CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012139
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone deacetylase 1 
Protein Synonyms/Alias
 HD1 
Gene Name
 HDAC1 
Gene Synonyms/Alias
 RPD3L1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
10QTQGTRRKVCYYYDGubiquitination[1, 2]
31YGQGHPMKPHRIRMTubiquitination[2]
50LNYGLYRKMEIYRPHubiquitination[2]
58MEIYRPHKANAEEMTubiquitination[2, 3]
66ANAEEMTKYHSDDYIacetylation[4]
66ANAEEMTKYHSDDYIubiquitination[1, 2, 3, 5, 6, 7, 8, 9]
74YHSDDYIKFLRSIRPacetylation[10, 11]
74YHSDDYIKFLRSIRPubiquitination[1, 2, 3, 5, 6, 8, 9, 12]
89DNMSEYSKQMQRFNVacetylation[10]
89DNMSEYSKQMQRFNVubiquitination[1, 2, 5, 8, 12]
126ASAVKLNKQQTDIAVubiquitination[1, 2, 3, 6, 8]
143AGGLHHAKKSEASGFubiquitination[2, 8]
144GGLHHAKKSEASGFCubiquitination[2]
200VMTVSFHKYGEYFPGubiquitination[1, 2, 5, 12]
218LRDIGAGKGKYYAVNubiquitination[5]
220DIGAGKGKYYAVNYPacetylation[10]
220DIGAGKGKYYAVNYPubiquitination[2]
242ESYEAIFKPVMSKVMubiquitination[2, 5]
279GCFNLTIKGHAKCVEubiquitination[2]
283LTIKGHAKCVEFVKSubiquitination[2, 8]
361NTNEYLEKIKQRLFEacetylation[10]
361NTNEYLEKIKQRLFEubiquitination[1, 2, 5, 8, 9]
363NEYLEKIKQRLFENLubiquitination[2]
412ISICSSDKRIACEEEubiquitination[2, 8]
432EEGEGGRKNSSNFKKmethylation[13]
438RKNSSNFKKAKRVKTubiquitination[5]
444FKKAKRVKTEDEKEKsumoylation[14, 15]
476KPEAKGVKEEVKLA*sumoylation[14, 15]
480KGVKEEVKLA*****ubiquitination[2]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [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] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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]
 [12] 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]
 [13] Update on activities at the Universal Protein Resource (UniProt) in 2013.
 e="String">UniProt Consortium.
 Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. [PMID: 23161681]
 [14] SUMO-1 modification of histone deacetylase 1 (HDAC1) modulates its biological activities.
 David G, Neptune MA, DePinho RA.
 J Biol Chem. 2002 Jun 28;277(26):23658-63. [PMID: 11960997]
 [15] The adenovirus protein Gam1 interferes with sumoylation of histone deacetylase 1.
 Colombo R, Boggio R, Seiser C, Draetta GF, Chiocca S.
 EMBO Rep. 2002 Nov;3(11):1062-8. [PMID: 12393750] 
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. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST- mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Component 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 9 321 Histone deacetylase.
 ACT_SITE 141 141
 MOD_RES 74 74 N6-acetyllysine.
 MOD_RES 220 220 N6-acetyllysine.
 MOD_RES 393 393 Phosphoserine.
 MOD_RES 421 421 Phosphoserine; by CK2.
 MOD_RES 423 423 Phosphoserine; by CK2.
 MOD_RES 432 432 N6-methylated lysine; by EHMT2.
 CROSSLNK 444 444 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 476 476 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Chromatin regulator; Complete proteome; Host-virus interaction; Hydrolase; Isopeptide bond; Methylation; Nucleus; Phosphoprotein; Reference proteome; Repressor; Transcription; Transcription regulation; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 482 AA 
Protein Sequence
MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN 60
AEEMTKYHSD DYIKFLRSIR PDNMSEYSKQ MQRFNVGEDC PVFDGLFEFC QLSTGGSVAS 120
AVKLNKQQTD IAVNWAGGLH HAKKSEASGF CYVNDIVLAI LELLKYHQRV LYIDIDIHHG 180
DGVEEAFYTT DRVMTVSFHK YGEYFPGTGD LRDIGAGKGK YYAVNYPLRD GIDDESYEAI 240
FKPVMSKVME MFQPSAVVLQ CGSDSLSGDR LGCFNLTIKG HAKCVEFVKS FNLPMLMLGG 300
GGYTIRNVAR CWTYETAVAL DTEIPNELPY NDYFEYFGPD FKLHISPSNM TNQNTNEYLE 360
KIKQRLFENL RMLPHAPGVQ MQAIPEDAIP EESGDEDEDD PDKRISICSS DKRIACEEEF 420
SDSEEEGEGG RKNSSNFKKA KRVKTEDEKE KDPEEKKEVT EEEKTKEEKP EAKGVKEEVK 480
LA 482 
Gene Ontology
 GO:0005829; C:cytosol; IDA:UniProtKB.
 GO:0016581; C:NuRD complex; IDA:UniProtKB.
 GO:0016580; C:Sin3 complex; IDA:BHF-UCL.
 GO:0001047; F:core promoter binding; IDA:UniProtKB.
 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:0001106; F:RNA polymerase II transcription corepressor activity; IDA:BHF-UCL.
 GO:0003700; F:sequence-specific DNA binding transcription factor activity; TAS:ProtInc.
 GO:0008134; F:transcription factor binding; TAS:UniProtKB.
 GO:0007596; P:blood coagulation; TAS:Reactome.
 GO:0006338; P:chromatin remodeling; IC:BHF-UCL.
 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:0070932; P:histone H3 deacetylation; IDA:BHF-UCL.
 GO:0070933; P:histone H4 deacetylation; IDA:BHF-UCL.
 GO:0000278; P:mitotic cell cycle; TAS:Reactome.
 GO:0043922; P:negative regulation by host of viral transcription; IMP:UniProtKB.
 GO:0060766; P:negative regulation of androgen receptor signaling pathway; IDA:BHF-UCL.
 GO:0043066; P:negative regulation of apoptotic process; ISS:BHF-UCL.
 GO:0045786; P:negative regulation of cell cycle; TAS:Reactome.
 GO:0048011; P:neurotrophin TRK receptor signaling pathway; TAS:Reactome.
 GO:0007219; P:Notch 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:0010870; P:positive regulation of receptor biosynthetic process; IMP:BHF-UCL.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:BHF-UCL.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome.
 GO:0007179; P:transforming growth factor beta receptor signaling pathway; TAS:Reactome.
 GO:0019048; P:virus-host interaction; 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.