Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Histone deacetylase 3

Gene

Hdac3

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), and some other non-histone substrates. 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. Participates in the BCL6 transcriptional repressor activity by deacetylating the H3 'Lys-27' (H3K27) on enhancer elements, antagonizing EP300 acetyltransferase activity and repressing proximal gene expression. Probably participates in the regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1 repression activity. Required to repress transcription of the POU1F1 transcription factor. Acts as a molecular chaperone for shuttling phosphorylated NR2C1 to PML bodies for sumoylation. Contributes, together with XBP1, to the activation of NFE2L2-mediated HMOX1 transcription factor gene expression in a PI3K/mTORC2/Akt-dependent signaling pathway leading to endothelial cell (EC) survival under disturbed flow/oxidative stress (By similarity).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 sitei135 – 1351By similarity

GO - Molecular functioni

  1. chromatin binding Source: UniProtKB
  2. GTPase binding Source: RGD
  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 corepressor activity Source: UniProtKB
  8. transcription factor binding Source: RGD

GO - Biological processi

  1. cellular response to fluid shear stress Source: UniProtKB
  2. cellular response to mechanical stimulus Source: RGD
  3. cellular response to parathyroid hormone stimulus Source: RGD
  4. histone H3 deacetylation Source: RGD
  5. negative regulation of interleukin-1 production Source: RGD
  6. negative regulation of protein export from nucleus Source: RGD
  7. negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  8. negative regulation of tumor necrosis factor production Source: RGD
  9. positive regulation of neuron apoptotic process Source: RGD
  10. positive regulation of protein phosphorylation Source: UniProtKB
  11. positive regulation of TOR signaling Source: UniProtKB
  12. positive regulation of transcription factor import into nucleus Source: UniProtKB
  13. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  14. positive regulation of type B pancreatic cell apoptotic process Source: RGD
  15. regulation of protein stability Source: UniProtKB
  16. response to dexamethasone Source: RGD
  17. response to drug Source: RGD
  18. response to nutrient levels Source: RGD
  19. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiREACT_283076. p75NTR negatively regulates cell cycle via SC1.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 3 (EC:3.5.1.98)
Short name:
HD3
Gene namesi
Name:Hdac3
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Unplaced

Organism-specific databases

RGDi619977. Hdac3.

Subcellular locationi

  1. Nucleus By similarity
  2. Cytoplasm By similarity

  3. Note: Colocalizes with XBP1 and AKT1 in the cytoplasm (By similarity).By similarity

GO - Cellular componenti

  1. chromatin Source: RGD
  2. cytoplasm Source: RGD
  3. nucleoplasm Source: Reactome
  4. nucleus Source: RGD
  5. transcriptional repressor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 428428Histone deacetylase 3PRO_0000281030Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki44 – 44Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei424 – 4241PhosphoserineBy similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

PTM databases

PhosphoSiteiQ6P6W3.

Expressioni

Gene expression databases

GenevestigatoriQ6P6W3.

Interactioni

Subunit structurei

Interacts with BTBD14B (PubMed:16033423). Interacts with HDAC7 and HDAC9. Forms a heterologous complex at least with YY1. Interacts with HDAC10, DAXX and DACH1. Found in a complex with NCOR1 and NCOR2. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Interacts with BCOR, MJD2A/JHDM3A, NRIP1, PRDM6 and SRY. Interacts with GLIS2. Interacts (via the DNA-binding domain) with NR2C1; the interaction recruits phosphorylated NR2C1 to PML bodies for sumoylation. Component of the Notch corepressor complex. Interacts with CBFA2T3 and NKAP. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with and deacetylates MAPK14. Interacts with ZMYND15. Interacts with SMRT/NCOR2 and BCL6 on DNA enhancer elements. Interacts with INSM1. Interacts with XBP1; the interaction occurs in endothelial cell (EC) under disturbed flow (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi250009. 2 interactions.
STRINGi10116.ENSRNOP00000057161.

Structurei

3D structure databases

ProteinModelPortaliQ6P6W3.
SMRiQ6P6W3. Positions 2-370.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni3 – 316314Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiQ6P6W3.
KOiK11404.
PhylomeDBiQ6P6W3.

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.

Q6P6W3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKTVAYFYD PDVGNFHYGA GHPMKPHRLA LTHSLVLHYG LYKKMIVFKP
60 70 80 90 100
YQASQHDMCR FHSEDYIDFL QRVSPTNMQG FTKSLNAFNV GDDCPVFPGL
110 120 130 140 150
FEFCSRYTGA SLQGATQLNN KICDIAINWA GGLHHAKKFE ASGFCYVNDI
160 170 180 190 200
VIGILELLKY HPRVLYIDID IHHGDGVQEA FYLTDRVMTV SFHKYGNYFF
210 220 230 240 250
PGTGDMYEVG AESGRYYCLN VPLRDGIDDQ SYKHLFQPVI SQVVDFYQPT
260 270 280 290 300
CIVLQCGADS LGCDRLGCFN LSIRGHGECV EYVKSFNIPL LVLGGGGYTV
310 320 330 340 350
RNVARCWTYE TSLLVEEAIS EELPYSEYFE YFAPDFTLHP DVSTRIENQN
360 370 380 390 400
SRQYLDQIRQ TIFENLKMLN HAPSVQIHDV PADLLTYDRT DEADAEERGP
410 420
EENYSRPEAP NEFYDGDHDN DKESDVEI
Length:428
Mass (Da):48,821
Last modified:July 5, 2004 - v1
Checksum:i1CB84DE250C3BB2C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF321131 mRNA. Translation: AAK11184.1.
BC061988 mRNA. Translation: AAH61988.1.
RefSeqiNP_445900.1. NM_053448.1.
UniGeneiRn.17284.

Genome annotation databases

GeneIDi84578.
KEGGirno:84578.
UCSCiRGD:619977. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF321131 mRNA. Translation: AAK11184.1.
BC061988 mRNA. Translation: AAH61988.1.
RefSeqiNP_445900.1. NM_053448.1.
UniGeneiRn.17284.

3D structure databases

ProteinModelPortaliQ6P6W3.
SMRiQ6P6W3. Positions 2-370.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi250009. 2 interactions.
STRINGi10116.ENSRNOP00000057161.

Chemistry

ChEMBLiCHEMBL2095943.

PTM databases

PhosphoSiteiQ6P6W3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi84578.
KEGGirno:84578.
UCSCiRGD:619977. rat.

Organism-specific databases

CTDi8841.
RGDi619977. Hdac3.

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiQ6P6W3.
KOiK11404.
PhylomeDBiQ6P6W3.

Enzyme and pathway databases

ReactomeiREACT_283076. p75NTR negatively regulates cell cycle via SC1.

Miscellaneous databases

NextBioi617139.
PROiQ6P6W3.

Gene expression databases

GenevestigatoriQ6P6W3.

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

« Hide 'large scale' publications
  1. "Expression pattern of rat histone deacetylases."
    Wilquet V., Chavez M., Korbers R., Geerts A.
    Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Wistar.
    Tissue: Testis.
  2. "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: Prostate.
  3. "The POZ/BTB protein NAC1 interacts with two different histone deacetylases in neuronal-like cultures."
    Korutla L., Wang P.J., Mackler S.A.
    J. Neurochem. 94:786-793(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH BTBD14B.

Entry informationi

Entry nameiHDAC3_RAT
AccessioniPrimary (citable) accession number: Q6P6W3
Secondary accession number(s): Q99PA0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: July 5, 2004
Last modified: April 1, 2015
This is version 90 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.