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Q8RX28

- HDA5_ARATH

UniProt

Q8RX28 - HDA5_ARATH

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
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
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    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

    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-SubCell

    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

    MAMAGESSGK KIGDCDGKVA GNRQRKVGLI YDETMCKHDT PDGEDHPECP    50
    DRIRVIWEKL QLAGVSQRCV VLGSSKAEDK HLQLVHTKDH VNLVKSISTK 100
    QKDYRRNRIA SQLNSIYLNG GSSEAAYLAA GSVVKLAEKV AEGELDCGFA 150
    IVRPPGHHAE ADEAMGFCLF NNVAVAASFL LNERPDLGVK KILIVDWDVH 200
    HGNGTQKMFW KDPRVLFFSV HRHEYGGFYP AGDDGDYNMV GEGPGEGFNI 250
    NVPWDQGRCG DADYLAAWDH ILIPVAREFN PDVIFLSAGF DAAINDPLGG 300
    CCVTPYGYSV MLKKLMEFAQ GKIVLALEGG YNLDSIAKSS LACVQVLLED 350
    KQIQGPPEAY PFESTWRVIQ AVRKRLCTYW PSLADELSWK LINQKTPTPI 400
    ILISSSDSET EDNAQGLLDQ MSKLSIENPQ GTLLENHQVE PASTSWRADL 450
    AKVDVWYASF GSNMWKPRFL CYIQGGQVDG LKKVCVGSMD KSPPKETVWE 500
    TFPHRLFFGR ESSVGWGVGG VAFTNPLANL IDQTHMCLYR ITLEQFNDVL 550
    SQENGLNVDS DSPVFDLAAL QLVDNKGSIL EAPLNSWYGN VVCLGKERDI 600
    PILTMTCTLS AVEKFKSGEI PIRPPAKAYA NTLIRGLVEG GRLSKEEAEA 650
    YIDKAVSKPL 660
    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.
    The sequence BAB10370.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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

    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 1, 2014
    This is version 83 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