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Q9FML2

- HDA6_ARATH

UniProt

Q9FML2 - HDA6_ARATH

Protein

Histone deacetylase 6

Gene

HDA6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    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.4 Publications

    Catalytic activityi

    Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

    Enzyme regulationi

    Inhibited by trichostatin A.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei153 – 1531By similarity

    GO - Molecular functioni

    1. histone deacetylase activity Source: TAIR
    2. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
    3. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
    4. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
    5. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
    6. protein binding Source: IntAct

    GO - Biological processi

    1. embryo development ending in seed dormancy Source: TAIR
    2. gene silencing Source: TAIR
    3. histone deacetylation Source: TAIR
    4. posttranscriptional gene silencing Source: TAIR
    5. regulation of transcription, DNA-templated Source: UniProtKB-KW
    6. response to abscisic acid Source: TAIR
    7. response to salt stress Source: TAIR
    8. seed maturation Source: TAIR
    9. transcription, DNA-templated Source: UniProtKB-KW
    10. vegetative to reproductive phase transition of meristem Source: TAIR

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciARA:AT5G63110-MONOMER.
    ReactomeiREACT_187702. G0 and Early G1.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone deacetylase 6 (EC:3.5.1.98)
    Gene namesi
    Name:HDA6
    Synonyms:RPD3B
    Ordered Locus Names:At5g63110
    ORF Names:MDC12.7
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G63110.

    Subcellular locationi

    Nucleusnucleolus 1 Publication

    GO - Cellular componenti

    1. chloroplast envelope Source: TAIR
    2. nucleolus Source: UniProtKB-SubCell
    3. nucleus Source: TAIR

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi16 – 161G → R in sil1; suppression of transgene silencing. 2 Publications
    Mutagenesisi127 – 1271G → R in axe1-1; suppression of transgene silencing. 2 Publications
    Mutagenesisi284 – 2841G → D in axe1-2; suppression of transgene silencing. 2 Publications
    Mutagenesisi294 – 2941A → V in axe1-3; suppression of transgene silencing. 2 Publications
    Mutagenesisi459 – 47113Missing in rts1-2; suppression of transgene silencing. 1 PublicationAdd
    BLAST

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 471471Histone deacetylase 6PRO_0000280085Add
    BLAST

    Proteomic databases

    PaxDbiQ9FML2.
    PRIDEiQ9FML2.

    Expressioni

    Tissue specificityi

    Not detected in leaves, stems, flowers and young siliques.1 Publication

    Inductioni

    By jasmonic acid and ethylene.1 Publication

    Gene expression databases

    GenevestigatoriQ9FML2.

    Interactioni

    Subunit structurei

    Interacts with Coi1, which functions in an SCF complex that recruits regulators for ubiquitination.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    COI1O041973EBI-639608,EBI-401159

    Protein-protein interaction databases

    BioGridi21674. 18 interactions.
    DIPiDIP-33452N.
    IntActiQ9FML2. 2 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9FML2.
    SMRiQ9FML2. Positions 18-385.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni20 – 333314Histone deacetylaseAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi311 – 3144Poly-Gly
    Compositional biasi428 – 46538Asp-richAdd
    BLAST

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0123.
    HOGENOMiHOG000225180.
    InParanoidiQ9FML2.
    KOiK06067.
    OMAiEAHRDWK.
    PhylomeDBiQ9FML2.

    Family and domain databases

    Gene3Di3.40.800.20. 1 hit.
    InterProiIPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view]
    PANTHERiPTHR10625. PTHR10625. 1 hit.
    PfamiPF00850. Hist_deacetyl. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSiPR01270. HDASUPER.
    PR01271. HISDACETLASE.

    Sequencei

    Sequence statusi: Complete.

