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   22-JUL-2008, entry version 40.
DE   RecName: Full=Histone deacetylase 6;
DE            EC=3.5.1.98;
GN   Name=HDA6; Synonyms=RPD3B; OrderedLocusNames=At5g63110;
GN   ORFNames=MDC12.7;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
OC   rosids; eurosids II; Brassicales; Brassicaceae; 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
RT   Arabidopsis thaliana.";
RL   Plant Mol. Biol. 44:167-176(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   MEDLINE=98162728; 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.
RT   Sequence features of the regions of 1,191,918 bp covered by seventeen
RT   physically assigned P1 clones.";
RL   DNA Res. 4:401-414(1997).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   MEDLINE=22954850; PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [4]
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   [5]
RP   FUNCTION, AND MUTAGENESIS OF GLY-127; GLY-284 AND ALA-294.
RX   PubMed=11340181; DOI=10.1105/tpc.13.5.1047;
RA   Murfett J., Wang X.-J., Hagen G., Guilfoyle T.J.;
RT   "Identification of Arabidopsis histone deacetylase HDA6 mutants that
RT   affect transgene expression.";
RL   Plant Cell 13:1047-1061(2001).
RN   [6]
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
RT   methylation induced by double-stranded RNA.";
RL   EMBO J. 21:6832-6841(2002).
RN   [7]
RP   GENE FAMILY, AND NOMENCLATURE.
RX   MEDLINE=22354691; 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
RT   families of Arabidopsis thaliana suggests functional diversification
RT   of chromatin modification among multicellular eukaryotes.";
RL   Nucleic Acids Res. 30:5036-5055(2002).
RN   [8]
RP   INTERACTION WITH COI1.
RX   MEDLINE=22337574; PubMed=12445118;
RX   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-
RT   ligase complex in Arabidopsis.";
RL   Plant J. 32:457-466(2002).
RN   [9]
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
RT   rDNA repeats.";
RL   Plant Cell 16:1021-1034(2004).
RN   [10]
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
RT   signaling of pathogen response in Arabidopsis.";
RL   Plant Cell 17:1196-1204(2005).
RN   [11]
RP   FUNCTION, SUBCELLULAR LOCATION, AND ENZYME REGULATION.
RX   PubMed=16648464; DOI=10.1101/gad.1417706;
RA   Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J.,
RA   Silva M., Neves N., Gross M., Viegas W., Pikaard C.S.;
RT   "Erasure of histone acetylation by Arabidopsis HDA6 mediates large-
RT   scale gene silencing in nucleolar dominance.";
RL   Genes Dev. 20:1283-1293(2006).
CC   -!- FUNCTION: Responsible for the deacetylation of lysine residues on
CC       the N-terminal part of the core histones (H2A, H2B, H3 and H4).
CC       Might remove acetyl residues only from specific targets, such as
CC       rDNA repeats or complex transgenes. Histone deacetylation gives a
CC       tag for epigenetic repression and plays an important role in
CC       transcriptional regulation, cell cycle progression and
CC       developmental events. Histone deacetylases act via the formation
CC       of large multiprotein complexes. Required for rRNA gene silencing
CC       in nucleolar dominance. Plays a role in transgene silencing, but
CC       this effect seems to bee independent of the histone deacetylase
CC       activity.
CC   -!- CATALYTIC ACTIVITY: Hydrolysis of an N(6)-acetyl-lysine residue of
CC       a histone to yield a deacetylated histone.
CC   -!- ENZYME REGULATION: Inhibited by trichostatin A.
CC   -!- SUBUNIT: Interacts with Coi1, which functions in an SCF complex
CC       that recruits regulators for ubiquitination.
CC   -!- INTERACTION:
CC       O04197:COI1; NbExp=3; IntAct=EBI-639608, EBI-401159;
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus.
CC   -!- TISSUE SPECIFICITY: Not detected in leaves, stems, flowers and
CC       young siliques.
CC   -!- INDUCTION: By jasmonic acid and ethylene.
CC   -!- MISCELLANEOUS: HDA6 mutations induce high acetylation of histone
CC       H4, increased methylation of histone H3 'Lys-4' and
CC       hypomethylation of DNA at particular loci, such as the rDNA
CC       repeats.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. Type 1
CC       subfamily.
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DR   EMBL; AF195548; AAG28475.1; -; mRNA.
DR   EMBL; AB008265; BAB10553.1; -; 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; -.
DR   UniGene; At.8834; -.
DR   HSSP; O67135; 1C3P.
DR   IntAct; Q9FML2; -.
DR   GeneID; 836431; -.
DR   GenomeReviews; BA000015_GR; AT5G63110.
DR   KEGG; ath:AT5G63110; -.
DR   NMPDR; fig|3702.1.peg.28357; -.
DR   TAIR; At5g63110; -.
DR   ArrayExpress; Q9FML2; -.
DR   GO; GO:0005515; F:protein binding; IPI:IntAct.
DR   InterPro; IPR000286; His_deacetylse.
DR   InterPro; IPR003084; His_deacetylse_1.
DR   Gene3D; G3DSA:3.40.800.20; His_deacetylse; 1.
DR   PANTHER; PTHR10625; His_deacetylse; 1.
DR   PANTHER; PTHR10625:SF28; His_deacetylse_1; 1.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   PRINTS; PR01271; HISDACETLASE.
PE   1: Evidence at protein level;
KW   Chromatin regulator; Complete proteome; Hydrolase; Nucleus; Repressor;
KW   Transcription; Transcription regulation.
FT   CHAIN         1    471       Histone deacetylase 6.
FT                                /FTId=PRO_0000280085.
FT   REGION       20    333       Histone deacetylase.
FT   COMPBIAS    311    314       Poly-Gly.
FT   COMPBIAS    428    465       Asp-rich.
FT   ACT_SITE    153    153       By similarity.
FT   MUTAGEN      16     16       G->R: In sil1; suppression of transgene
FT                                silencing.
FT   MUTAGEN     127    127       G->R: In axe1-1; suppression of transgene
FT                                silencing.
FT   MUTAGEN     284    284       G->D: In axe1-2; suppression of transgene
FT                                silencing.
FT   MUTAGEN     294    294       A->V: In axe1-3; suppression of transgene
FT                                silencing.
FT   MUTAGEN     459    471       Missing: In rts1-2; suppression of
FT                                transgene silencing.
FT   CONFLICT    313    313       G -> E (in Ref. 1; AAG28475).
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
//