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Protein

Histone deacetylase 1

Gene

Hdac1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation.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 sitei141 – 1411By similarity

GO - Molecular functioni

GO - Biological processi

  • cellular response to oxidative stress Source: RGD
  • cellular response to tumor necrosis factor Source: RGD
  • circadian regulation of gene expression Source: UniProtKB
  • histone H3 deacetylation Source: RGD
  • histone H4 deacetylation Source: UniProtKB
  • negative regulation of cell proliferation Source: RGD
  • negative regulation of insulin secretion Source: RGD
  • negative regulation of neuron apoptotic process Source: RGD
  • negative regulation of peptidyl-lysine acetylation Source: RGD
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of cell proliferation Source: RGD
  • positive regulation of chemokine (C-X-C motif) ligand 2 production Source: RGD
  • positive regulation of interleukin-1 production Source: RGD
  • positive regulation of oligodendrocyte differentiation Source: RGD
  • positive regulation of tumor necrosis factor production Source: RGD
  • positive regulation of type B pancreatic cell apoptotic process Source: RGD
  • positive regulation of tyrosine phosphorylation of Stat3 protein Source: RGD
  • response to amphetamine Source: RGD
  • response to caffeine Source: RGD
  • response to drug Source: RGD
  • response to hyperoxia Source: RGD
  • response to lipopolysaccharide Source: RGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiREACT_274139. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_274349. formation of the beta-catenin:TCF transactivating complex.
REACT_275619. Factors involved in megakaryocyte development and platelet production.
REACT_280841. RNA Polymerase I Transcription Initiation.
REACT_283076. p75NTR negatively regulates cell cycle via SC1.
REACT_308234. repression of WNT target genes.
REACT_315119. NoRC negatively regulates rRNA expression.
REACT_319651. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_345252. deactivation of the beta-catenin transactivating complex.
REACT_349406. G0 and Early G1.
REACT_361585. HDACs deacetylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 1 (EC:3.5.1.98)
Short name:
HD1
Gene namesi
Name:Hdac1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi619975. Hdac1.

Subcellular locationi

GO - Cellular componenti

  • chromatin Source: RGD
  • neuron projection Source: RGD
  • nucleoplasm Source: Reactome
  • nucleus Source: RGD
  • perinuclear region of cytoplasm Source: RGD
  • protein complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 482482Histone deacetylase 1PRO_0000304731Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei74 – 741N6-acetyllysineBy similarity
Modified residuei220 – 2201N6-acetyllysineBy similarity
Modified residuei393 – 3931Phosphoserine1 Publication
Modified residuei421 – 4211PhosphoserineBy similarity
Modified residuei423 – 4231PhosphoserineBy similarity
Modified residuei432 – 4321N6-methylated lysine; by EHMT2By similarity
Cross-linki444 – 444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki476 – 476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity

Post-translational modificationi

Sumoylated on Lys-444 and Lys-476; which promotes enzymatic activity. Desumoylated by SENP1.By similarity
Phosphorylation on Ser-421 and Ser-423 promotes enzymatic activity and interactions with NuRD and SIN3 complexes. Phosphorylated by CDK5.By similarity
Ubiquitinated by CHFR and KCTD11, leading to its degradation by the proteasome.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ4QQW4.
PRIDEiQ4QQW4.

PTM databases

PhosphoSiteiQ4QQW4.

Expressioni

Gene expression databases

GenevestigatoriQ4QQW4.

Interactioni

Subunit structurei

Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core complex associates with MTA2, MBD2, MBD3, MTA1L1, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylation (NuRD) complex, or with SIN3, SAP18 and SAP30 to form the SIN3 HDAC complex. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Found in a trimeric complex with APBB1 and TSHZ3; the interaction between HDAC1 and APBB1 is mediated by TSHZ3. Component of a RCOR/GFI/KDM1A/HDAC complex. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Associates with the 9-1-1 complex; interacts with HUS1. Found in a complex with DNMT3A and HDAC7. Interacts with the non-histone region of H2AFY. Interacts with TRIM28; the interaction recruits HDAC1 to E2F1 and inhibits its acetylation. Interacts with SP1; the interaction deacetylates SP1 and regulates its transcriptional activity. Interacts with SP3; the interaction deacetylates SP3 and regulates its transcriptional activity. In vitro, C(18) ceramides increase this interaction and the subsequent SP3 deacetylation and SP3-mediated repression of the TERT promoter. Interacts with TSHZ3 (via N-terminus); the interaction is direct. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with DNTTIP1 (By similarity). Identified in a histone deacetylase complex that contains DNTTIP1, HDAC1 and ELMSAN1; this complex assembles into a tetramer that contains four copies of each protein chain (By similarity). Interacts with C10orf90/FATS (via its N-terminal); the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the acetylation and stabilization of CDKN1A/p21. Interacts with CDKN1A/p21. Interacts with CDK5 complexed to CDK5R1 (p25). Interacts directly with GFI1 and GFI1B. Interacts with NR1D2 (via C-terminus). Interacts with TSC22D3 isoform 1; this interaction affects HDAC1 activity on MYOG promoter and thus inhibits MYOD1 transcriptional activity. Interacts with BAZ2A/TIP5, BANP, BCL6, BCOR, BHLHE40/DEC1, BRMS1, BRMS1L, CBFA2T3, CHFR, CIART, CRY1, DAXX, DDIT3/CHOP, DDX5, DNMT1, E4F1, EP300, HCFC1, HDAC9, INSM1, NFE4, NR4A2/NURR1, MIER1, KDM4A, KDM5B, KLF1, MINT, NRIP1, PCAF, PHB2, PRDM6, PRDM16, RB1, RERE, SAMSN1, SAP30L, SETDB1, SMAD3, SMARCA4/BRG1, SMYD2, SUV39H1, TGIF, TGIF2, TRAF6, UHRF1, UHRF2, ZMYND15, ZNF431 and ZNF541. Interacts with KDM5A.By similarity

