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Protein

Histone deacetylase 1

Gene

Hdac1

Organism
Mus musculus (Mouse)
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.5 Publications

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

  • ATP-dependent chromatin remodeling Source: MGI
  • chromatin modification Source: UniProtKB
  • chromatin silencing at rDNA Source: Reactome
  • circadian regulation of gene expression Source: UniProtKB
  • circadian rhythm Source: UniProtKB
  • embryonic digit morphogenesis Source: BHF-UCL
  • endoderm development Source: MGI
  • epidermal cell differentiation Source: BHF-UCL
  • eyelid development in camera-type eye Source: BHF-UCL
  • fungiform papilla formation Source: BHF-UCL
  • hair follicle placode formation Source: BHF-UCL
  • hippocampus development Source: MGI
  • histone deacetylation Source: MGI
  • histone H3 deacetylation Source: UniProtKB
  • histone H4 deacetylation Source: UniProtKB
  • negative regulation by host of viral transcription Source: MGI
  • negative regulation of androgen receptor signaling pathway Source: MGI
  • negative regulation of apoptotic process Source: BHF-UCL
  • negative regulation of canonical Wnt signaling pathway Source: MGI
  • negative regulation of gene expression Source: MGI
  • negative regulation of I-kappaB kinase/NF-kappaB signaling Source: MGI
  • negative regulation of intrinsic apoptotic signaling pathway Source: MGI
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • neuron differentiation Source: MGI
  • odontogenesis of dentin-containing tooth Source: BHF-UCL
  • positive regulation of cell proliferation Source: BHF-UCL
  • positive regulation of oligodendrocyte differentiation Source: MGI
  • positive regulation of receptor biosynthetic process Source: MGI
  • positive regulation of transcription, DNA-templated Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • protein deacetylation Source: MGI
  • 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

ReactomeiR-MMU-1538133. G0 and Early G1.
R-MMU-201722. Formation of the beta-catenin:TCF transactivating complex.
R-MMU-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-MMU-3769402. Deactivation of the beta-catenin transactivating complex.
R-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-6804758. Regulation of TP53 Activity through Acetylation.
R-MMU-73762. RNA Polymerase I Transcription Initiation.
SABIO-RKO09106.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 1 (EC:3.5.1.98)
Short name:
HD1
Gene namesi
Name:Hdac1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:108086. Hdac1.

Subcellular locationi

GO - Cellular componenti

  • chromatin Source: MGI
  • cytoplasm Source: UniProtKB
  • cytosol Source: MGI
  • heterochromatin Source: MGI
  • histone deacetylase complex Source: UniProtKB
  • neuronal cell body Source: MGI
  • nuclear chromatin Source: BHF-UCL
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
  • NuRD complex Source: MGI
  • protein complex Source: MGI
  • Sin3 complex Source: MGI
  • transcriptional repressor complex Source: MGI
  • transcription factor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL4001.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 482482Histone deacetylase 1PRO_0000114688Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei74 – 741N6-acetyllysineBy similarity
Modified residuei220 – 2201N6-acetyllysineBy similarity
Modified residuei261 – 2611S-nitrosocysteineBy similarity
Modified residuei273 – 2731S-nitrosocysteineBy similarity
Modified residuei393 – 3931PhosphoserineBy similarity
Modified residuei409 – 4091PhosphoserineBy similarity
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); alternateBy similarity
Cross-linki444 – 444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Cross-linki457 – 457Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki476 – 476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity
Cross-linki476 – 476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy 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, S-nitrosylation, Ubl conjugation

Proteomic databases

EPDiO09106.
PaxDbiO09106.
PeptideAtlasiO09106.
PRIDEiO09106.

PTM databases

iPTMnetiO09106.
PhosphoSiteiO09106.

Expressioni

Tissue specificityi

Widely expressed with higher levels in thymus and testis and lower levels in liver. Present in muscle (at protein level).1 Publication

Inductioni

By interleukin-2.

Gene expression databases

BgeeiENSMUSG00000028800.
CleanExiMM_HDAC1.
ExpressionAtlasiO09106. baseline and differential.
GenevisibleiO09106. MM.

