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Protein

Histone deacetylase 1

Gene

hda-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: -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. Involved in the endoderm determination possibly by repressing end-1 expression. Also involved in vulval development, possibly by repressing lag-2 expression.2 Publications

Catalytic activityi

Hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei145By similarity1

GO - Molecular functioni

  • histone deacetylase activity Source: WormBase
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  • RNA polymerase II repressing transcription factor binding Source: WormBase

GO - Biological processi

  • cell differentiation Source: WormBase
  • embryo development ending in birth or egg hatching Source: WormBase
  • embryonic digestive tract morphogenesis Source: WormBase
  • gonad development Source: WormBase
  • histone deacetylation Source: WormBase
  • negative regulation of Notch signaling pathway Source: WormBase
  • negative regulation of Ras protein signal transduction Source: WormBase
  • negative regulation of stress response to copper ion Source: WormBase
  • negative regulation of transcription by RNA polymerase II Source: WormBase
  • negative regulation of vulval development Source: WormBase
  • nematode male tail tip morphogenesis Source: WormBase
  • positive regulation of transcription by RNA polymerase II Source: WormBase
  • regulation of cell differentiation Source: WormBase
  • regulation of cell migration Source: WormBase
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Developmental protein, Hydrolase, Repressor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-CEL-3214815 HDACs deacetylate histones
R-CEL-4551638 SUMOylation of chromatin organization proteins
R-CEL-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-CEL-8943724 Regulation of PTEN gene transcription

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 1 (EC:3.5.1.98)
Gene namesi
Name:hda-1Imported
ORF Names:C53A5.3Imported
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome V

Organism-specific databases

WormBaseiC53A5.3 ; CE08952 ; WBGene00001834 ; hda-1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

RNAi-mediated knockdown results in embryonic lethality.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi145H → F: Loss of function. 1
Mutagenesisi186G → E in gon-10; specific defects in gonadogenesis and vulval development. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001147191 – 461Histone deacetylase 1Add BLAST461

Post-translational modificationi

Sumoylated.1 Publication

Keywords - PTMi

Ubl conjugation

Proteomic databases

EPDiO17695
PaxDbiO17695
PeptideAtlasiO17695
PRIDEiO17695

PTM databases

iPTMnetiO17695

Expressioni

Tissue specificityi

Ubiquitously expressed throughout embryonic and postembryonic development.1 Publication

Developmental stagei

Expressed both maternally and zygotically.1 Publication

Gene expression databases

BgeeiWBGene00001834

Interactioni

Subunit structurei

Probable component of a NuRD-like complex, composed of at least lin-53 and hda-1 (PubMed:17075059). Interacts with lin-53 (PubMed:9875852, PubMed:17075059). Interacts with pop-1 (PubMed:11742996).3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • RNA polymerase II repressing transcription factor binding Source: WormBase

Protein-protein interaction databases

BioGridi44961, 22 interactors
DIPiDIP-26427N
IntActiO17695, 13 interactors
MINTiO17695
STRINGi6239.C53A5.3.2

Structurei

3D structure databases

ProteinModelPortaliO17695
SMRiO17695
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni13 – 325Histone deacetylaseAdd BLAST313

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1342 Eukaryota
COG0123 LUCA
GeneTreeiENSGT00910000144047
HOGENOMiHOG000225180
InParanoidiO17695
KOiK06067
OMAiRMTHHLL
OrthoDBiEOG091G067J
PhylomeDBiO17695

Family and domain databases

Gene3Di3.40.800.20, 1 hit
InterProiView protein in InterPro
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf
PANTHERiPTHR10625 PTHR10625, 1 hit
PfamiView protein in Pfam
PF00850 Hist_deacetyl, 1 hit
PIRSFiPIRSF037913 His_deacetylse_1, 1 hit
PRINTSiPR01270 HDASUPER
PR01271 HISDACETLASE
SUPFAMiSSF52768 SSF52768, 1 hit

Sequencei

Sequence statusi: Complete.

O17695-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSNGPLMEH GKRRVAYYYD SNIGNYYYGQ GHVMKPHRIR MTHHLVLNYG
60 70 80 90 100
LYRNLEIFRP FPASFEDMTR FHSDEYMTFL KSANPDNLKS FNKQMLKFNV
110 120 130 140 150
GEDCPLFDGL YEFCQLSSGG SLAAATKLNK QKVDIAINWM GGLHHAKKSE
160 170 180 190 200
ASGFCYTNDI VLGILELLKY HKRVLYVDID VHHGDGVEEA FYTTDRVMTV
210 220 230 240 250
SFHKYGDFFP GTGDLKDIGA GKGKLYSVNV PLRDGITDVS YQSIFKPIMT
260 270 280 290 300
KVMERFDPCA VVLQCGADSL NGDRLGPFNL TLKGHGECAR FFRSYNVPLM
310 320 330 340 350
MVGGGGYTPR NVARCWTYET SIAVDKEVPN ELPYNDYFEY FGPNYRLHIE
360 370 380 390 400
SSNAANENSS DMLAKLQTDV IANLEQLTFV PSVQMRPIPE DALSALNDDS
410 420 430 440 450
LIADQANPDK RLPPQITDGM IQDDGDFYDG EREGDDRRNE SDAKRAAQFE
460
SEGGEKRQKT E
Length:461
Mass (Da):52,138
Last modified:January 1, 1998 - v1
Checksum:i9A104E88C5A1C07A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z81486 Genomic DNA Translation: CAB03984.1
PIRiT20163
RefSeqiNP_506599.1, NM_074198.7
UniGeneiCel.17341

Genome annotation databases

EnsemblMetazoaiC53A5.3; C53A5.3; WBGene00001834
GeneIDi179959
KEGGicel:CELE_C53A5.3
UCSCiC53A5.3.1 c. elegans

Similar proteinsi

Entry informationi

Entry nameiHDA1_CAEEL
AccessioniPrimary (citable) accession number: O17695
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 1, 1998
Last modified: March 28, 2018
This is version 136 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health