UniProt Accession

 HDAC2_HUMAN; Q92769; B4DL58; E1P561; Q5SRI8; Q5SZ86; Q8NEH4 

Genbank Protein ID

 U31814; AK296856; AL590398; FO393415; CH471051; CH471051; BC031055 

Genbank Nucleotide ID

 AAC50814.1; BAG59420.1; EAW48254.1; EAW48255.1; AAH31055.2 

Protein Name

 Histone deacetylase 2 

Protein Synonyms/Alias

 HD2 

Gene Name

 HDAC2 

Gene Synonyms/Alias

  

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
9	AYSQGGGKKKVCYYY	ubiquitination	[1]
10	YSQGGGKKKVCYYYD	ubiquitination	[1]
11	SQGGGKKKVCYYYDG	ubiquitination	[2, 3]
59	MEIYRPHKATAEEMT	ubiquitination	[1]
67	ATAEEMTKYHSDEYI	ubiquitination	[1, 2, 3, 4]
75	YHSDEYIKFLRSIRP	acetylation	[5]
75	YHSDEYIKFLRSIRP	ubiquitination	[1, 2, 3, 4, 6, 7]
90	DNMSEYSKQMQRFNV	ubiquitination	[4, 6, 7, 8]
144	AGGLHHAKKSEASGF	ubiquitination	[4]
145	GGLHHAKKSEASGFC	ubiquitination	[1]
201	VMTVSFHKYGEYFPG	ubiquitination	[4, 6]
221	DIGAGKGKYYAVNFP	ubiquitination	[1, 4]
243	ESYGQIFKPIISKVM	ubiquitination	[1, 2, 3, 4, 6, 7, 8, 9, 10]
284	LTVKGHAKCVEVVKT	ubiquitination	[1]
362	NTPEYMEKIKQRLFE	ubiquitination	[1, 4, 7]
364	PEYMEKIKQRLFENL	ubiquitination	[1]
439	RRNVADHKKGAKKAR	ubiquitination	[10]
440	RNVADHKKGAKKARI	ubiquitination	[10]
462	EDKKTDVKEEDKSKD	sumoylation	[11]

Reference

 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [4] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [5] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [6] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [7] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [8] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [9] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [10] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [11] Dynamically regulated sumoylation of HDAC2 controls p53 deacetylation and restricts apoptosis following genotoxic stress.
 Brandl A, Wagner T, Uhlig KM, Knauer SK, Stauber RH, Melchior F, Schneider G, Heinzel T, Krämer OH.
 J Mol Cell Biol. 2012 Oct;4(5):284-93. [PMID: 22493095] 

Functional Description

 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. 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. 

Sequence Annotation

 REGION 9 322 Histone deacetylase.
 ACT_SITE 142 142 By similarity.
 MOD_RES 262 262 S-nitrosocysteine (By similarity).
 MOD_RES 274 274 S-nitrosocysteine (By similarity).
 MOD_RES 394 394 Phosphoserine.
 MOD_RES 422 422 Phosphoserine.
 MOD_RES 424 424 Phosphoserine.  

Keyword

 3D-structure; Acetylation; Chromatin regulator; Complete proteome; Hydrolase; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repressor; S-nitrosylation; Transcription; Transcription regulation. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 488 AA 

Protein Sequence

Gene Ontology

 GO:0005737; C:cytoplasm; TAS:UniProtKB.
 GO:0035098; C:ESC/E(Z) complex; IDA:UniProtKB.
 GO:0000792; C:heterochromatin; IEA:Compara.
 GO:0016581; C:NuRD complex; IDA:UniProtKB.
 GO:0005657; C:replication fork; IEA:Compara.
 GO:0016580; C:Sin3 complex; IDA:UniProtKB.
 GO:0005667; C:transcription factor complex; IEA:Compara.
 GO:0003682; F:chromatin binding; ISS:UniProtKB.
 GO:0031490; F:chromatin DNA binding; IEA:Compara.
 GO:0004407; F:histone deacetylase activity; IDA:BHF-UCL.
 GO:0032041; F:NAD-dependent histone deacetylase activity (H3-K14 specific); IEA:EC.
 GO:0097372; F:NAD-dependent histone deacetylase activity (H3-K18 specific); IEA:EC.
 GO:0046969; F:NAD-dependent histone deacetylase activity (H3-K9 specific); IEA:EC.
 GO:0046970; F:NAD-dependent histone deacetylase activity (H4-K16 specific); IEA:EC.
 GO:0043565; F:sequence-specific DNA binding; IDA:BHF-UCL.
 GO:0003700; F:sequence-specific DNA binding transcription factor activity; IEA:Compara.
 GO:0007596; P:blood coagulation; TAS:Reactome.
 GO:0006338; P:chromatin remodeling; IC:BHF-UCL.
 GO:0016358; P:dendrite development; ISS:UniProtKB.
 GO:0042733; P:embryonic digit morphogenesis; ISS:BHF-UCL.
 GO:0009913; P:epidermal cell differentiation; ISS:BHF-UCL.
 GO:0061029; P:eyelid development in camera-type eye; ISS:BHF-UCL.
 GO:0061198; P:fungiform papilla formation; ISS:BHF-UCL.
 GO:0060789; P:hair follicle placode formation; ISS:BHF-UCL.
 GO:0021766; P:hippocampus development; IEA:Compara.
 GO:0070932; P:histone H3 deacetylation; IEA:GOC.
 GO:0070933; P:histone H4 deacetylation; IEA:GOC.
 GO:0006344; P:maintenance of chromatin silencing; IMP:BHF-UCL.
 GO:0043066; P:negative regulation of apoptotic process; ISS:BHF-UCL.
 GO:0090090; P:negative regulation of canonical Wnt receptor signaling pathway; IEA:Compara.
 GO:0045786; P:negative regulation of cell cycle; TAS:Reactome.
 GO:0045347; P:negative regulation of MHC class II biosynthetic process; IC:BHF-UCL.
 GO:0010977; P:negative regulation of neuron projection development; ISS:BHF-UCL.
 GO:0043433; P:negative regulation of sequence-specific DNA binding transcription factor activity; IMP:BHF-UCL.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:BHF-UCL.
 GO:0048011; P:neurotrophin TRK receptor signaling pathway; TAS:Reactome.
 GO:0042475; P:odontogenesis of dentin-containing tooth; ISS:BHF-UCL.
 GO:0008284; P:positive regulation of cell proliferation; IMP:BHF-UCL.
 GO:0032967; P:positive regulation of collagen biosynthetic process; IC:BHF-UCL.
 GO:0048714; P:positive regulation of oligodendrocyte differentiation; IEA:Compara.
 GO:0045862; P:positive regulation of proteolysis; IMP:BHF-UCL.
 GO:0010870; P:positive regulation of receptor biosynthetic process; IMP:BHF-UCL.
 GO:0051091; P:positive regulation of sequence-specific DNA binding transcription factor activity; IEA:Compara.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IMP:BHF-UCL.
 GO:0090311; P:regulation of protein deacetylation; IEA:Compara.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 

Interpro

 IPR000286; His_deacetylse.
 IPR003084; His_deacetylse_1.
 IPR023801; His_deacetylse_dom. 

Pfam

 PF00850; Hist_deacetyl 

SMART

  

PROSITE

  

PRINTS

 PR01270; HDASUPER.
 PR01271; HISDACETLASE.