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Protein

Histone deacetylase 6

Gene

HDA6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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 (PubMed:11340181, PubMed:12486004, PubMed:15037732, PubMed:16648464). Part of the AS1 repressor complex to regulate the KNOX expression in leaf development (PubMed:23271976). Binds to KNAT1, KNAT2, and KNATM chromatin (PubMed:23271976).5 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

  • histone deacetylase activity Source: TAIR
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC

GO - Biological processi

  • embryo development ending in seed dormancy Source: TAIR
  • gene silencing Source: TAIR
  • histone deacetylation Source: TAIR
  • posttranscriptional gene silencing Source: TAIR
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • response to abscisic acid Source: TAIR
  • response to salt stress Source: TAIR
  • seed maturation Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
  • 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.

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
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G63110.

Subcellular locationi

GO - Cellular componenti

  • chloroplast envelope Source: TAIR
  • nucleolus Source: UniProtKB-SubCell
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Curling and serrated leaves. Down curling phenotype on both the distal and lateral axis.1 Publication

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

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ9FML2.
PRIDEiQ9FML2.

PTM databases

iPTMnetiQ9FML2.

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

ExpressionAtlasiQ9FML2. baseline.
GenevisibleiQ9FML2. AT.

Interactioni

Subunit structurei

Interacts with Coi1, which functions in an SCF complex that recruits regulators for ubiquitination. Interacts with AHL22 (PubMed:12445118, PubMed:22442143). Interacts with AS1 (PubMed:23271976). Part of the AS1 repressor complex composed of AS1, LBD6/AS2 and HDA6 (PubMed:23271976). Binds to EBS and SHL (PubMed:25281686).4 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi21674. 18 interactions.
DIPiDIP-33452N.
IntActiQ9FML2. 2 interactions.
STRINGi3702.AT5G63110.1.

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

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
InParanoidiQ9FML2.
KOiK06067.
OMAiHRRRVSY.
OrthoDBiEOG093609CH.
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:
EMBLi
GenBanki
DDBJi
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.
GrameneiAT5G63110.1; AT5G63110.1; AT5G63110.
KEGGiath:AT5G63110.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

BioGridi21674. 18 interactions.
DIPiDIP-33452N.
IntActiQ9FML2. 2 interactions.
STRINGi3702.AT5G63110.1.

PTM databases

iPTMnetiQ9FML2.

Proteomic databases

PaxDbiQ9FML2.
PRIDEiQ9FML2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G63110.1; AT5G63110.1; AT5G63110.
GeneIDi836431.
GrameneiAT5G63110.1; AT5G63110.1; AT5G63110.
KEGGiath:AT5G63110.

Organism-specific databases

TAIRiAT5G63110.

Phylogenomic databases

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
InParanoidiQ9FML2.
KOiK06067.
OMAiHRRRVSY.
OrthoDBiEOG093609CH.
PhylomeDBiQ9FML2.

Enzyme and pathway databases

BioCyciARA:AT5G63110-MONOMER.

Miscellaneous databases

PROiQ9FML2.

Gene expression databases

ExpressionAtlasiQ9FML2. baseline.
GenevisibleiQ9FML2. AT.

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.
ProtoNetiSearch...

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: September 7, 2016
This is version 105 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.