CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022845
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone deacetylase 6 
Protein Synonyms/Alias
 HD6 
Gene Name
 HDAC6 
Gene Synonyms/Alias
 KIAA0901; JM21 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
32QDSSVTSKRNIKKGAacetylation[1]
36VTSKRNIKKGAVPRSacetylation[1]
37TSKRNIKKGAVPRSIacetylation[1]
51IPNLAEVKKKGKMKKacetylation[1]
52PNLAEVKKKGKMKKLacetylation[1]
53NLAEVKKKGKMKKLGacetylation[1]
55AEVKKKGKMKKLGQAacetylation[1]
57VKKKGKMKKLGQAMEacetylation[1]
58KKKGKMKKLGQAMEEacetylation[1]
116PERLHAIKEQLIQEGubiquitination[2, 3]
553GHLRATEKMKTRELHacetylation[1]
555LRATEKMKTRELHREacetylation[1]
849REGPSSSKLVTKKAPacetylation[1]
849REGPSSSKLVTKKAPubiquitination[3]
853SSSKLVTKKAPQPAKacetylation[1]
854SSKLVTKKAPQPAKPacetylation[1]
872ERMTTREKKVLEAGMacetylation[1]
873RMTTREKKVLEAGMGacetylation[1]
Reference
 [1] Gcn5p-dependent acetylation induces degradation of the meiotic transcriptional repressor Ume6p.
 Mallory MJ, Law MJ, Sterner DE, Berger SL, Strich R.
 Mol Biol Cell. 2012 May;23(9):1609-17. [PMID: 22438583]
 [2] 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]
 [3] 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] 
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 (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin. 
Sequence Annotation
 ZN_FING 1131 1192 UBP-type.
 REGION 87 404 Histone deacetylase 1.
 REGION 482 800 Histone deacetylase 2.
 REGION 1154 1156 Ubiquitin binding.
 REGION 1182 1189 Ubiquitin binding.
 ACT_SITE 216 216 1.
 ACT_SITE 611 611 2.
 METAL 1113 1113 Zinc 1.
 METAL 1115 1115 Zinc 1.
 METAL 1133 1133 Zinc 3.
 METAL 1136 1136 Zinc 3.
 METAL 1145 1145 Zinc 2.
 METAL 1148 1148 Zinc 2.
 METAL 1153 1153 Zinc 3.
 METAL 1160 1160 Zinc 3.
 METAL 1164 1164 Zinc 2.
 METAL 1170 1170 Zinc 2.
 METAL 1183 1183 Zinc 1.
 METAL 1186 1186 Zinc 1.
 MOD_RES 16 16 Phosphoserine (By similarity).  
Keyword
 3D-structure; Actin-binding; Alternative splicing; Autophagy; Chromatin regulator; Complete proteome; Cytoplasm; Hydrolase; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Repressor; Transcription; Transcription regulation; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1215 AA 
Protein Sequence
MTSTGQDSTT TRQRRSRQNP QSPPQDSSVT SKRNIKKGAV PRSIPNLAEV KKKGKMKKLG 60
QAMEEDLIVG LQGMDLNLEA EALAGTGLVL DEQLNEFHCL WDDSFPEGPE RLHAIKEQLI 120
QEGLLDRCVS FQARFAEKEE LMLVHSLEYI DLMETTQYMN EGELRVLADT YDSVYLHPNS 180
YSCACLASGS VLRLVDAVLG AEIRNGMAII RPPGHHAQHS LMDGYCMFNH VAVAARYAQQ 240
KHRIRRVLIV DWDVHHGQGT QFTFDQDPSV LYFSIHRYEQ GRFWPHLKAS NWSTTGFGQG 300
QGYTINVPWN QVGMRDADYI AAFLHVLLPV ALEFQPQLVL VAAGFDALQG DPKGEMAATP 360
AGFAQLTHLL MGLAGGKLIL SLEGGYNLRA LAEGVSASLH TLLGDPCPML ESPGAPCRSA 420
QASVSCALEA LEPFWEVLVR STETVERDNM EEDNVEESEE EGPWEPPVLP ILTWPVLQSR 480
TGLVYDQNMM NHCNLWDSHH PEVPQRILRI MCRLEELGLA GRCLTLTPRP ATEAELLTCH 540
SAEYVGHLRA TEKMKTRELH RESSNFDSIY ICPSTFACAQ LATGAACRLV EAVLSGEVLN 600
GAAVVRPPGH HAEQDAACGF CFFNSVAVAA RHAQTISGHA LRILIVDWDV HHGNGTQHMF 660
EDDPSVLYVS LHRYDHGTFF PMGDEGASSQ IGRAAGTGFT VNVAWNGPRM GDADYLAAWH 720
RLVLPIAYEF NPELVLVSAG FDAARGDPLG GCQVSPEGYA HLTHLLMGLA SGRIILILEG 780
GYNLTSISES MAACTRSLLG DPPPLLTLPR PPLSGALASI TETIQVHRRY WRSLRVMKVE 840
DREGPSSSKL VTKKAPQPAK PRLAERMTTR EKKVLEAGMG KVTSASFGEE STPGQTNSET 900
AVVALTQDQP SEAATGGATL AQTISEAAIG GAMLGQTTSE EAVGGATPDQ TTSEETVGGA 960
ILDQTTSEDA VGGATLGQTT SEEAVGGATL AQTTSEAAME GATLDQTTSE EAPGGTELIQ 1020
TPLASSTDHQ TPPTSPVQGT TPQISPSTLI GSLRTLELGS ESQGASESQA PGEENLLGEA 1080
AGGQDMADSM LMQGSRGLTD QAIFYAVTPL PWCPHLVAVC PIPAAGLDVT QPCGDCGTIQ 1140
ENWVCLSCYQ VYCGRYINGH MLQHHGNSGH PLVLSYIDLS AWCYYCQAYV HHQALLDVKN 1200
IAHQNKFGED MPHPH 1215 
Gene Ontology
 GO:0016235; C:aggresome; IDA:BHF-UCL.
