HDA6_ARATH
ID HDA6_ARATH Reviewed; 471 AA.
AC Q9FML2; Q9FVE5;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Histone deacetylase 6 {ECO:0000303|PubMed:11340181, ECO:0000303|PubMed:28229965};
DE Short=AtHDA6 {ECO:0000303|PubMed:11340181, ECO:0000303|PubMed:28229965};
DE EC=3.5.1.98 {ECO:0000269|PubMed:21398257};
GN Name=HDA6 {ECO:0000303|PubMed:11340181, ECO:0000303|PubMed:28229965};
GN Synonyms=RPD3B {ECO:0000303|PubMed:11117260};
GN OrderedLocusNames=At5g63110 {ECO:0000312|Araport:AT5G63110};
GN ORFNames=MDC12.7 {ECO:0000312|EMBL:BAB10553.1};
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 [MRNA], AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=11117260; DOI=10.1023/a:1006498413543;
RA Wu K., Malik K., Tian L., Brown D., Miki B.;
RT "Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis
RT thaliana.";
RL Plant Mol. Biol. 44:167-176(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND MUTAGENESIS OF GLY-127; GLY-284 AND ALA-294.
RX PubMed=11340181; DOI=10.2307/3871363;
RA Murfett J., Wang X.-J., Hagen G., Guilfoyle T.J.;
RT "Identification of Arabidopsis histone deacetylase HDA6 mutants that affect
RT transgene expression.";
RL Plant Cell 13:1047-1061(2001).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF 459-ASP--SER-471.
RX PubMed=12486004; DOI=10.1093/emboj/cdf663;
RA Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J.M.;
RT "HDA6, a putative histone deacetylase needed to enhance DNA methylation
RT induced by double-stranded RNA.";
RL EMBO J. 21:6832-6841(2002).
RN [8]
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 [9]
RP INTERACTION WITH COI1.
RX PubMed=12445118; DOI=10.1046/j.1365-313x.2002.01432.x;
RA Devoto A., Nieto-Rostro M., Xie D., Ellis C., Harmston R., Patrick E.,
RA Davis J., Sherratt L., Coleman M., Turner J.G.;
RT "COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase
RT complex in Arabidopsis.";
RL Plant J. 32:457-466(2002).
RN [10]
RP FUNCTION, AND MUTAGENESIS OF GLY-16.
RX PubMed=15037732; DOI=10.1105/tpc.018754;
RA Probst A.V., Fagard M., Proux F., Mourrain P., Boutet S., Earley K.,
RA Lawrence R.J., Pikaard C.S., Murfett J., Furner I., Vaucheret H.,
RA Mittelsten Scheid O.;
RT "Arabidopsis histone deacetylase HDA6 is required for maintenance of
RT transcriptional gene silencing and determines nuclear organization of rDNA
RT repeats.";
RL Plant Cell 16:1021-1034(2004).
RN [11]
RP INDUCTION.
RX PubMed=15749761; DOI=10.1105/tpc.104.028514;
RA Zhou C., Zhang L., Duan J., Miki B., Wu K.;
RT "HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling
RT of pathogen response in Arabidopsis.";
RL Plant Cell 17:1196-1204(2005).
RN [12]
RP FUNCTION, SUBCELLULAR LOCATION, AND ACTIVITY REGULATION.
RX PubMed=16648464; DOI=10.1101/gad.1417706;
RA Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M.,
RA Neves N., Gross M., Viegas W., Pikaard C.S.;
RT "Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale
RT gene silencing in nucleolar dominance.";
RL Genes Dev. 20:1283-1293(2006).
RN [13]
RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH FLD.
RX PubMed=21398257; DOI=10.1104/pp.111.174417;
RA Yu C.-W., Liu X., Luo M., Chen C., Lin X., Tian G., Lu Q., Cui Y., Wu K.;
RT "HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates
RT flowering in Arabidopsis.";
RL Plant Physiol. 156:173-184(2011).
RN [14]
RP INTERACTION WITH AHL22.
RX PubMed=22442143; DOI=10.1074/jbc.m111.318477;
RA Yun J., Kim Y.S., Jung J.H., Seo P.J., Park C.M.;
RT "The AT-hook motif-containing protein AHL22 regulates flowering initiation
RT by modifying FLOWERING LOCUS T chromatin in Arabidopsis.";
RL J. Biol. Chem. 287:15307-15316(2012).
RN [15]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [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 [16]
RP FUNCTION, INTERACTION WITH AS1, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=23271976; DOI=10.1371/journal.pgen.1003114;
RA Luo M., Yu C.W., Chen F.F., Zhao L., Tian G., Liu X., Cui Y., Yang J.Y.,
RA Wu K.;
RT "Histone deacetylase HDA6 is functionally associated with AS1 in repression
RT of KNOX genes in arabidopsis.";
RL PLoS Genet. 8:E1003114-E1003114(2012).
