HDA5_ARATH
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 03-AUG-2022, entry version 130.
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.AT5G61060.2; -.
DR iPTMnet; Q8RX28; -.
DR PaxDb; Q8RX28; -.
DR PRIDE; Q8RX28; -.
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 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 Genevisible; Q8RX28; AT.
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:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0016575; P:histone deacetylation; 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; 3.40.800.20; -; 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 Pfam; PF00850; Hist_deacetyl; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
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