 GO:0005901; C:caveola; IDA:BHF-UCL.
 GO:0031252; C:cell leading edge; IDA:BHF-UCL.
 GO:0005881; C:cytoplasmic microtubule; IEA:Compara.
 GO:0005829; C:cytosol; ISS:UniProtKB.
 GO:0000118; C:histone deacetylase complex; IDA:UniProtKB.
 GO:0005874; C:microtubule; IDA:UniProtKB.
 GO:0005875; C:microtubule associated complex; IDA:BHF-UCL.
 GO:0048471; C:perinuclear region of cytoplasm; IDA:BHF-UCL.
 GO:0043014; F:alpha-tubulin binding; IDA:BHF-UCL.
 GO:0070840; F:dynein complex binding; IDA:BHF-UCL.
 GO:0019899; F:enzyme binding; ISS:UniProtKB.
 GO:0004407; F:histone deacetylase activity; IDA:BHF-UCL.
 GO:0051879; F:Hsp90 protein binding; IDA:BHF-UCL.
 GO:0008017; F:microtubule binding; ISS: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:0031593; F:polyubiquitin binding; IDA:BHF-UCL.
 GO:0048156; F:tau protein binding; IDA:BHF-UCL.
 GO:0042903; F:tubulin deacetylase activity; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0070842; P:aggresome assembly; IMP:BHF-UCL.
 GO:0070301; P:cellular response to hydrogen peroxide; IMP:BHF-UCL.
 GO:0071218; P:cellular response to misfolded protein; IEA:Compara.
 GO:0035967; P:cellular response to topologically incorrect protein; IMP:BHF-UCL.
 GO:0070932; P:histone H3 deacetylation; IEA:GOC.
 GO:0070933; P:histone H4 deacetylation; IEA:GOC.
 GO:0070846; P:Hsp90 deacetylation; IMP:BHF-UCL.
 GO:0032418; P:lysosome localization; IMP:BHF-UCL.
 GO:0016236; P:macroautophagy; IMP:BHF-UCL.
 GO:0006515; P:misfolded or incompletely synthesized protein catabolic process; IMP:BHF-UCL.
 GO:0010727; P:negative regulation of hydrogen peroxide metabolic process; IC:BHF-UCL.
 GO:0007026; P:negative regulation of microtubule depolymerization; IEA:Compara.
 GO:0051354; P:negative regulation of oxidoreductase activity; IC:BHF-UCL.
 GO:0043242; P:negative regulation of protein complex disassembly; IMP:BHF-UCL.
 GO:0045861; P:negative regulation of proteolysis; IMP:BHF-UCL.
 GO:0045892; P:negative regulation of transcription, DNA-dependent; ISS:UniProtKB.
 GO:0034983; P:peptidyl-lysine deacetylation; IMP:BHF-UCL.
 GO:0070845; P:polyubiquitinated misfolded protein transport; IMP:BHF-UCL.
 GO:0090035; P:positive regulation of chaperone-mediated protein complex assembly; IMP:BHF-UCL.
 GO:0010634; P:positive regulation of epithelial cell migration; IMP:BHF-UCL.
 GO:1901300; P:positive regulation of hydrogen peroxide-mediated programmed cell death; IDA:BHF-UCL.
 GO:0010870; P:positive regulation of receptor biosynthetic process; IMP:BHF-UCL.
 GO:0009967; P:positive regulation of signal transduction; IMP:BHF-UCL.
 GO:0043241; P:protein complex disassembly; IEA:Compara.
 GO:0000209; P:protein polyubiquitination; IEA:Compara.
 GO:0060765; P:regulation of androgen receptor signaling pathway; TAS:BHF-UCL.
 GO:0060632; P:regulation of microtubule-based movement; IC:BHF-UCL.
 GO:0010469; P:regulation of receptor activity; IMP:BHF-UCL.
 GO:0070848; P:response to growth factor stimulus; IMP:BHF-UCL.
 GO:0051788; P:response to misfolded protein; IMP:BHF-UCL.
 GO:0009636; P:response to toxic substance; IMP:BHF-UCL.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0043162; P:ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; IEA:Compara. 
Interpro
 IPR000286; His_deacetylse.
 IPR023801; His_deacetylse_dom.
 IPR013083; Znf_RING/FYVE/PHD.
 IPR001607; Znf_UBP. 
Pfam
 PF00850; Hist_deacetyl
 PF02148; zf-UBP 
SMART
 SM00290; ZnF_UBP 
PROSITE
 PS50271; ZF_UBP 
PRINTS
 PR01270; HDASUPER.