ID   HDA5_ARATH              Reviewed;         660 AA.
AC   Q8RX28; Q9FNQ7; Q9FNQ8;
DT   06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   27-MAR-2024, entry version 138.
DE   RecName: Full=Histone deacetylase 5 {ECO:0000303|PubMed:12466527};
DE            EC=3.5.1.98 {ECO:0000269|PubMed:25922987};
GN   Name=HDA5 {ECO:0000303|PubMed:12466527};
GN   OrderedLocusNames=At5g61060 {ECO:0000312|EMBL:AED97417.1};
GN   ORFNames=MAF19.7 {ECO:0000312|EMBL:BAB10369.1};
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;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA   Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT   features of the regions of 1,044,062 bp covered by thirteen physically
RT   assigned P1 clones.";
RL   DNA Res. 4:291-300(1997).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
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).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA   Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA   Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA   Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA   Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA   Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA   Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA   Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA   Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA   Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA   Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA   Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [4]
RP   GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=12466527; DOI=10.1093/nar/gkf660;
RA   Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S.,
RA   Richards E.J., Bender J., Mount D.W., Jorgensen R.A.;
RT   "Analysis of histone acetyltransferase and histone deacetylase families of
RT   Arabidopsis thaliana suggests functional diversification of chromatin
RT   modification among multicellular eukaryotes.";
RL   Nucleic Acids Res. 30:5036-5055(2002).
RN   [5]
RP   FUNCTION.
RX   PubMed=16176989; DOI=10.1073/pnas.0503143102;
RA   Xu C.-R., Liu C., Wang Y.-L., Li L.-C., Chen W.-Q., Xu Z.-H., Bai S.-N.;
RT   "Histone acetylation affects expression of cellular patterning genes in the
RT   Arabidopsis root epidermis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 102:14469-14474(2005).
RN   [6]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP   METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP   [LARGE SCALE ANALYSIS].
RX   PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA   Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA   Giglione C.;
RT   "Comparative large-scale characterisation of plant vs. mammal proteins
RT   reveals similar and idiosyncratic N-alpha acetylation features.";
RL   Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN   [7]
RP   SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX   PubMed=22363501; DOI=10.1371/journal.pone.0030846;
RA   Alinsug M.V., Chen F.F., Luo M., Tai R., Jiang L., Wu K.;
RT   "Subcellular localization of class II HDAs in Arabidopsis thaliana:
RT   nucleocytoplasmic shuttling of HDA15 is driven by light.";
RL   PLoS ONE 7:e30846-e30846(2012).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, INTERACTION WITH HDA6,
RP   DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-198; HIS-200 AND ASP-291.
RX   PubMed=25922987; DOI=10.1111/tpj.12868;
RA   Luo M., Tai R., Yu C.W., Yang S., Chen C.Y., Lin W.D., Schmidt W., Wu K.;
RT   "Regulation of flowering time by the histone deacetylase HDA5 in
RT   Arabidopsis.";
RL   Plant J. 82:925-936(2015).
CC   -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC       N-terminal part of the core histones (H2A, H2B, H3 and H4) (Probable).
CC       Histone deacetylation gives a tag for epigenetic repression and plays
CC       an important role in transcriptional regulation, cell cycle progression
CC       and developmental events (Probable). Histone deacetylases act via the
CC       formation of large multiprotein complexes (PubMed:25922987). Involved
CC       in the regulation of flowering time by repressing FLC and AGL27/MAF1
CC       expression (PubMed:25922987). Forms a histone deacetylase complex with
CC       HDA6, FLD and MSI4/FVE that represses FLC gene expression to control
CC       flowering time (PubMed:25922987). Unlike its tandem duplication HDA18,
CC       HDA5 does not seem to be required for the cellular patterning in the
CC       root epidermis (PubMed:16176989). {ECO:0000269|PubMed:16176989,
CC       ECO:0000269|PubMed:25922987, ECO:0000305|PubMed:25922987}.
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:0000269|PubMed:25922987};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:58197;
CC         Evidence={ECO:0000269|PubMed:25922987};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000250|UniProtKB:Q8GXJ1};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q8GXJ1};
CC   -!- ACTIVITY REGULATION: Inhibited by trichostatin A (TSA), a well-known
CC       histone deacetylase inhibitor. {ECO:0000269|PubMed:25922987}.
CC   -!- SUBUNIT: Interacts with HDA6. {ECO:0000269|PubMed:25922987}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22363501}. Cytoplasm
CC       {ECO:0000269|PubMed:22363501}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=1;
CC         Comment=A number of isoforms are produced. According to EST
CC         sequences.;
CC       Name=1;
CC         IsoId=Q8RX28-1; Sequence=Displayed;
CC   -!- TISSUE SPECIFICITY: Expressed in stems, leaves, flowers, siliques and
CC       mature seeds. {ECO:0000269|PubMed:22363501}.
CC   -!- DISRUPTION PHENOTYPE: Delayed flowering under both long-day (LD) and
CC       short-day (SD) conditions. {ECO:0000269|PubMed:25922987}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB10369.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAB10370.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB006696; BAB10369.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AB006696; BAB10370.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED97417.1; -; Genomic_DNA.
DR   EMBL; AY090936; AAM13986.1; -; mRNA.
DR   EMBL; AY120784; AAM53342.1; -; mRNA.
DR   EMBL; BT000073; AAN15392.1; -; mRNA.