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. Interacts with CCAR2 (By similarity). Interacts with PPHLN1 (By similarity). Found in a complex with YY1, SIN3A and GON4L (PubMed:21454521).By similarity36 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CremP276993EBI-301912,EBI-8744406
Dnmt1P138643EBI-301912,EBI-301927
GscQ025912EBI-301912,EBI-7457485
Nfkb1P257992EBI-301912,EBI-643958
RelaQ042072EBI-301912,EBI-644400
Zbtb7aO889392EBI-301912,EBI-595063
Znf431E9QAG83EBI-301912,EBI-9549639

GO - Molecular functioni

Protein-protein interaction databases

BioGridi241423. 91 interactions.
DIPiDIP-31499N.
IntActiO09106. 34 interactions.
MINTiMINT-2568222.
STRINGi10090.ENSMUSP00000099657.

Chemistry

BindingDBiO09106.

Structurei

3D structure databases

ProteinModelPortaliO09106.
SMRiO09106. Positions 8-376.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiO09106.
KOiK06067.
OMAiHASCVKF.
OrthoDBiEOG091G067J.
PhylomeDBiO09106.
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.

O09106-1 [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 LA
Length:482
Mass (Da):55,075
Last modified:July 1, 1997 - v1
Checksum:i7F64D3C17F5E4844
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X98207 mRNA. Translation: CAA66870.1.
U80780 mRNA. Translation: AAB68398.1.
CCDSiCCDS18696.1.
RefSeqiNP_032254.1. NM_008228.2.
UniGeneiMm.202504.
Mm.391033.

Genome annotation databases

EnsembliENSMUST00000102597; ENSMUSP00000099657; ENSMUSG00000028800.
GeneIDi433759.
KEGGimmu:433759.
UCSCiuc008uxg.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X98207 mRNA. Translation: CAA66870.1.
U80780 mRNA. Translation: AAB68398.1.
CCDSiCCDS18696.1.
RefSeqiNP_032254.1. NM_008228.2.
UniGeneiMm.202504.
Mm.391033.

3D structure databases

ProteinModelPortaliO09106.
SMRiO09106. Positions 8-376.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi241423. 91 interactions.
DIPiDIP-31499N.
IntActiO09106. 34 interactions.
MINTiMINT-2568222.
STRINGi10090.ENSMUSP00000099657.

Chemistry

BindingDBiO09106.
ChEMBLiCHEMBL4001.

PTM databases

iPTMnetiO09106.
PhosphoSiteiO09106.

Proteomic databases

EPDiO09106.
PaxDbiO09106.
PeptideAtlasiO09106.
PRIDEiO09106.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000102597; ENSMUSP00000099657; ENSMUSG00000028800.
GeneIDi433759.
KEGGimmu:433759.
UCSCiuc008uxg.1. mouse.

Organism-specific databases

CTDi3065.
MGIiMGI:108086. Hdac1.

Phylogenomic databases

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiO09106.
KOiK06067.
OMAiHASCVKF.
OrthoDBiEOG091G067J.
PhylomeDBiO09106.
TreeFamiTF106171.

Enzyme and pathway databases

ReactomeiR-MMU-1538133. G0 and Early G1.
R-MMU-201722. Formation of the beta-catenin:TCF transactivating complex.
R-MMU-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-MMU-3769402. Deactivation of the beta-catenin transactivating complex.
R-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-6804758. Regulation of TP53 Activity through Acetylation.
R-MMU-73762. RNA Polymerase I Transcription Initiation.
SABIO-RKO09106.

Miscellaneous databases

PROiO09106.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000028800.
CleanExiMM_HDAC1.
ExpressionAtlasiO09106. baseline and differential.
GenevisibleiO09106. MM.

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...

Entry informationi

Entry nameiHDAC1_MOUSE
AccessioniPrimary (citable) accession number: O09106
Secondary accession number(s): P97476
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 1, 1997
Last modified: September 7, 2016
This is version 173 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.