Protein-protein interaction databases

BioGridi255695. 5 interactions.
IntActiQ4QQW4. 1 interaction.
STRINGi10116.ENSRNOP00000012854.

Structurei

3D structure databases

ProteinModelPortaliQ4QQW4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 321313Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062889.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiQ4QQW4.
KOiK06067.
OMAiQIAHEYC.
OrthoDBiEOG7DNNTW.
PhylomeDBiQ4QQW4.
TreeFamiTF106171.

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.

Q4QQW4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQTQGTKRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK
60 70 80 90 100
MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSKQ MQRFNVGEDC
110 120 130 140 150
PVFDGLFEFC QLSTGGSVAS AVKLNKQQTD IAVNWAGGLH HAKKSEASGF
160 170 180 190 200
CYVNDIVLAI LELLKYHQRV LYIDIDIHHG DGVEEAFYTT DRVMTVSFHK
210 220 230 240 250
YGEYFPGTGD LRDIGAGKGK YYAVNYPLRD GIDDESYEAI FKPVMSKVME
260 270 280 290 300
MFQPSAVVLQ CGSDSLSGDR LGCFNLTIKG HAKCVEFVKS FNLPMLMLGG
310 320 330 340 350
GGYTIRNVAR CWTYETAVAL DTEIPNELPY NDYFEYFGPD FKLHISPSNM
360 370 380 390 400
TNQNTNEYLE KIKQRLFENL RMLPHAPGVQ MQAIPEDAIP EESGDEDEED
410 420 430 440 450
PDKRISICSS DKRIACEEEF SDSDEEGEGG RKNSSNFKKA KRVKTEDEKE
460 470 480
KDPEEKKEVT EEEKTKEEKP EAKGVKEEVK MA
Length:482
Mass (Da):55,093
Last modified:July 19, 2005 - v1
Checksum:i7F6563C17F5E4844
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097943 mRNA. Translation: AAH97943.1.
BC107476 mRNA. Translation: AAI07477.1.
RefSeqiNP_001020580.1. NM_001025409.1.
UniGeneiRn.1863.

Genome annotation databases

EnsembliENSRNOT00000012854; ENSRNOP00000012854; ENSRNOG00000009568.
GeneIDi297893.
KEGGirno:297893.
UCSCiRGD:619975. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097943 mRNA. Translation: AAH97943.1.
BC107476 mRNA. Translation: AAI07477.1.
RefSeqiNP_001020580.1. NM_001025409.1.
UniGeneiRn.1863.

3D structure databases

ProteinModelPortaliQ4QQW4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi255695. 5 interactions.
IntActiQ4QQW4. 1 interaction.
STRINGi10116.ENSRNOP00000012854.

Chemistry

BindingDBiQ4QQW4.
ChEMBLiCHEMBL2915.

PTM databases

PhosphoSiteiQ4QQW4.

Proteomic databases

PaxDbiQ4QQW4.
PRIDEiQ4QQW4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000012854; ENSRNOP00000012854; ENSRNOG00000009568.
GeneIDi297893.
KEGGirno:297893.
UCSCiRGD:619975. rat.

Organism-specific databases

CTDi3065.
RGDi619975. Hdac1.

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062889.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiQ4QQW4.
KOiK06067.
OMAiQIAHEYC.
OrthoDBiEOG7DNNTW.
PhylomeDBiQ4QQW4.
TreeFamiTF106171.

Enzyme and pathway databases

ReactomeiREACT_274139. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_274349. formation of the beta-catenin:TCF transactivating complex.
REACT_275619. Factors involved in megakaryocyte development and platelet production.
REACT_280841. RNA Polymerase I Transcription Initiation.
REACT_283076. p75NTR negatively regulates cell cycle via SC1.
REACT_308234. repression of WNT target genes.
REACT_315119. NoRC negatively regulates rRNA expression.
REACT_319651. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_345252. deactivation of the beta-catenin transactivating complex.
REACT_349406. G0 and Early G1.
REACT_361585. HDACs deacetylate histones.

Miscellaneous databases

NextBioi642799.
PROiQ4QQW4.

Gene expression databases

GenevestigatoriQ4QQW4.

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.
ProtoNetiSearch...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Placenta.
  2. "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites."
    Hoffert J.D., Pisitkun T., Wang G., Shen R.-F., Knepper M.A.
    Proc. Natl. Acad. Sci. U.S.A. 103:7159-7164(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-393, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiHDAC1_RAT
AccessioniPrimary (citable) accession number: Q4QQW4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: July 19, 2005
Last modified: May 27, 2015
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.