DR   RefSeq; NP_200914.2; NM_125499.5. [Q8RX28-1]
DR   AlphaFoldDB; Q8RX28; -.
DR   SMR; Q8RX28; -.
DR   BioGRID; 21471; 6.
DR   STRING; 3702.Q8RX28; -.
DR   iPTMnet; Q8RX28; -.
DR   PaxDb; 3702-AT5G61060-2; -.
DR   ProteomicsDB; 230373; -. [Q8RX28-1]
DR   EnsemblPlants; AT5G61060.1; AT5G61060.1; AT5G61060. [Q8RX28-1]
DR   GeneID; 836227; -.
DR   Gramene; AT5G61060.1; AT5G61060.1; AT5G61060. [Q8RX28-1]
DR   KEGG; ath:AT5G61060; -.
DR   Araport; AT5G61060; -.
DR   TAIR; AT5G61060; HDA05.
DR   eggNOG; KOG1343; Eukaryota.
DR   InParanoid; Q8RX28; -.
DR   OMA; FYPAEGD; -.
DR   PhylomeDB; Q8RX28; -.
DR   PRO; PR:Q8RX28; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q8RX28; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR   GO; GO:0000118; C:histone deacetylase complex; IDA:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0004407; F:histone deacetylase activity; IDA:UniProtKB.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR   GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IDA:UniProtKB.
DR   GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   GO; GO:0048510; P:regulation of timing of transition from vegetative to reproductive phase; IMP:UniProtKB.
DR   Gene3D; 3.10.490.10; Gamma-glutamyl cyclotransferase-like; 1.
DR   Gene3D; 3.40.800.20; Histone deacetylase domain; 1.
DR   InterPro; IPR000286; His_deacetylse.
DR   InterPro; IPR023801; His_deacetylse_dom.
DR   InterPro; IPR037138; His_deacetylse_dom_sf.
DR   InterPro; IPR023696; Ureohydrolase_dom_sf.
DR   PANTHER; PTHR10625:SF37; HISTONE DEACETYLASE 18-RELATED; 1.
DR   PANTHER; PTHR10625; HISTONE DEACETYLASE HDAC1-RELATED; 1.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   SUPFAM; SSF52768; Arginase/deacetylase; 1.
DR   Genevisible; Q8RX28; AT.
PE   1: Evidence at protein level;
KW   Acetylation; Alternative splicing; Chromatin regulator; Cytoplasm;
KW   Flowering; Hydrolase; Metal-binding; Nucleus; Reference proteome;
KW   Repressor; Transcription; Transcription regulation; Zinc.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0007744|PubMed:22223895"
FT   CHAIN           2..660
FT                   /note="Histone deacetylase 5"
FT                   /id="PRO_0000280084"
FT   REGION          26..349
FT                   /note="Histone deacetylase"
FT   ACT_SITE        158
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         198
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         200
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         291
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   SITE            331
FT                   /note="Polarizes the scissile carbonyl of the substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   MOD_RES         2
FT                   /note="N-acetylalanine"
FT                   /evidence="ECO:0007744|PubMed:22223895"
FT   MUTAGEN         198
FT                   /note="D->A: Loss of enzymatic activity."
FT                   /evidence="ECO:0000269|PubMed:25922987"
FT   MUTAGEN         200
FT                   /note="H->A: Loss of enzymatic activity."
FT                   /evidence="ECO:0000269|PubMed:25922987"
FT   MUTAGEN         291
FT                   /note="D->A: Loss of enzymatic activity."
FT                   /evidence="ECO:0000269|PubMed:25922987"
SQ   SEQUENCE   660 AA;  72723 MW;  A40906BF82B397DE CRC64;
     MAMAGESSGK KIGDCDGKVA GNRQRKVGLI YDETMCKHDT PDGEDHPECP DRIRVIWEKL
     QLAGVSQRCV VLGSSKAEDK HLQLVHTKDH VNLVKSISTK QKDYRRNRIA SQLNSIYLNG
     GSSEAAYLAA GSVVKLAEKV AEGELDCGFA IVRPPGHHAE ADEAMGFCLF NNVAVAASFL
     LNERPDLGVK KILIVDWDVH HGNGTQKMFW KDPRVLFFSV HRHEYGGFYP AGDDGDYNMV
     GEGPGEGFNI NVPWDQGRCG DADYLAAWDH ILIPVAREFN PDVIFLSAGF DAAINDPLGG
     CCVTPYGYSV MLKKLMEFAQ GKIVLALEGG YNLDSIAKSS LACVQVLLED KQIQGPPEAY
     PFESTWRVIQ AVRKRLCTYW PSLADELSWK LINQKTPTPI ILISSSDSET EDNAQGLLDQ
     MSKLSIENPQ GTLLENHQVE PASTSWRADL AKVDVWYASF GSNMWKPRFL CYIQGGQVDG
     LKKVCVGSMD KSPPKETVWE TFPHRLFFGR ESSVGWGVGG VAFTNPLANL IDQTHMCLYR
     ITLEQFNDVL SQENGLNVDS DSPVFDLAAL QLVDNKGSIL EAPLNSWYGN VVCLGKERDI
     PILTMTCTLS AVEKFKSGEI PIRPPAKAYA NTLIRGLVEG GRLSKEEAEA YIDKAVSKPL
//