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Protein

Histone deacetylase 2

Gene

Hdac2

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 (By similarity). Forms transcriptional repressor complexes by associating with MAD, SIN3, YY1 and N-COR. Interacts in the late S-phase of DNA-replication with DNMT1 in the other transcriptional repressor complex composed of DNMT1, DMAP1, PCNA, CAF1. Deacetylates TSHZ3 and regulates its transcriptional repressor 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. May be involved in the transcriptional repression of circadian target genes, such as PER1, mediated by CRY1 through histone deacetylation. Involved in MTA1-mediated transcriptional corepression of TFF1 and CDKN1A.By similarity3 Publications

Catalytic activityi

Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei142By similarity1

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • chromatin DNA binding Source: MGI
  • deacetylase activity Source: UniProtKB
  • enzyme binding Source: UniProtKB
  • histone deacetylase activity Source: UniProtKB
  • histone deacetylase activity (H4-K16 specific) Source: CACAO
  • Krueppel-associated box domain binding Source: UniProtKB
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  • NF-kappaB binding Source: MGI
  • poly(A) RNA binding Source: MGI
  • protein deacetylase activity Source: BHF-UCL
  • RNA polymerase II core promoter sequence-specific DNA binding Source: MGI
  • RNA polymerase II repressing transcription factor binding Source: MGI
  • RNA polymerase II transcription corepressor binding Source: BHF-UCL
  • sequence-specific DNA binding Source: MGI
  • transcription factor activity, sequence-specific DNA binding Source: MGI
  • transcription factor binding Source: UniProtKB

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: MGI
  • cardiac muscle cell development Source: MGI
  • cellular response to trichostatin A Source: MGI
  • chromatin organization Source: UniProtKB
  • chromatin silencing at rDNA Source: Reactome
  • circadian regulation of gene expression Source: UniProtKB
  • dendrite development Source: UniProtKB
  • embryonic digit morphogenesis Source: BHF-UCL
  • 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 H3-K27 methylation Source: MGI
  • histone H4 deacetylation Source: UniProtKB
  • maintenance of chromatin silencing Source: MGI
  • negative regulation of apoptotic process Source: BHF-UCL
  • negative regulation of canonical Wnt signaling pathway Source: MGI
  • negative regulation of cardiac muscle cell proliferation Source: MGI
  • negative regulation of intrinsic apoptotic signaling pathway Source: MGI
  • negative regulation of neuron projection development Source: BHF-UCL
  • negative regulation of pri-miRNA transcription from RNA polymerase II promoter Source: BHF-UCL
  • negative regulation of sequence-specific DNA binding transcription factor activity Source: MGI
  • negative regulation of transcription, DNA-templated Source: BHF-UCL
  • 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 proteolysis Source: MGI
  • positive regulation of receptor biosynthetic process Source: MGI
  • positive regulation of sequence-specific DNA binding transcription factor activity Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • protein deacetylation Source: BHF-UCL
  • regulation of protein deacetylation Source: MGI
  • regulation of protein kinase B signaling Source: MGI
  • regulation of sarcomere organization 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

BRENDAi3.5.1.98. 3474.
ReactomeiR-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-573389. NoRC negatively regulates rRNA expression.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 2 (EC:3.5.1.98)
Short name:
HD2
Alternative name(s):
YY1 transcription factor-binding protein
Gene namesi
Name:Hdac2
Synonyms:Yy1bp
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1097691. Hdac2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • ESC/E(Z) complex Source: UniProtKB
  • heterochromatin Source: MGI
  • histone deacetylase complex Source: UniProtKB
  • nuclear chromatin Source: BHF-UCL
  • nucleoplasm Source: Reactome
  • nucleus Source: MGI
  • NuRD complex Source: MGI
  • protein complex Source: MGI
  • replication fork Source: MGI
  • RNA polymerase II transcription repressor complex Source: BHF-UCL
  • Sin3 complex Source: MGI
  • transcriptional repressor complex Source: MGI
  • transcription factor complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi152C → A: Does not affect S-nitrosylation. 1 Publication1
Mutagenesisi262C → A: Impairs S-nitrosylation. Abolishes S-nitrosylation; when associated with A-274. 1 Publication1
Mutagenesisi274C → A: Impairs S-nitrosylation. Abolishes S-nitrosylation; when associated with A-262. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001146941 – 488Histone deacetylase 2Add BLAST488

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei75N6-acetyllysineBy similarity1
Modified residuei221N6-acetyllysineBy similarity1
Modified residuei262S-nitrosocysteine1 Publication1
Modified residuei274S-nitrosocysteine1 Publication1
Modified residuei394PhosphoserineCombined sources1
Modified residuei407PhosphoserineBy similarity1
Modified residuei422PhosphoserineCombined sources1
Modified residuei424PhosphoserineCombined sources1
Cross-linki462Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki481Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Post-translational modificationi

S-nitrosylated by GAPDH. In neurons, S-Nitrosylation at Cys-262 and Cys-274 does not affect the enzyme activity but abolishes chromatin-binding, leading to increases acetylation of histones and activate genes that are associated with neuronal development. In embryonic cortical neurons, S-Nitrosylation regulates dendritic growth and branching. S-Nitrosylation interferes with its interaction with MTA1.3 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, S-nitrosylation, Ubl conjugation

Proteomic databases

EPDiP70288.
MaxQBiP70288.
PaxDbiP70288.
PeptideAtlasiP70288.
PRIDEiP70288.

PTM databases

iPTMnetiP70288.
PhosphoSitePlusiP70288.

Expressioni

Gene expression databases

BgeeiENSMUSG00000019777.
CleanExiMM_HDAC2.

