Q9FML2 (HDA6_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase 6
EC=3.5.1.98

Gene names

Name:	HDA6
Synonyms:	RPD3B
Ordered Locus Names:	At5g63110
ORF Names:	MDC12.7

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	471 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nucleolus 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 process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	embryo development ending in seed dormancy Inferred from mutant phenotype PubMed 21330492. Source: TAIR histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC posttranscriptional gene silencing Inferred from mutant phenotype Ref.7. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to abscisic acid stimulus 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-dependent Inferred from electronic annotation. Source: UniProtKB-KW vegetative to reproductive phase transition of meristem Inferred from mutant phenotype PubMed 21398257. Source: TAIR
Cellular_component	chloroplast 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_function	NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K18 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from electronic annotation. Source: EC histone deacetylase activity Inferred from mutant phenotype PubMed 21398257. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
COI1	O04197	3	EBI-639608,EBI-401159

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 471	471	Histone deacetylase 6		PRO_0000280085
Regions
	Region	20 – 333	314	Histone deacetylase
	Compositional bias	311 – 314	4	Poly-Gly
	Compositional bias	428 – 465	38	Asp-rich
Sites
	Active site	153	1	By similarity
Experimental info
	Mutagenesis	16	1	G → R in sil1; suppression of transgene silencing. Ref.10
	Mutagenesis	127	1	G → R in axe1-1; suppression of transgene silencing. Ref.6
	Mutagenesis	284	1	G → D in axe1-2; suppression of transgene silencing. Ref.6
	Mutagenesis	294	1	A → V in axe1-3; suppression of transgene silencing. Ref.6
	Mutagenesis	459 – 471	13	Missing in rts1-2; suppression of transgene silencing. Ref.7
	Sequence conflict	313	1	G → E in AAG28475. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9FML2 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: CA16C2640D1B1732	FASTA	471	52,652
	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

References

	« Hide 'large scale' referencesShow '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. , 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.
+	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.
IPI	IPI00533304.
RefSeq	NP_201116.1. NM_125705.3.
UniGene	At.8834.
3D structure databases
HSSP	HSSP built from PDB template 1W22 based on UniProtKB Q9BY41.
ProteinModelPortal	Q9FML2.
SMR	Q9FML2. Positions 18-385.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9FML2. 2 interactions.
Proteomic databases
PaxDb	Q9FML2.
PRIDE	Q9FML2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G63110.1; AT5G63110.1; AT5G63110.
GeneID	836431.
KEGG	ath:AT5G63110.
Organism-specific databases
TAIR	At5g63110.
Phylogenomic databases
eggNOG	COG0123.
HOGENOM	HOG000225180.
InParanoid	Q9FML2.
KO	K06067.
OMA	WSAQSAV.
PhylomeDB	Q9FML2.
ProtClustDB	CLSN2687541.
Gene expression databases
ArrayExpress	Q9FML2.
Genevestigator	Q9FML2.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR003084. His_deacetylse_1. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PIRSF	PIRSF037913. His_deacetylse_1. 1 hit.
PRINTS	PR01270. HDASUPER. PR01271. HISDACETLASE.
ProtoNet	Search...

Entry information

Entry name

HDA6_ARATH

Accession

Primary (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:	May 1, 2013
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program