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Q55BW2

- HDA12_DICDI

UniProt

Q55BW2 - HDA12_DICDI

Protein

Histone deacetylase B

Gene

hdaB

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      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 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. May play a role in the regulation of the timing of gene expression during the development and in the definition aspects of the phenotype that mediate social behavior in genetically heterogeneous groups.By similarity1 Publication

    Catalytic activityi

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

    Enzyme regulationi

    Its activity is inhibited by trichostatin A (TSA), a well known histone deacetylase inhibitor. Cytosolic activity is refractory to inhibition by TSA, while the nuclear activity is inhibited completely.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei102 – 1021SubstrateBy similarity
    Active sitei144 – 1441Proton acceptorBy similarity
    Binding sitei152 – 1521Substrate; via carbonyl oxygenBy similarity
    Metal bindingi179 – 1791Divalent metal cationBy similarity
    Metal bindingi181 – 1811Divalent metal cationBy similarity
    Metal bindingi268 – 2681Divalent metal cationBy similarity
    Binding sitei307 – 3071SubstrateBy similarity

    GO - Molecular functioni

    1. histone deacetylase activity Source: dictyBase
    2. metal ion binding Source: UniProtKB-KW
    3. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
    4. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
    5. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
    6. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC

    GO - Biological processi

    1. histone deacetylation Source: dictyBase
    2. regulation of transcription, DNA-templated Source: UniProtKB-KW
    3. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone deacetylase B
    Short name:
    DdHdaB
    Alternative name(s):
    Type-1 histone deacetylase 2 (EC:3.5.1.98)
    Gene namesi
    Name:hdaB
    ORF Names:DDB_G0270338
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 1, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0270338. hdaB.

    Subcellular locationi

    Nucleus 1 Publication. Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleus Source: dictyBase

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Develop normally but when mixed with wild type cells they sporulate less efficiently than the wild type. Do not show major alterations in gross histone acetylation levels.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 422422Histone deacetylase BPRO_0000331370Add
    BLAST

    Expressioni

    Developmental stagei

    Expressed throughout growth and development.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi44689.DDBDRAFT_0190980.

    Structurei

    3D structure databases

    ProteinModelPortaliQ55BW2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi303 – 3064Poly-Gly

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0123.
    KOiK11404.
    OMAiNFHYGPG.
    PhylomeDBiQ55BW2.

    Family and domain databases

    Gene3Di3.40.800.20. 1 hit.
    InterProiIPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view]
    PANTHERiPTHR10625. PTHR10625. 1 hit.
    PfamiPF00850. Hist_deacetyl. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSiPR01270. HDASUPER.
    PR01271. HISDACETLASE.

    Sequencei

    Sequence statusi: Complete.

    Q55BW2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEYNTILNNT SKTRVCYFFD QDVGNYFYGP YHPMKPHRLC LTNNLVLNYG    50
    LHKKMHLYKA RPADAEDMLK FHSEDYVDFL ERVTPENINE WKDVKRFHIG 100
    EDCPVFPGLY DYCSIYSGGS IEGALKLNHR MYDIAINWSG GLHHARKDEA 150
    SGFCYVNDIV LAILELLKFH ARVLYIDIDV HHGDGVQEAF YLTDRVMTVS 200
    FHKFGGDFFP GTGDIDEIGA KTGKLYSVNV PLADGIDDKN YLNIFKPVIQ 250
    GVMDYYRPSV IVLQCGADSL RFDRLGCFNL TIKGHAECVR FVKSFNIPTL 300
    VLGGGGYTVR NVARCWTYET SVCVDTEVNN ELPYNDYIQF YSPDFQLIPD 350
    YTGLPFKYEN ANTKSYLESL RIKILENLRI LQWAPSVQIQ DVPPDIMPID 400
    FDRDEDSKEN MDKRKKKHND FS 422
    Length:422
    Mass (Da):48,641
    Last modified:May 24, 2005 - v1
    Checksum:i732B1FFDAF4F21DC
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000005 Genomic DNA. Translation: EAL72519.1.
    RefSeqiXP_646719.1. XM_641627.1.

    Genome annotation databases

    EnsemblProtistsiDDB0237652; DDB0237652; DDB_G0270338.
    GeneIDi8617692.
    KEGGiddi:DDB_G0270338.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000005 Genomic DNA. Translation: EAL72519.1 .
    RefSeqi XP_646719.1. XM_641627.1.

    3D structure databases

    ProteinModelPortali Q55BW2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDBDRAFT_0190980.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0237652 ; DDB0237652 ; DDB_G0270338 .
    GeneIDi 8617692.
    KEGGi ddi:DDB_G0270338.

    Organism-specific databases

    dictyBasei DDB_G0270338. hdaB.

    Phylogenomic databases

    eggNOGi COG0123.
    KOi K11404.
    OMAi NFHYGPG.
    PhylomeDBi Q55BW2.

    Miscellaneous databases

    PROi Q55BW2.

    Family and domain databases

    Gene3Di 3.40.800.20. 1 hit.
    InterProi IPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view ]
    PANTHERi PTHR10625. PTHR10625. 1 hit.
    Pfami PF00850. Hist_deacetyl. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSi PR01270. HDASUPER.
    PR01271. HISDACETLASE.
    ProtoNeti Search...

    Publicationsi

    1. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.
    2. "Histone deacetylases regulate multicellular development in the social amoeba Dictyostelium discoideum."
      Sawarkar R., Visweswariah S.S., Nellen W., Nanjundiah V.
      J. Mol. Biol. 391:833-848(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME REGULATION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION.

    Entry informationi

    Entry nameiHDA12_DICDI
    AccessioniPrimary (citable) accession number: Q55BW2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 29, 2008
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 64 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3