Histone deacetylase 5 - Arabidopsis thaliana (Mouse-ear cress)

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Q8RX28 (HDA5_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone deacetylase 5
EC=3.5.1.98

Gene names

Name:	HDA5
Ordered Locus Names:	At5g61060
ORF Names:	MAF19.7

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	660 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript 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). 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 By similarity. Ref.5
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subcellular location	Nucleus By similarity.
Miscellaneous	Unlike its tandem duplication HDA18, HDA5 is not required for the cellular patterning in the root epidermis.
Sequence similarities	Belongs to the histone deacetylase family. HD type 2 subfamily.
Sequence caution	The sequence BAB10369.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence BAB10370.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select] Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q8RX28-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 660

660

Histone deacetylase 5

PRO_0000280084

Regions

Region

26 – 349

324

Histone deacetylase

Sites

Active site

158

By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Isoform 1 [UniParc].

Last modified June 1, 2002. Version 1.
Checksum: A40906BF82B397DE
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FASTA

660

72,723

        10         20         30         40         50         60 
MAMAGESSGK KIGDCDGKVA GNRQRKVGLI YDETMCKHDT PDGEDHPECP DRIRVIWEKL 

        70         80         90        100        110        120 
QLAGVSQRCV VLGSSKAEDK HLQLVHTKDH VNLVKSISTK QKDYRRNRIA SQLNSIYLNG 

       130        140        150        160        170        180 
GSSEAAYLAA GSVVKLAEKV AEGELDCGFA IVRPPGHHAE ADEAMGFCLF NNVAVAASFL 

       190        200        210        220        230        240 
LNERPDLGVK KILIVDWDVH HGNGTQKMFW KDPRVLFFSV HRHEYGGFYP AGDDGDYNMV 

       250        260        270        280        290        300 
GEGPGEGFNI NVPWDQGRCG DADYLAAWDH ILIPVAREFN PDVIFLSAGF DAAINDPLGG 

       310        320        330        340        350        360 
CCVTPYGYSV MLKKLMEFAQ GKIVLALEGG YNLDSIAKSS LACVQVLLED KQIQGPPEAY 

       370        380        390        400        410        420 
PFESTWRVIQ AVRKRLCTYW PSLADELSWK LINQKTPTPI ILISSSDSET EDNAQGLLDQ 

       430        440        450        460        470        480 
MSKLSIENPQ GTLLENHQVE PASTSWRADL AKVDVWYASF GSNMWKPRFL CYIQGGQVDG 

       490        500        510        520        530        540 
LKKVCVGSMD KSPPKETVWE TFPHRLFFGR ESSVGWGVGG VAFTNPLANL IDQTHMCLYR 

       550        560        570        580        590        600 
ITLEQFNDVL SQENGLNVDS DSPVFDLAAL QLVDNKGSIL EAPLNSWYGN VVCLGKERDI 

       610        620        630        640        650        660 
PILTMTCTLS AVEKFKSGEI PIRPPAKAYA NTLIRGLVEG GRLSKEEAEA YIDKAVSKPL

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones." Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N., Tabata S. DNA Res. 4:291-300(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"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. Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"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.
[5]	"Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis." Xu C.-R., Liu C., Wang Y.-L., Li L.-C., Chen W.-Q., Xu Z.-H., Bai S.-N. Proc. Natl. Acad. Sci. U.S.A. 102:14469-14474(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB006696 Genomic DNA. Translation: BAB10369.1. Sequence problems. AB006696 Genomic DNA. Translation: BAB10370.1. Sequence problems. CP002688 Genomic DNA. Translation: AED97417.1. AY090936 mRNA. Translation: AAM13986.1. AY120784 mRNA. Translation: AAM53342.1. BT000073 mRNA. Translation: AAN15392.1.
IPI	IPI00522955.
RefSeq	NP_200914.2. NM_125499.4.
UniGene	At.44759. At.75645.
3D structure databases
HSSP	HSSP built from PDB template 1ZZ0 based on UniProtKB Q70I53.
ProteinModelPortal	Q8RX28.
SMR	Q8RX28. Positions 28-380.
ModBase	Search...
Proteomic databases
PaxDb	Q8RX28.
PRIDE	Q8RX28.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G61060.1; AT5G61060.1; AT5G61060.
GeneID	836227.
KEGG	ath:AT5G61060.
Organism-specific databases
TAIR	At5g61060.
Phylogenomic databases
eggNOG	COG0123.
HOGENOM	HOG000225183.
InParanoid	Q8RX28.
KO	K11407.
PhylomeDB	Q8RX28.
ProtClustDB	CLSN2690255.
Gene expression databases
ArrayExpress	Q8RX28.
Genevestigator	Q8RX28.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PRINTS	PR01270. HDASUPER.
ProtoNet	Search...

Entry information

Entry name

HDA5_ARATH

Accession

Primary (citable) accession number: Q8RX28
Secondary accession number(s): Q9FNQ7, Q9FNQ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	June 1, 2002
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents