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Q9FML2 (HDA6_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone deacetylase 6

EC=3.5.1.98
Gene names
Name:HDA6
Synonyms:RPD3B
Ordered Locus Names:At5g63110
ORF Names:MDC12.7
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length471 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (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. Ref.6 Ref.7 Ref.10 Ref.12

Catalytic activity

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

Enzyme regulation

Inhibited by trichostatin A. Ref.12

Subunit structure

Interacts with Coi1, which functions in an SCF complex that recruits regulators for ubiquitination. Ref.9

Subcellular location

Nucleusnucleolus Ref.12.

Tissue specificity

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

Induction

By jasmonic acid and ethylene. Ref.11 Ref.12

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.

Sequence similarities

Belongs to the histone deacetylase family. HD type 1 subfamily.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Molecular functionChromatin regulator
Hydrolase
Repressor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processembryo development ending in seed dormancy

Inferred from mutant phenotype PubMed 21330492. Source: TAIR

gene silencing

Inferred from mutant phenotype PubMed 9611181. Source: TAIR

histone deacetylation

Inferred from mutant phenotype Ref.12. Source: TAIR

posttranscriptional gene silencing

Inferred from mutant phenotype Ref.7. Source: TAIR

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

response to abscisic acid

Inferred from mutant phenotype PubMed 20519338. Source: TAIR

response to salt stress

Inferred from mutant phenotype PubMed 20519338. Source: TAIR

seed maturation

Inferred from mutant phenotype PubMed 21330492. Source: TAIR

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

vegetative to reproductive phase transition of meristem

Inferred from mutant phenotype PubMed 21398257. Source: TAIR

   Cellular_componentchloroplast envelope

Inferred from direct assay PubMed 12938931. Source: TAIR

nucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay Ref.12PubMed 21398257. Source: TAIR

   Molecular_functionNAD-dependent histone deacetylase activity (H3-K14 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K18 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K9 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H4-K16 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

histone deacetylase activity

Inferred from mutant phenotype PubMed 21398257. Source: TAIR

protein binding

Inferred from physical interaction Ref.9. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

COI1O041973EBI-639608,EBI-401159

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 471471Histone deacetylase 6
PRO_0000280085

Regions

Region20 – 333314Histone deacetylase
Compositional bias311 – 3144Poly-Gly
Compositional bias428 – 46538Asp-rich

Sites

Active site1531 By similarity

Experimental info

Mutagenesis161G → R in sil1; suppression of transgene silencing. Ref.10
Mutagenesis1271G → R in axe1-1; suppression of transgene silencing. Ref.6
Mutagenesis2841G → D in axe1-2; suppression of transgene silencing. Ref.6
Mutagenesis2941A → V in axe1-3; suppression of transgene silencing. Ref.6
Mutagenesis459 – 47113Missing in rts1-2; suppression of transgene silencing. Ref.7
Sequence conflict3131G → E in AAG28475. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q9FML2 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: CA16C2640D1B1732

FASTA47152,652
        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 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_201116.1. NM_125705.3.
UniGeneAt.8834.

3D structure databases

ProteinModelPortalQ9FML2.
SMRQ9FML2. Positions 18-385.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid21674. 18 interactions.
DIPDIP-33452N.
IntActQ9FML2. 2 interactions.

Proteomic databases

PaxDbQ9FML2.
PRIDEQ9FML2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G63110.1; AT5G63110.1; AT5G63110.
GeneID836431.
KEGGath:AT5G63110.

Organism-specific databases

TAIRAT5G63110.

Phylogenomic databases

eggNOGCOG0123.
HOGENOMHOG000225180.
InParanoidQ9FML2.
KOK06067.
OMAEAHRDWK.
PhylomeDBQ9FML2.

Enzyme and pathway databases

BioCycARA:AT5G63110-MONOMER.

Gene expression databases

GenevestigatorQ9FML2.

Family and domain databases

Gene3D3.40.800.20. 1 hit.
InterProIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERPTHR10625. PTHR10625. 1 hit.
PfamPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSPR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNetSearch...

Entry information

Entry nameHDA6_ARATH
AccessionPrimary (citable) accession number: Q9FML2
Secondary accession number(s): Q9FVE5
Entry history
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 1, 2001
Last modified: June 11, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names