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Q4QQW4

- HDAC1_RAT

UniProt

Q4QQW4 - HDAC1_RAT

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Protein

Histone deacetylase 1

Gene

Hdac1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - 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

  1. deacetylase activity Source: UniProtKB
  2. histone deacetylase activity Source: UniProtKB
  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
  7. transcription regulatory region sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  1. circadian regulation of gene expression Source: UniProtKB
  2. histone H4 deacetylation Source: UniProtKB
  3. negative regulation of transcription, DNA-templated Source: UniProtKB
  4. 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_194639. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_196232. Factors involved in megakaryocyte development and platelet production.
REACT_198659. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_198750. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_198752. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_199174. G0 and Early G1.
REACT_206206. RNA Polymerase I Transcription Initiation.
REACT_214025. deactivation of the beta-catenin transactivating complex.
REACT_223113. NoRC negatively regulates rRNA expression.
REACT_226234. formation of the beta-catenin:TCF transactivating complex.
REACT_231997. repression of WNT target genes.
REACT_235467. p75NTR negatively regulates cell cycle via SC1.
REACT_258496. 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: Chromosome 5

Organism-specific databases

RGDi619975. Hdac1.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleoplasm Source: Reactome
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 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.
OMAiLRRDHQN.
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 .
RefSeqi NP_001020580.1. NM_001025409.1.
UniGenei Rn.1863.

3D structure databases

ProteinModelPortali Q4QQW4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 255695. 5 interactions.
IntActi Q4QQW4. 1 interaction.
STRINGi 10116.ENSRNOP00000012854.

Chemistry

BindingDBi Q4QQW4.
ChEMBLi CHEMBL2915.

PTM databases

PhosphoSitei Q4QQW4.

Proteomic databases

PaxDbi Q4QQW4.
PRIDEi Q4QQW4.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000012854 ; ENSRNOP00000012854 ; ENSRNOG00000009568 .
GeneIDi 297893.
KEGGi rno:297893.
UCSCi RGD:619975. rat.

Organism-specific databases

CTDi 3065.
RGDi 619975. Hdac1.

Phylogenomic databases

eggNOGi COG0123.
GeneTreei ENSGT00530000062889.
HOGENOMi HOG000225180.
HOVERGENi HBG057112.
InParanoidi Q4QQW4.
KOi K06067.
OMAi LRRDHQN.
OrthoDBi EOG7DNNTW.
PhylomeDBi Q4QQW4.
TreeFami TF106171.

Enzyme and pathway databases

Reactomei REACT_194639. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_196232. Factors involved in megakaryocyte development and platelet production.
REACT_198659. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_198750. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_198752. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_199174. G0 and Early G1.
REACT_206206. RNA Polymerase I Transcription Initiation.
REACT_214025. deactivation of the beta-catenin transactivating complex.
REACT_223113. NoRC negatively regulates rRNA expression.
REACT_226234. formation of the beta-catenin:TCF transactivating complex.
REACT_231997. repression of WNT target genes.
REACT_235467. p75NTR negatively regulates cell cycle via SC1.
REACT_258496. HDACs deacetylate histones.

Miscellaneous databases

NextBioi 642799.
PROi Q4QQW4.

Gene expression databases

Genevestigatori Q4QQW4.

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

  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: November 26, 2014
This is version 89 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