Interactioni

Subunit structurei

Interacts with SNW1, PELP1, ATR, DNMT1, MINT, HDAC10, HCFC1, NRIP1, KDM4A, CHFR and SAP30L. Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core complex associates with MTA2, 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. Interacts (CK2 phosphorylated form) with SP3. Interacts with TSHZ3 (via its N-terminus). Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Part of a complex containing the core histones H2A, H2B, H3 and H4, DEK and unphosphorylated DAXX. Part of a complex containing ATR and CHD4. Forms a heterologous complex at least with YY1. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3, ARID4B, HDAC1 and HDAC2. Interacts with CBFA2T3, HDAC7, PRDM6, SAP30, SETDB1 and SUV39H1. Interacts with the H2AFY (via the non-histone region). Component of a RCOR/GFI/KDM1A/HDAC complex. Interacts directly with GFI1 and GFI1B. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Interacts with FAM64A. Interacts with BCL6 (non-acetylated form). Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. Interacts with CRY1, INSM1 and ZNF431. Interacts with NACC2 (By similarity). Interacts with MTA1, with a preference for sumoylated MTA1. Interacts with SIX3. Interacts with BEND3 (By similarity). Component of a histone deacetylase complex containing DNTTIP1, ZNF541, HDAC1 and HDAC2 (By similarity).By similarity14 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Znf431E9QAG83EBI-302251,EBI-9549639

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • Krueppel-associated box domain binding Source: UniProtKB
  • NF-kappaB binding Source: MGI
  • RNA polymerase II repressing transcription factor binding Source: MGI
  • RNA polymerase II transcription corepressor binding Source: BHF-UCL
  • transcription factor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi200260. 52 interactors.
DIPiDIP-32854N.
IntActiP70288. 28 interactors.
MINTiMINT-146936.
STRINGi10090.ENSMUSP00000019911.

Structurei

3D structure databases

ProteinModelPortaliP70288.
SMRiP70288.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni9 – 322Histone deacetylaseAdd BLAST314

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi300 – 303Poly-Gly4

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiP70288.
KOiK06067.
PhylomeDBiP70288.
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.

P70288-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAYSQGGGKK KVCYYYDGDI GNYYYGQGHP MKPHRIRMTH NLLLNYGLYR
60 70 80 90 100
KMEIYRPHKA TAEEMTKYHS DEYIKFLRSI RPDNMSEYSK QMQRFNVGED
110 120 130 140 150
CPVFDGLFEF CQLSTGGSVA GAVKLNRQQT DMAVNWAGGL HHAKKSEASG
160 170 180 190 200
FCYVNDIVLA ILELLKYHQR VLYIDIDIHH GDGVEEAFYT TDRVMTVSFH
210 220 230 240 250
KYGEYFPGTG DLRDIGAGKG KYYAVNFPMR DGIDDESYGQ IFKPIISKVM
260 270 280 290 300
EMYQPSAVVL QCGADSLSGD RLGCFNLTVK GHAKCVEVAK TFNLPLLMLG
310 320 330 340 350
GGGYTIRNVA RCWTYETAVA LDCEIPNELP YNDYFEYFGP DFKLHISPSN
360 370 380 390 400
MTNQNTPEYM EKIKQRLFEN LRMLPHAPGV QMQAIPEDAV HEDSGDEDGE
410 420 430 440 450
DPDKRISIRA SDKRIACDEE FSDSEDEGEG GRRNVADHKK GAKKARIEED
460 470 480
KKETEDKKTD VKEEDKSKDN SGEKTDPKGA KSEQLSNP
Length:488
Mass (Da):55,302
Last modified:February 1, 1997 - v1
Checksum:iB9843D24A775157C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti289A → V in EDL04897 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31758 mRNA. Translation: AAC52889.1.
CH466540 Genomic DNA. Translation: EDL04897.1.
BC138517 mRNA. Translation: AAI38518.1.
CCDSiCCDS23783.1.
RefSeqiNP_032255.2. NM_008229.2.
UniGeneiMm.19806.

Genome annotation databases

GeneIDi15182.
KEGGimmu:15182.
UCSCiuc007evf.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31758 mRNA. Translation: AAC52889.1.
CH466540 Genomic DNA. Translation: EDL04897.1.
BC138517 mRNA. Translation: AAI38518.1.
CCDSiCCDS23783.1.
RefSeqiNP_032255.2. NM_008229.2.
UniGeneiMm.19806.

3D structure databases

ProteinModelPortaliP70288.
SMRiP70288.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200260. 52 interactors.
DIPiDIP-32854N.
IntActiP70288. 28 interactors.
MINTiMINT-146936.
STRINGi10090.ENSMUSP00000019911.

PTM databases

iPTMnetiP70288.
PhosphoSitePlusiP70288.

Proteomic databases

EPDiP70288.
MaxQBiP70288.
PaxDbiP70288.
PeptideAtlasiP70288.
PRIDEiP70288.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi15182.
KEGGimmu:15182.
UCSCiuc007evf.1. mouse.

Organism-specific databases

CTDi3066.
MGIiMGI:1097691. Hdac2.

Phylogenomic databases

eggNOGiKOG1342. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiP70288.
KOiK06067.
PhylomeDBiP70288.
TreeFamiTF106171.

Enzyme and pathway databases

BRENDAi3.5.1.98. 3474.
ReactomeiR-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-573389. NoRC negatively regulates rRNA expression.

Miscellaneous databases

ChiTaRSiHdac2. mouse.
PROiP70288.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000019777.
CleanExiMM_HDAC2.

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 nameiHDAC2_MOUSE
AccessioniPrimary (citable) accession number: P70288
Secondary accession number(s): B2RRP3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: February 1, 1997
Last modified: November 30, 2016
This is version 171 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.