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Q8RX28 (HDA5_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 80. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone deacetylase 5

EC=3.5.1.98
Gene names
Name:HDA5
Ordered Locus Names:At5g61060
ORF Names:MAF19.7
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length660 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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). 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.

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 660659Histone deacetylase 5
PRO_0000280084

Regions

Region26 – 349324Histone deacetylase

Sites

Active site1581 By similarity

Amino acid modifications

Modified residue21N-acetylalanine Ref.6

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

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

FASTA66072,723
        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' 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. 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.
[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.
[6]"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: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

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.
RefSeqNP_200914.2. NM_125499.4.
UniGeneAt.44759.
At.75645.

3D structure databases

ProteinModelPortalQ8RX28.
SMRQ8RX28. Positions 28-380.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid21471. 4 interactions.

Proteomic databases

PaxDbQ8RX28.
PRIDEQ8RX28.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G61060.1; AT5G61060.1; AT5G61060. [Q8RX28-1]
GeneID836227.
KEGGath:AT5G61060.

Organism-specific databases

TAIRAT5G61060.

Phylogenomic databases

eggNOGCOG0123.
HOGENOMHOG000225183.
InParanoidQ8RX28.
KOK11407.
PhylomeDBQ8RX28.
ProtClustDBCLSN2690255.

Enzyme and pathway databases

BioCycARA:AT5G61060-MONOMER.
ARA:GQT-1316-MONOMER.

Gene expression databases

GenevestigatorQ8RX28.

Family and domain databases

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

Entry information

Entry nameHDA5_ARATH
AccessionPrimary (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: April 16, 2014
This is version 80 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