_deacetylse_dom.
DR   InterPro; IPR037138; His_deacetylse_dom_sf.
DR   InterPro; IPR023696; Ureohydrolase_dom_sf.
DR   PANTHER; PTHR10625:SF44; 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   1: Evidence at protein level;
KW   Chromatin regulator {ECO:0000256|ARBA:ARBA00022853,
KW   ECO:0000256|PIRNR:PIRNR037913};
KW   Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|PIRNR:PIRNR037913};
KW   Metal-binding {ECO:0000256|PIRSR:PIRSR037913-3};
KW   Nucleus {ECO:0000256|ARBA:ARBA00023242, ECO:0000256|PIRNR:PIRNR037913};
KW   Proteomics identification {ECO:0007829|PeptideAtlas:A8MSD0,
KW   ECO:0007829|ProteomicsDB:A8MSD0};
KW   Reference proteome {ECO:0000313|Proteomes:UP000006548};
KW   Repressor {ECO:0000256|ARBA:ARBA00022491};
KW   Transcription {ECO:0000256|ARBA:ARBA00023163,
KW   ECO:0000256|PIRNR:PIRNR037913};
KW   Transcription regulation {ECO:0000256|ARBA:ARBA00023015,
KW   ECO:0000256|PIRNR:PIRNR037913}.
FT   DOMAIN          36..324
FT                   /note="Histone deacetylase"
FT                   /evidence="ECO:0000259|Pfam:PF00850"
FT   REGION          383..469
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        397..407
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        422..457
FT                   /note="Basic and acidic 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   469 AA;  52780 MW;  63AA007E54AD2328 CRC64;
     MDTGGNSLAS GPDGVKRKVC YFYDPEVGNY YYGQGHPMKP HRIRMTHALL AHYGLLQHMQ
     VLKPFPARDR DLCRFHADDY VSFLRSITPE TQQDQIRQLK RFNVGEDCPV FDGLYSFCQT
     YAGGSVGGSV KLNHGLCDIA INWAGGLHHA KKCEASGFCY VNDIVLAILE LLKQHERVLY
     VDIDIHHGDG VEEAFYATDR VMTVSFHKFG DYFPGTGHIQ DIGYGSGKYY SLNVPLDDGI
     DDESYHLLFK PIMGKVMEIF RPGAVVLQCG ADSLSGDRLG CFNLSIKGHA ECVKFMRSFN
     VPLLLLGGGG YTIRNVARCW CYETGVALGV EVEDKMPEHE YYEYFGPDYT LHVAPSNMEN
     KNSRQMLEEI RNDLLHNLSK LQHAPSVPFQ ERPPDTETPE VDEDQEDGDK RWDPDSDMDV
     DDDRKPIPSR VKREAVEPDT KDKDGLKGIM ERGKGCEVEV DESGSTKVK
//