Q55BW2 (HDA12_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase B
Short name=DdHdaB

Alternative name(s):
Type-1 histone deacetylase 2
EC=3.5.1.98

Gene names

Name:	hdaB
ORF Names:	DDB_G0270338

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	422 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript 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 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. Ref.2
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Enzyme regulation	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. Ref.2
Subcellular location	Nucleus. Cytoplasm Ref.2.
Developmental stage	Expressed throughout growth and development. Ref.2
Disruption phenotype	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. Ref.2
Sequence similarities	Belongs to the histone deacetylase family. HD type 1 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Ligand	Metal-binding
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay Ref.2. Source: dictyBase
Molecular_function	NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K18 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from electronic annotation. Source: EC histone deacetylase activity Inferred from mutant phenotype Ref.2. Source: dictyBase metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 422	422	Histone deacetylase B		PRO_0000331370
Regions
	Compositional bias	303 – 306	4	Poly-Gly
Sites
	Active site	144	1	Proton acceptor By similarity
	Metal binding	179	1	Divalent metal cation By similarity
	Metal binding	181	1	Divalent metal cation By similarity
	Metal binding	268	1	Divalent metal cation By similarity
	Binding site	102	1	Substrate By similarity
	Binding site	152	1	Substrate; via carbonyl oxygen By similarity
	Binding site	307	1	Substrate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q55BW2 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: 732B1FFDAF4F21DC	FASTA	422	48,641
	10 20 30 40 50 60 MEYNTILNNT SKTRVCYFFD QDVGNYFYGP YHPMKPHRLC LTNNLVLNYG LHKKMHLYKA 70 80 90 100 110 120 RPADAEDMLK FHSEDYVDFL ERVTPENINE WKDVKRFHIG EDCPVFPGLY DYCSIYSGGS 130 140 150 160 170 180 IEGALKLNHR MYDIAINWSG GLHHARKDEA SGFCYVNDIV LAILELLKFH ARVLYIDIDV 190 200 210 220 230 240 HHGDGVQEAF YLTDRVMTVS FHKFGGDFFP GTGDIDEIGA KTGKLYSVNV PLADGIDDKN 250 260 270 280 290 300 YLNIFKPVIQ GVMDYYRPSV IVLQCGADSL RFDRLGCFNL TIKGHAECVR FVKSFNIPTL 310 320 330 340 350 360 VLGGGGYTVR NVARCWTYET SVCVDTEVNN ELPYNDYIQF YSPDFQLIPD YTGLPFKYEN 370 380 390 400 410 420 ANTKSYLESL RIKILENLRI LQWAPSVQIQ DVPPDIMPID FDRDEDSKEN MDKRKKKHND FS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000005 Genomic DNA. Translation: EAL72519.1.
RefSeq	XP_646719.1. XM_641627.1.
3D structure databases
HSSP	HSSP built from PDB template 1T67 based on UniProtKB Q9BY41.
ProteinModelPortal	Q55BW2.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDBDRAFT_0190980.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0237652; DDB0237652; DDB_G0270338.
GeneID	8617692.
KEGG	ddi:DDB_G0270338.
Organism-specific databases
dictyBase	DDB_G0270338. hdaB.
Phylogenomic databases
eggNOG	COG0123.
OMA	RDDEYYE.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR003084. His_deacetylse_1. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PIRSF	PIRSF037913. His_deacetylse_1. 1 hit.
PRINTS	PR01270. HDASUPER. PR01271. HISDACETLASE.
ProtoNet	Search...

Entry information

Entry name

HDA12_DICDI

Accession

Primary (citable) accession number: Q55BW2

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 29, 2008
Last sequence update:	May 24, 2005
Last modified:	May 1, 2013
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)