    Q9FML2-1 [UniParc]FASTAAdd to Basket

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    MEADESGISL PSGPDGRKRR VSYFYEPTIG DYYYGQGHPM KPHRIRMAHS    50
    LIIHYHLHRR LEISRPSLAD ASDIGRFHSP EYVDFLASVS PESMGDPSAA 100
    RNLRRFNVGE DCPVFDGLFD FCRASAGGSI GAAVKLNRQD ADIAINWGGG 150
    LHHAKKSEAS GFCYVNDIVL GILELLKMFK RVLYIDIDVH HGDGVEEAFY 200
    TTDRVMTVSF HKFGDFFPGT GHIRDVGAEK GKYYALNVPL NDGMDDESFR 250
    SLFRPLIQKV MEVYQPEAVV LQCGADSLSG DRLGCFNLSV KGHADCLRFL 300
    RSYNVPLMVL GGGGYTIRNV ARCWCYETAV AVGVEPDNKL PYNEYFEYFG 350
    PDYTLHVDPS PMENLNTPKD MERIRNTLLE QLSGLIHAPS VQFQHTPPVN 400
    RVLDEPEDDM ETRPKPRIWS GTATYESDSD DDDKPLHGYS CRGGATTDRD 450
    STGEDEMDDD NPEPDVNPPS S 471
    Length:471
    Mass (Da):52,652
    Last modified:March 1, 2001 - v1
    Checksum:iCA16C2640D1B1732
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti313 – 3131G → E in AAG28475. (PubMed:11117260)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF195548 mRNA. Translation: AAG28475.1.
    AB008265 Genomic DNA. Translation: BAB10553.1.
    CP002688 Genomic DNA. Translation: AED97705.1.
    AY142660 mRNA. Translation: AAN13198.1.
    AY072201 mRNA. Translation: AAL60022.1.
    AY088314 mRNA. Translation: AAM65853.1.
    RefSeqiNP_201116.1. NM_125705.3.
    UniGeneiAt.8834.

    Genome annotation databases

    EnsemblPlantsiAT5G63110.1; AT5G63110.1; AT5G63110.
    GeneIDi836431.
    KEGGiath:AT5G63110.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF195548 mRNA. Translation: AAG28475.1 .
    AB008265 Genomic DNA. Translation: BAB10553.1 .
    CP002688 Genomic DNA. Translation: AED97705.1 .
    AY142660 mRNA. Translation: AAN13198.1 .
    AY072201 mRNA. Translation: AAL60022.1 .
    AY088314 mRNA. Translation: AAM65853.1 .
    RefSeqi NP_201116.1. NM_125705.3.
    UniGenei At.8834.

    3D structure databases

    ProteinModelPortali Q9FML2.
    SMRi Q9FML2. Positions 18-385.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 21674. 18 interactions.
    DIPi DIP-33452N.
    IntActi Q9FML2. 2 interactions.

    Proteomic databases

    PaxDbi Q9FML2.
    PRIDEi Q9FML2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G63110.1 ; AT5G63110.1 ; AT5G63110 .
    GeneIDi 836431.
    KEGGi ath:AT5G63110.

    Organism-specific databases

    TAIRi AT5G63110.

    Phylogenomic databases

    eggNOGi COG0123.
    HOGENOMi HOG000225180.
    InParanoidi Q9FML2.
    KOi K06067.
    OMAi EAHRDWK.
    PhylomeDBi Q9FML2.

    Enzyme and pathway databases

    BioCyci ARA:AT5G63110-MONOMER.
    Reactomei REACT_187702. G0 and Early G1.

    Gene expression databases

    Genevestigatori Q9FML2.

    Family and domain databases

    Gene3Di 3.40.800.20. 1 hit.
    InterProi IPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view ]
    PANTHERi PTHR10625. PTHR10625. 1 hit.
    Pfami PF00850. Hist_deacetyl. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSi PR01270. HDASUPER.
    PR01271. HISDACETLASE.
    ProtoNeti Search...

    Publicationsi

    1. "Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana."
      Wu K., Malik K., Tian L., Brown D., Miki B.
      Plant Mol. Biol. 44:167-176(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
      Strain: cv. Columbia.
    2. "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."
      Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S.
      DNA Res. 4:401-414(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      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.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression."
      Murfett J., Wang X.-J., Hagen G., Guilfoyle T.J.
      Plant Cell 13:1047-1061(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF GLY-127; GLY-284 AND ALA-294.
    7. "HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA."
      Aufsatz W., Mette M.F., van der Winden J., Matzke M., Matzke A.J.M.
      EMBO J. 21:6832-6841(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF 459-ASP--SER-471.
    8. "Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes."
      Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A.
      Nucleic Acids Res. 30:5036-5055(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE.
    9. "COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis."
      Devoto A., Nieto-Rostro M., Xie D., Ellis C., Harmston R., Patrick E., Davis J., Sherratt L., Coleman M., Turner J.G.
      Plant J. 32:457-466(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH COI1.
    10. "Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats."
      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.
      Plant Cell 16:1021-1034(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF GLY-16.
    11. "HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis."
      Zhou C., Zhang L., Duan J., Miki B., Wu K.
      Plant Cell 17:1196-1204(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    12. "Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance."
      Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J., Silva M., Neves N., Gross M., Viegas W., Pikaard C.S.
      Genes Dev. 20:1283-1293(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, ENZYME REGULATION.
    13. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiHDA6_ARATH
    AccessioniPrimary (citable) accession number: Q9FML2
    Secondary accession number(s): Q9FVE5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 6, 2007
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 91 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3