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UniProtKB/Swiss-Prot entry Q9FML2


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name HDA6_ARATH
Primary accession number Q9FML2
Secondary accession number Q9FVE5
Integrated into Swiss-Prot on March 6, 2007
Sequence was last modified on March 1, 2001 (Sequence version 1)
Annotations were last modified on    April 29, 2008 (Entry version 39)
Name and origin of the protein
Protein name Histone deacetylase 6
Synonym EC 3.5.1.98
Gene name
Name: HDA6
Synonyms: RPD3B
OrderedLocusNames: At5g63110
ORFNames: MDC12.7
From
Arabidopsis thaliana (Mouse-ear cress) [TaxID: 3702] 
Taxonomy Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
STRAIN=cv. Columbia;
DOI=10.1023/A:1006498413543; PubMed=11117260 [NCBI, ExPASy, EBI, Israel, Japan]
Wu K., Malik K., Tian L., Brown D., Miki B.;
"Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana.";
Plant Mol. Biol. 44:167-176(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
DOI=10.1093/dnares/4.6.401; PubMed=9501997 [NCBI, ExPASy, EBI, Israel, Japan]
Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones.";
DNA Res. 4:401-414(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
DOI=10.1126/science.1088305; PubMed=14593172 [NCBI, ExPASy, EBI, Israel, Japan]
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis genome.";
Science 302:842-846(2003).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[5]
FUNCTION, AND MUTAGENESIS OF GLY-127; GLY-284 AND ALA-294.
DOI=10.1105/tpc.13.5.1047; PubMed=11340181 [NCBI, ExPASy, EBI, Israel, Japan]
Murfett J., Wang X.-J., Hagen G., Guilfoyle T.J.;
"Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression.";
Plant Cell 13:1047-1061(2001).
[6]
FUNCTION, AND MUTAGENESIS OF 459-ASP--SER-471.
DOI=10.1093/emboj/cdf663; PubMed=12486004 [NCBI, ExPASy, EBI, Israel, Japan]
Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J.M.;
"HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA.";
EMBO J. 21:6832-6841(2002).
[7]
GENE FAMILY, AND NOMENCLATURE.
DOI=10.1093/nar/gkf660; PubMed=12466527 [NCBI, ExPASy, EBI, Israel, Japan]
Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A.;
"Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.";
Nucleic Acids Res. 30:5036-5055(2002).
[8]
INTERACTION WITH COI1.
DOI=10.1046/j.1365-313X.2002.01432.x; PubMed=12445118 [NCBI, ExPASy, EBI, Israel, Japan]
Devoto A., Nieto-Rostro M., Xie D., Ellis C., Harmston R., Patrick E., Davis J., Sherratt L., Coleman M., Turner J.G.;
"COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis.";
Plant J. 32:457-466(2002).
[9]
FUNCTION, AND MUTAGENESIS OF GLY-16.
DOI=10.1105/tpc.018754; PubMed=15037732 [NCBI, ExPASy, EBI, Israel, Japan]
Probst A.V., Fagard M., Proux F., Mourrain P., Boutet S., Earley K., Lawrence R.J., Pikaard C.S., Murfett J., Furner I., Vaucheret H., Mittelsten Scheid O.;
"Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.";
Plant Cell 16:1021-1034(2004).
[10]
INDUCTION.
DOI=10.1105/tpc.104.028514; PubMed=15749761 [NCBI, ExPASy, EBI, Israel, Japan]
Zhou C., Zhang L., Duan J., Miki B., Wu K.;
"HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis.";
Plant Cell 17:1196-1204(2005).
[11]
FUNCTION, SUBCELLULAR LOCATION, AND ENZYME REGULATION.
DOI=10.1101/gad.1417706; PubMed=16648464 [NCBI, ExPASy, EBI, Israel, Japan]
Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M., Neves N., Gross M., Viegas W., Pikaard C.S.;
"Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance.";
Genes Dev. 20:1283-1293(2006).
Comments
  • FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Might remove acetyl residues only from specific targets, such as rDNA repeats or complex transgenes. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Required for rRNA gene silencing in nucleolar dominance. Plays a role in transgene silencing, but this effect seems to bee independent of the histone deacetylase activity.
  • CATALYTIC ACTIVITY: Hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone.
  • ENZYME REGULATION: Inhibited by trichostatin A.
  • SUBUNIT: Interacts with Coi1, which functions in an SCF complex that recruits regulators for ubiquitination.
  • INTERACTION:
    O04197:COI1; NbExp=3; IntAct=EBI-639608, EBI-401159;
  • SUBCELLULAR LOCATION: Nucleus, nucleolus.
  • TISSUE SPECIFICITY: Not detected in leaves, stems, flowers and young siliques.
  • INDUCTION: By jasmonic acid and ethylene.
  • MISCELLANEOUS: HDA6 mutations induce high acetylation of histone H4, increased methylation of histone H3 'Lys-4' and hypomethylation of DNA at particular loci, such as the rDNA repeats.
  • SIMILARITY: Belongs to the histone deacetylase family. Type 1 subfamily.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AF195548; AAG28475.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AB008265; BAB10553.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY142660; AAN13198.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY072201; AAL60022.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY088314; AAM65853.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
RefSeq NP_201116.1; -.
UniGene At.8834
3D structure databases
HSSP O67135; 1C3P. [HSSP ENTRY / PDB]
ModBase Q9FML2.
Protein-protein interaction databases
IntAct Q9FML2; -.
Organism-specific databases
TAIR At5g63110; -.
Gene expression databases
ArrayExpress Q9FML2; -.
Ontologies
GO
GO:0005515; Molecular function: protein binding (inferred from physical interaction from IntAct).
QuickGo view.
Family and domain databases
InterPro IPR000286; His_deacetylse.
IPR003084; His_deacetylse_1.
Graphical view of domain structure.
Gene3D G3DSA:3.40.800.20; His_deacetylse; 1.
PANTHER PTHR10625; His_deacetylse; 1.
PTHR10625:SF28; His_deacetylse_1; 1.
Pfam PF00850; Hist_deacetyl; 1.
Pfam graphical view of domain structure.
PIRSF PIRSF037913; His_deacetylse_1; 1.
PRINTS PR01270; HDASUPER.
PR01271; HISDACETLASE.
BLOCKS Q9FML2.
Genome annotation databases
GeneID 836431; -.
GenomeReviews BA000015_GR; AT5G63110.
KEGG ath:AT5G63110; -.
NMPDR fig|3702.1.peg.28357; -.
Other
ProtoNet Q9FML2.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Chromatin regulator; Complete proteome; Hydrolase; Nucleus; Repressor; Transcription; Transcription regulation.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   471  471     Histone deacetylase 6. PRO_0000280085
REGION   20   333  314     Histone deacetylase. 
COMPBIAS   311   314  4     Poly-Gly. 
COMPBIAS   428   465  38     Asp-rich. 
ACT_SITE   153   153        By similarity. 
MUTAGEN   16    16        G->R: In sil1; suppression of transgene silencing. 
MUTAGEN   127   127        G->R: In axe1-1; suppression of transgene silencing. 
MUTAGEN   284   284        G->D: In axe1-2; suppression of transgene silencing. 
MUTAGEN   294   294        A->V: In axe1-3; suppression of transgene silencing. 
MUTAGEN   459   471        Missing: In rts1-2; suppression of transgene silencing. 
CONFLICT   313   313        G -> E (in Ref. 1; AAG28475). 
Sequence information
Length: 471 AA [This is the length of the unprocessed precursor] Molecular weight: 52652 Da [This is the MW of the unprocessed precursor] CRC64: CA16C2640D1B1732 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MEADESGISL PSGPDGRKRR VSYFYEPTIG DYYYGQGHPM KPHRIRMAHS LIIHYHLHRR 

