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Q8RX28

- HDA5_ARATH

UniProt

Q8RX28 - HDA5_ARATH

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Protein

Histone deacetylase 5

Gene

HDA5

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 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). 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).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei158 – 1581By similarity

GO - Molecular functioni

  1. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  2. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
  3. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
  4. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC

GO - Biological processi

  1. regulation of transcription, DNA-templated Source: UniProtKB-KW
  2. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 5 (EC:3.5.1.98)
Gene namesi
Name:HDA5
Ordered Locus Names:At5g61060
ORF Names:MAF19.7
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G61060.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 660659Histone deacetylase 5PRO_0000280084Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ8RX28.
PRIDEiQ8RX28.

Expressioni

Gene expression databases

GenevestigatoriQ8RX28.

Interactioni

Protein-protein interaction databases

BioGridi21471. 4 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ8RX28.
SMRiQ8RX28. Positions 28-383.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni26 – 349324Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000225183.
InParanoidiQ8RX28.
KOiK11407.
PhylomeDBiQ8RX28.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PRINTSiPR01270. HDASUPER.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 1 isoform i produced by alternative splicing. Align

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q8RX28-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MAMAGESSGK KIGDCDGKVA GNRQRKVGLI YDETMCKHDT PDGEDHPECP
60 70 80 90 100
DRIRVIWEKL QLAGVSQRCV VLGSSKAEDK HLQLVHTKDH VNLVKSISTK
110 120 130 140 150
QKDYRRNRIA SQLNSIYLNG GSSEAAYLAA GSVVKLAEKV AEGELDCGFA
160 170 180 190 200
IVRPPGHHAE ADEAMGFCLF NNVAVAASFL LNERPDLGVK KILIVDWDVH
210 220 230 240 250
HGNGTQKMFW KDPRVLFFSV HRHEYGGFYP AGDDGDYNMV GEGPGEGFNI
260 270 280 290 300
NVPWDQGRCG DADYLAAWDH ILIPVAREFN PDVIFLSAGF DAAINDPLGG
310 320 330 340 350
CCVTPYGYSV MLKKLMEFAQ GKIVLALEGG YNLDSIAKSS LACVQVLLED
360 370 380 390 400
KQIQGPPEAY PFESTWRVIQ AVRKRLCTYW PSLADELSWK LINQKTPTPI
410 420 430 440 450
ILISSSDSET EDNAQGLLDQ MSKLSIENPQ GTLLENHQVE PASTSWRADL
460 470 480 490 500
AKVDVWYASF GSNMWKPRFL CYIQGGQVDG LKKVCVGSMD KSPPKETVWE
510 520 530 540 550
TFPHRLFFGR ESSVGWGVGG VAFTNPLANL IDQTHMCLYR ITLEQFNDVL
560 570 580 590 600
SQENGLNVDS DSPVFDLAAL QLVDNKGSIL EAPLNSWYGN VVCLGKERDI
610 620 630 640 650
PILTMTCTLS AVEKFKSGEI PIRPPAKAYA NTLIRGLVEG GRLSKEEAEA
660
YIDKAVSKPL
Length:660
Mass (Da):72,723
Last modified:June 1, 2002 - v1
Checksum:iA40906BF82B397DE
GO

Sequence cautioni

The sequence BAB10369.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence BAB10370.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
RefSeqiNP_200914.2. NM_125499.4. [Q8RX28-1]
UniGeneiAt.44759.
At.75645.

Genome annotation databases

EnsemblPlantsiAT5G61060.1; AT5G61060.1; AT5G61060. [Q8RX28-1]
GeneIDi836227.
KEGGiath:AT5G61060.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
RefSeqi NP_200914.2. NM_125499.4. [Q8RX28-1 ]
UniGenei At.44759.
At.75645.

3D structure databases

ProteinModelPortali Q8RX28.
SMRi Q8RX28. Positions 28-383.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 21471. 4 interactions.

Proteomic databases

PaxDbi Q8RX28.
PRIDEi Q8RX28.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G61060.1 ; AT5G61060.1 ; AT5G61060 . [Q8RX28-1 ]
GeneIDi 836227.
KEGGi ath:AT5G61060.

Organism-specific databases

TAIRi AT5G61060.

Phylogenomic databases

eggNOGi COG0123.
HOGENOMi HOG000225183.
InParanoidi Q8RX28.
KOi K11407.
PhylomeDBi Q8RX28.

Enzyme and pathway databases

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

Gene expression databases

Genevestigatori Q8RX28.

Family and domain databases

Gene3Di 3.40.800.20. 1 hit.
InterProi IPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
[Graphical view ]
PANTHERi PTHR10625. PTHR10625. 1 hit.
Pfami PF00850. Hist_deacetyl. 1 hit.
[Graphical view ]
PRINTSi PR01270. HDASUPER.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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].

Entry informationi

Entry nameiHDA5_ARATH
AccessioniPrimary (citable) accession number: Q8RX28
Secondary accession number(s): Q9FNQ7, Q9FNQ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: June 1, 2002
Last modified: October 29, 2014
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Unlike its tandem duplication HDA18, HDA5 is not required for the cellular patterning in the root epidermis.

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

External Data

Dasty 3