CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-030531
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone deacetylase 
Protein Synonyms/Alias
  
Gene Name
 HDAC2 
Gene Synonyms/Alias
 hCG_21384 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
21LNYGLYRKMEIYRPHubiquitination[1, 2]
29MEIYRPHKATAEEMTubiquitination[1]
37ATAEEMTKYHSDEYIacetylation[3]
37ATAEEMTKYHSDEYIubiquitination[1, 2, 4, 5, 6]
45YHSDEYIKFLRSIRPubiquitination[1, 2, 4, 5, 6, 7, 8]
60DNMSEYSKQMQRFNVacetylation[2, 3, 9]
60DNMSEYSKQMQRFNVubiquitination[1, 2, 4, 5, 6, 7, 8, 10, 11]
115GGLHHAKKSEASGFCubiquitination[1]
171VMTVSFHKYGEYFPGubiquitination[1, 2, 4, 5, 6]
191DIGAGKGKYYAVNFPacetylation[9]
191DIGAGKGKYYAVNFPubiquitination[1, 6]
213ESYGQIFKPIISKVMubiquitination[1, 2, 4, 5, 6, 8, 11, 12]
250GCFNLTVKGHAKCVEubiquitination[6]
254LTVKGHAKCVEVVKTubiquitination[1, 2]
332NTPEYMEKIKQRLFEacetylation[3]
332NTPEYMEKIKQRLFEubiquitination[1, 5, 6, 8]
334PEYMEKIKQRLFENLubiquitination[1]
409RRNVADHKKGAKKARubiquitination[11]
410RNVADHKKGAKKARIubiquitination[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] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [3] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [4] 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]
 [5] 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]
 [6] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [7] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [8] 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]
 [9] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [10] A data set of human endogenous protein ubiquitination sites.
 Shi Y, Chan DW, Jung SY, Malovannaya A, Wang Y, Qin J.
 Mol Cell Proteomics. 2011 May;10(5):M110.002089. [PMID: 20972266]
 [11] 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]
 [12] 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] 
Functional Description
  
Sequence Annotation
  
Keyword
 Chromatin regulator; Complete proteome; Hydrolase; Nucleus; Reference proteome; Transcription; Transcription regulation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 458 AA 
Protein Sequence
MKPHRIRMTH NLLLNYGLYR KMEIYRPHKA TAEEMTKYHS DEYIKFLRSI RPDNMSEYSK 60
QMQRFNVGED CPVFDGLFEF CQLSTGGSVA GAVKLNRQQT DMAVNWAGGL HHAKKSEASG 120
FCYVNDIVLA ILELLKYHQR VLYIDIDIHH GDGVEEAFYT TDRVMTVSFH KYGEYFPGTG 180
DLRDIGAGKG KYYAVNFPMR DGIDDESYGQ IFKPIISKVM EMYQPSAVVL QCGADSLSGD 240
RLGCFNLTVK GHAKCVEVVK TFNLPLLMLG GGGYTIRNVA RCWTYETAVA LDCEIPNELP 300
YNDYFEYFGP DFKLHISPSN MTNQNTPEYM EKIKQRLFEN LRMLPHAPGV QMQAIPEDAV 360
HEDSGDEDGE DPDKRISIRA SDKRIACDEE FSDSEDEGEG GRRNVADHKK GAKKARIEED 420
KKETEDKKTD VKEEDKSKDN SGEKTDTKGT KSEQLSNP 458 
Gene Ontology
 GO:0000792; C:heterochromatin; IEA:Compara.
 GO:0000790; C:nuclear chromatin; IEA:Compara.
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0005657; C:replication fork; IEA:Compara.
 GO:0005667; C:transcription factor complex; IEA:Compara.
 GO:0017053; C:transcriptional repressor complex; IEA:Compara.
 GO:0031490; F:chromatin DNA binding; IEA:Compara.
 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:0003700; F:sequence-specific DNA binding transcription factor activity; IEA:Compara.
 GO:0016358; P:dendrite development; IEA:Compara.
 GO:0042733; P:embryonic digit morphogenesis; IEA:Compara.
 GO:0009913; P:epidermal cell differentiation; IEA:Compara.
 GO:0061029; P:eyelid development in camera-type eye; IEA:Compara.
 GO:0061198; P:fungiform papilla formation; IEA:Compara.
 GO:0060789; P:hair follicle placode formation; IEA:Compara.
 GO:0021766; P:hippocampus development; 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; IEA:Compara.
 GO:0090090; P:negative regulation of canonical Wnt receptor signaling pathway; IEA:Compara.
 GO:0010977; P:negative regulation of neuron projection development; IEA:Compara.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0042475; P:odontogenesis of dentin-containing tooth; IEA:Compara.
 GO:0008284; P:positive regulation of cell proliferation; IEA:Compara.
 GO:0048714; P:positive regulation of oligodendrocyte differentiation; IEA:Compara.
 GO:0051091; P:positive regulation of sequence-specific DNA binding transcription factor activity; IEA:Compara.
 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.