        70         80         90        100        110        120 
LEISRPSLAD ASDIGRFHSP EYVDFLASVS PESMGDPSAA RNLRRFNVGE DCPVFDGLFD 

       130        140        150        160        170        180 
FCRASAGGSI GAAVKLNRQD ADIAINWGGG LHHAKKSEAS GFCYVNDIVL GILELLKMFK 

       190        200        210        220        230        240 
RVLYIDIDVH HGDGVEEAFY TTDRVMTVSF HKFGDFFPGT GHIRDVGAEK GKYYALNVPL 

       250        260        270        280        290        300 
NDGMDDESFR SLFRPLIQKV MEVYQPEAVV LQCGADSLSG DRLGCFNLSV KGHADCLRFL 

       310        320        330        340        350        360 
RSYNVPLMVL GGGGYTIRNV ARCWCYETAV AVGVEPDNKL PYNEYFEYFG PDYTLHVDPS 

       370        380        390        400        410        420 
PMENLNTPKD MERIRNTLLE QLSGLIHAPS VQFQHTPPVN RVLDEPEDDM ETRPKPRIWS 

       430        440        450        460        470 
GTATYESDSD DDDKPLHGYS CRGGATTDRD STGEDEMDDD NPEPDVNPPS S 

Q9FML2 in FASTA format

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