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Q55BW2

- HDA12_DICDI

UniProt

Q55BW2 - HDA12_DICDI

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Protein

Histone deacetylase B

Gene

hdaB

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript 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 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
Complete GO annotation...

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-KW
  2. nucleus Source: dictyBase
Complete GO annotation...

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.
InParanoidiQ55BW2.
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

        10         20         30         40         50
MEYNTILNNT SKTRVCYFFD QDVGNYFYGP YHPMKPHRLC LTNNLVLNYG
60 70 80 90 100
LHKKMHLYKA RPADAEDMLK FHSEDYVDFL ERVTPENINE WKDVKRFHIG
110 120 130 140 150
EDCPVFPGLY DYCSIYSGGS IEGALKLNHR MYDIAINWSG GLHHARKDEA
160 170 180 190 200
SGFCYVNDIV LAILELLKFH ARVLYIDIDV HHGDGVQEAF YLTDRVMTVS
210 220 230 240 250
FHKFGGDFFP GTGDIDEIGA KTGKLYSVNV PLADGIDDKN YLNIFKPVIQ
260 270 280 290 300
GVMDYYRPSV IVLQCGADSL RFDRLGCFNL TIKGHAECVR FVKSFNIPTL
310 320 330 340 350
VLGGGGYTVR NVARCWTYET SVCVDTEVNN ELPYNDYIQF YSPDFQLIPD
360 370 380 390 400
YTGLPFKYEN ANTKSYLESL RIKILENLRI LQWAPSVQIQ DVPPDIMPID
410 420
FDRDEDSKEN MDKRKKKHND FS
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.
InParanoidi Q55BW2.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 65 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