RN [17]
RP INTERACTION WITH EBS AND SHL.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=25281686; DOI=10.1105/tpc.114.130781;
RA Lopez-Gonzalez L., Mouriz A., Narro-Diego L., Bustos R.,
RA Martinez-Zapater J.M., Jarillo J.A., Pineiro M.;
RT "Chromatin-dependent repression of the Arabidopsis floral integrator genes
RT involves plant specific PHD-containing proteins.";
RL Plant Cell 26:3922-3938(2014).
RN [18]
RP FUNCTION, AND INTERACTION WITH HDA5.
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).
RN [19]
RP INTERACTION WITH MBD6.
RX PubMed=28229965; DOI=10.1007/s12038-016-9658-1;
RA Parida A.P., Sharma A., Sharma A.K.;
RT "AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in
RT Arabidopsis by interacting with RNA binding proteins.";
RL J. Biosci. 42:57-68(2017).
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4). Might
CC remove acetyl residues only from specific targets, such as rDNA repeats
CC or complex transgenes. Histone deacetylation gives a tag for epigenetic
CC repression and plays an important role in transcriptional regulation,
CC cell cycle progression and developmental events. Histone deacetylases
CC act via the formation of large multiprotein complexes. Required for
CC rRNA gene silencing in nucleolar dominance. Plays a role in transgene
CC silencing, but this effect seems to bee independent of the histone
CC deacetylase activity (PubMed:11340181, PubMed:12486004,
CC PubMed:15037732, PubMed:16648464). Part of the AS1 repressor complex to
CC regulate the KNOX expression in leaf development (PubMed:23271976).
CC Binds to KNAT1, KNAT2, and KNATM chromatin (PubMed:23271976). Involved
CC in the regulation of flowering time (PubMed:21398257, PubMed:25922987).
CC Forms a histone deacetylase complex with HDA5, FLD and MSI4/FVE that
CC represses FLC gene expression to control flowering time
CC (PubMed:21398257, PubMed:25922987). {ECO:0000269|PubMed:11340181,
CC ECO:0000269|PubMed:12486004, ECO:0000269|PubMed:15037732,
CC ECO:0000269|PubMed:16648464, ECO:0000269|PubMed:21398257,
CC ECO:0000269|PubMed:23271976, ECO:0000269|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:21398257};
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.
CC {ECO:0000269|PubMed:16648464}.
CC -!- SUBUNIT: Interacts with Coi1, which functions in an SCF complex that
CC recruits regulators for ubiquitination (PubMed:12445118). Interacts
CC with AHL22 (PubMed:12445118, PubMed:22442143). Interacts with AS1
CC (PubMed:23271976). Part of the AS1 repressor complex composed of AS1,
CC LBD6/AS2 and HDA6 (PubMed:23271976). Binds to EBS and SHL
CC (PubMed:25281686). Interacts with MBD6 (PubMed:28229965). Interacts
CC with HDA5 (PubMed:25922987). Interacts with FLD (PubMed:21398257).
CC {ECO:0000269|PubMed:12445118, ECO:0000269|PubMed:21398257,
CC ECO:0000269|PubMed:22442143, ECO:0000269|PubMed:23271976,
CC ECO:0000269|PubMed:25281686, ECO:0000269|PubMed:25922987,
CC ECO:0000269|PubMed:28229965}.
CC -!- INTERACTION:
CC Q9FML2; O04197: COI1; NbExp=3; IntAct=EBI-639608, EBI-401159;
CC Q9FML2; O24606: EIN3; NbExp=2; IntAct=EBI-639608, EBI-593576;
CC Q9FML2; Q9LMA8: TIFY10A; NbExp=4; IntAct=EBI-639608, EBI-1388539;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:16648464}.
CC Nucleus {ECO:0000269|PubMed:23271976}.
CC -!- TISSUE SPECIFICITY: Not detected in leaves, stems, flowers and young
CC siliques. {ECO:0000269|PubMed:11117260}.
CC -!- INDUCTION: By jasmonic acid and ethylene.
CC {ECO:0000269|PubMed:15749761}.
CC -!- DISRUPTION PHENOTYPE: Curling and serrated leaves. Down curling
CC phenotype on both the distal and lateral axis.
CC {ECO:0000269|PubMed:23271976}.
CC -!- MISCELLANEOUS: HDA6 mutations induce high acetylation of histone H4,
CC increased methylation of histone H3 'Lys-4' and hypomethylation of DNA
CC at particular loci, such as the rDNA repeats.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 1
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; AF195548; AAG28475.1; -; mRNA.
DR EMBL; AB008265; BAB10553.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97705.1; -; Genomic_DNA.
DR EMBL; AY142660; AAN13198.1; -; mRNA.
