CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000442
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone deacetylase 3 
Protein Synonyms/Alias
 HD3; RPD3-2; SMAP45 
Gene Name
 HDAC3 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
3*****MAKTVAYFYDubiquitination[1]
25YGAGHPMKPHRLALTubiquitination[1]
44LHYGLYKKMIVFKPYubiquitination[2, 3]
121GATQLNNKICDIAINubiquitination[1]
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] Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells.
 Tan F, Lu L, Cai Y, Wang J, Xie Y, Wang L, Gong Y, Xu BE, Wu J, Luo Y, Qiang B, Yuan J, Sun X, Peng X.
 Proteomics. 2008 Jul;8(14):2885-96. [PMID: 18655026]
 [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] 
Functional Description
 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. 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 (By similarity). 
Sequence Annotation
 REGION 3 316 Histone deacetylase.
 ACT_SITE 135 135 By similarity.
 MOD_RES 424 424 Phosphoserine.
 CROSSLNK 44 44 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Alternative splicing; Chromatin regulator; Complete proteome; Hydrolase; Isopeptide bond; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repressor; Transcription; Transcription regulation; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 428 AA 
Protein Sequence
MAKTVAYFYD PDVGNFHYGA GHPMKPHRLA LTHSLVLHYG LYKKMIVFKP YQASQHDMCR 60
FHSEDYIDFL QRVSPTNMQG FTKSLNAFNV GDDCPVFPGL FEFCSRYTGA SLQGATQLNN 120
KICDIAINWA GGLHHAKKFE ASGFCYVNDI VIGILELLKY HPRVLYIDID IHHGDGVQEA 180
FYLTDRVMTV SFHKYGNYFF PGTGDMYEVG AESGRYYCLN VPLRDGIDDQ SYKHLFQPVI 240
NQVVDFYQPT CIVLQCGADS LGCDRLGCFN LSIRGHGECV EYVKSFNIPL LVLGGGGYTV 300
RNVARCWTYE TSLLVEEAIS EELPYSEYFE YFAPDFTLHP DVSTRIENQN SRQYLDQIRQ 360
TIFENLKMLN HAPSVQIHDV PADLLTYDRT DEADAEERGP EENYSRPEAP NEFYDGDHDN 420
DKESDVEI 428 
Gene Ontology
 GO:0005737; C:cytoplasm; TAS:UniProtKB.
 GO:0000118; C:histone deacetylase complex; TAS:UniProtKB.
 GO:0005876; C:spindle microtubule; IDA:UniProtKB.
 GO:0017053; C:transcriptional repressor complex; IDA:UniProtKB.
 GO:0031490; F:chromatin DNA binding; IEA:Compara.
 GO:0004407; F:histone deacetylase activity; IMP:UniProtKB.
 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:0003714; F:transcription corepressor activity; IMP:UniProtKB.
 GO:0008134; F:transcription factor binding; TAS:UniProtKB.
 GO:0044255; P:cellular lipid metabolic process; TAS:Reactome.
 GO:0032922; P:circadian regulation of gene expression; IEA:Compara.
 GO:0070932; P:histone H3 deacetylation; IEA:GOC.
 GO:0070933; P:histone H4 deacetylation; IEA:GOC.
 GO:0043066; P:negative regulation of apoptotic process; TAS:ProtInc.
 GO:0045786; P:negative regulation of cell cycle; TAS:Reactome.
 GO:0046329; P:negative regulation of JNK cascade; IMP:UniProtKB.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:UniProtKB.
 GO:0048011; P:neurotrophin TRK receptor signaling pathway; TAS:Reactome.
 GO:0007219; P:Notch signaling pathway; TAS:Reactome.
 GO:0007346; P:regulation of mitotic cell cycle; IEA:Compara.
 GO:0040014; P:regulation of multicellular organism growth; IEA:Compara.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0051225; P:spindle assembly; IMP:UniProtKB.
 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.