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Q9FML2

- HDA6_ARATH

UniProt

Q9FML2 - HDA6_ARATH

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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

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

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
Complete GO annotation...

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. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

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

« Hide

        10         20         30         40         50
MEADESGISL PSGPDGRKRR VSYFYEPTIG DYYYGQGHPM KPHRIRMAHS
60 70 80 90 100
LIIHYHLHRR LEISRPSLAD ASDIGRFHSP EYVDFLASVS PESMGDPSAA
110 120 130 140 150
RNLRRFNVGE DCPVFDGLFD FCRASAGGSI GAAVKLNRQD ADIAINWGGG
160 170 180 190 200
LHHAKKSEAS GFCYVNDIVL GILELLKMFK RVLYIDIDVH HGDGVEEAFY
210 220 230 240 250
TTDRVMTVSF HKFGDFFPGT GHIRDVGAEK GKYYALNVPL NDGMDDESFR
260 270 280 290 300
SLFRPLIQKV MEVYQPEAVV LQCGADSLSG DRLGCFNLSV KGHADCLRFL
310 320 330 340 350
RSYNVPLMVL GGGGYTIRNV ARCWCYETAV AVGVEPDNKL PYNEYFEYFG
360 370 380 390 400
PDYTLHVDPS PMENLNTPKD MERIRNTLLE QLSGLIHAPS VQFQHTPPVN
410 420 430 440 450
RVLDEPEDDM ETRPKPRIWS GTATYESDSD DDDKPLHGYS CRGGATTDRD
460 470
STGEDEMDDD NPEPDVNPPS S
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

« Hide 'large scale' publications
  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 29, 2014
This is version 92 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