DR EMBL; AY072201; AAL60022.1; -; mRNA.
DR EMBL; AY088314; AAM65853.1; -; mRNA.
DR RefSeq; NP_201116.1; NM_125705.4.
DR AlphaFoldDB; Q9FML2; -.
DR SMR; Q9FML2; -.
DR BioGRID; 21674; 20.
DR DIP; DIP-33452N; -.
DR IntAct; Q9FML2; 7.
DR STRING; 3702.AT5G63110.1; -.
DR iPTMnet; Q9FML2; -.
DR PaxDb; Q9FML2; -.
DR PRIDE; Q9FML2; -.
DR ProteomicsDB; 230310; -.
DR EnsemblPlants; AT5G63110.1; AT5G63110.1; AT5G63110.
DR GeneID; 836431; -.
DR Gramene; AT5G63110.1; AT5G63110.1; AT5G63110.
DR KEGG; ath:AT5G63110; -.
DR Araport; AT5G63110; -.
DR TAIR; locus:2162017; AT5G63110.
DR eggNOG; KOG1342; Eukaryota.
DR HOGENOM; CLU_007727_7_12_1; -.
DR InParanoid; Q9FML2; -.
DR OMA; EIPMNEY; -.
DR OrthoDB; 732770at2759; -.
DR PhylomeDB; Q9FML2; -.
DR PRO; PR:Q9FML2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FML2; baseline and differential.
DR Genevisible; Q9FML2; AT.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0070822; C:Sin3-type complex; IDA:TAIR.
DR GO; GO:0004407; F:histone deacetylase activity; IMP:TAIR.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0016575; P:histone deacetylation; IMP:TAIR.
DR GO; GO:0016441; P:post-transcriptional gene silencing; IMP:TAIR.
DR GO; GO:0048510; P:regulation of timing of transition from vegetative to reproductive phase; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR GO; GO:0010431; P:seed maturation; IMP:TAIR.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:TAIR.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR003084; His_deacetylse_1.
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 PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR PRINTS; PR01270; HDASUPER.
DR PRINTS; PR01271; HISDACETLASE.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chromatin regulator; Hydrolase; Metal-binding; Nucleus;
KW Reference proteome; Repressor; Transcription; Transcription regulation;
KW Zinc.
FT CHAIN 1..471
FT /note="Histone deacetylase 6"
FT /id="PRO_0000280085"
FT REGION 20..333
FT /note="Histone deacetylase"
FT REGION 389..471
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 401..415
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 153
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 188
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 276
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT SITE 315
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00004"
FT MUTAGEN 16
FT /note="G->R: In sil1; suppression of transgene silencing."
FT /evidence="ECO:0000250"
FT MUTAGEN 127
FT /note="G->R: In axe1-1; suppression of transgene
FT silencing."
FT /evidence="ECO:0007744|PubMed:22223895"
FT MUTAGEN 284
FT /note="G->D: In axe1-2; suppression of transgene
FT silencing."
FT /evidence="ECO:0000269|PubMed:15037732"
FT MUTAGEN 294
FT /note="A->V: In axe1-3; suppression of transgene
FT silencing."
FT /evidence="ECO:0000269|PubMed:11340181"
FT MUTAGEN 459..471
FT /note="Missing: In rts1-2; suppression of transgene
FT silencing."
FT /evidence="ECO:0000269|PubMed:11340181"
FT CONFLICT 313
FT /note="G -> E (in Ref. 1; AAG28475)"
FT /evidence="ECO:0000269|PubMed:11340181"
SQ SEQUENCE 471 AA; 52652 MW; CA16C2640D1B1732 CRC64;
MEADESGISL PSGPDGRKRR VSYFYEPTIG DYYYGQGHPM KPHRIRMAHS LIIHYHLHRR
LEISRPSLAD ASDIGRFHSP EYVDFLASVS PESMGDPSAA RNLRRFNVGE DCPVFDGLFD
FCRASAGGSI GAAVKLNRQD ADIAINWGGG LHHAKKSEAS GFCYVNDIVL GILELLKMFK
RVLYIDIDVH HGDGVEEAFY TTDRVMTVSF HKFGDFFPGT GHIRDVGAEK GKYYALNVPL
NDGMDDESFR SLFRPLIQKV MEVYQPEAVV LQCGADSLSG DRLGCFNLSV KGHADCLRFL
RSYNVPLMVL GGGGYTIRNV ARCWCYETAV AVGVEPDNKL PYNEYFEYFG PDYTLHVDPS
PMENLNTPKD MERIRNTLLE QLSGLIHAPS VQFQHTPPVN RVLDEPEDDM ETRPKPRIWS
GTATYESDSD DDDKPLHGYS CRGGATTDRD STGEDEMDDD NPEPDVNPPS S
