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Protein

Histone deacetylase 6

Gene

Hdac6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.By similarity2 Publications
In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy (By similarity).By similarity

Catalytic activityi

Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

Cofactori

Zn2+By similarityNote: Binds 3 Zn2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei215 – 21511By similarity
Active sitei610 – 61012By similarity
Metal bindingi1047 – 10471Zinc 1By similarity
Metal bindingi1049 – 10491Zinc 1By similarity
Metal bindingi1067 – 10671Zinc 3By similarity
Metal bindingi1070 – 10701Zinc 3By similarity
Metal bindingi1079 – 10791Zinc 2By similarity
Metal bindingi1082 – 10821Zinc 2By similarity
Metal bindingi1087 – 10871Zinc 3By similarity
Metal bindingi1094 – 10941Zinc 3By similarity
Metal bindingi1098 – 10981Zinc 2By similarity
Metal bindingi1104 – 11041Zinc 2By similarity
Metal bindingi1117 – 11171Zinc 1By similarity
Metal bindingi1120 – 11201Zinc 1By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1065 – 112662UBP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. alpha-tubulin binding Source: MGI
  2. beta-catenin binding Source: MGI
  3. beta-tubulin binding Source: MGI
  4. core promoter binding Source: MGI
  5. dynein complex binding Source: MGI
  6. histone deacetylase activity Source: MGI
  7. histone deacetylase binding Source: MGI
  8. Hsp90 protein binding Source: MGI
  9. microtubule binding Source: UniProtKB
  10. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  11. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
  12. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
  13. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
  14. polyubiquitin binding Source: MGI
  15. tau protein binding Source: MGI
  16. tubulin deacetylase activity Source: UniProtKB
  17. ubiquitin binding Source: MGI
  18. zinc ion binding Source: InterPro

GO - Biological processi

  1. aggresome assembly Source: MGI
  2. cellular response to hydrogen peroxide Source: MGI
  3. cellular response to misfolded protein Source: MGI
  4. cellular response to topologically incorrect protein Source: MGI
  5. histone deacetylation Source: MGI
  6. Hsp90 deacetylation Source: MGI
  7. intracellular protein transport Source: MGI
  8. lysosome localization Source: MGI
  9. macroautophagy Source: MGI
  10. misfolded or incompletely synthesized protein catabolic process Source: MGI
  11. negative regulation of microtubule depolymerization Source: MGI
  12. negative regulation of protein complex disassembly Source: MGI
  13. negative regulation of proteolysis Source: MGI
  14. peptidyl-lysine deacetylation Source: MGI
  15. polyubiquitinated misfolded protein transport Source: MGI
  16. positive regulation of chaperone-mediated protein complex assembly Source: MGI
  17. positive regulation of epithelial cell migration Source: MGI
  18. positive regulation of hydrogen peroxide-mediated programmed cell death Source: MGI
  19. positive regulation of receptor biosynthetic process Source: MGI
  20. positive regulation of signal transduction Source: MGI
  21. protein complex disassembly Source: MGI
  22. protein deacetylation Source: MGI
  23. protein polyubiquitination Source: MGI
  24. regulation of establishment of protein localization Source: MGI
  25. regulation of fat cell differentiation Source: MGI
  26. regulation of gene expression, epigenetic Source: MGI
  27. regulation of receptor activity Source: MGI
  28. regulation of transcription, DNA-templated Source: UniProtKB-KW
  29. response to growth factor Source: MGI
  30. response to misfolded protein Source: MGI
  31. response to organic substance Source: MGI
  32. response to toxic substance Source: MGI
  33. transcription, DNA-templated Source: UniProtKB-KW
  34. tubulin deacetylation Source: UniProtKB
  35. ubiquitin-dependent protein catabolic process Source: MGI
  36. ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Actin-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_225256. HSF1 activation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 6 (EC:3.5.1.98)
Short name:
HD6
Alternative name(s):
Histone deacetylase mHDA2
Gene namesi
Name:Hdac6
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome X

Organism-specific databases

MGIiMGI:1333752. Hdac6.

Subcellular locationi

Nucleus. Cytoplasm. Perikaryon. Cell projectiondendrite. Cell projectionaxon
Note: It is mainly cytoplasmic, where it is associated with microtubules.

GO - Cellular componenti

  1. aggresome Source: MGI
  2. axon Source: UniProtKB
  3. caveola Source: MGI
  4. cell leading edge Source: MGI
  5. cytoplasm Source: MGI
  6. cytosol Source: UniProtKB
  7. dendrite Source: UniProtKB
  8. dynein complex Source: Ensembl
  9. histone deacetylase complex Source: MGI
  10. inclusion body Source: MGI
  11. microtubule Source: MGI
  12. microtubule associated complex Source: MGI
  13. nucleus Source: UniProtKB
  14. perikaryon Source: UniProtKB
  15. perinuclear region of cytoplasm Source: MGI
  16. protein complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11491149Histone deacetylase 6PRO_0000114704Add
BLAST

Post-translational modificationi

Phosphorylated by AURKA.By similarity
Ubiquitinated. Its polyubiquitination however does not lead to its degradation (By similarity).By similarity
Sumoylated in vitro.By similarity

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9Z2V5.
PaxDbiQ9Z2V5.
PRIDEiQ9Z2V5.

PTM databases

PhosphoSiteiQ9Z2V5.

Expressioni

Tissue specificityi

Expressed in neurons of the cortex. Expressed in Purkinje cells. Detected in keratinocytes (at protein level).2 Publications

Gene expression databases

BgeeiQ9Z2V5.
CleanExiMM_HDAC6.
ExpressionAtlasiQ9Z2V5. baseline and differential.
GenevestigatoriQ9Z2V5.

Interactioni

Subunit structurei

Interacts with BBIP10, DDIT3/CHOP, F-actin and HDAC11. Interacts with SIRT2 (via both phosphorylated, unphosphorylated, active or inactive forms); the interaction is necessary for the complex to interact with alpha-tubulin. Under proteasome impairment conditions, interacts with UBD via its histone deacetylase 1 and UBP-type zinc-finger regions (By similarity). Interacts with CBFA2T3, CYLD and ZMYND15. Interacts with FAM65B (By similarity).By similarity3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ADRBK1P211462EBI-1009256,EBI-1036401From a different organism.
CyldQ80TQ23EBI-1009256,EBI-943859

Protein-protein interaction databases

BioGridi200263. 16 interactions.
IntActiQ9Z2V5. 8 interactions.
MINTiMINT-220628.

Structurei

3D structure databases

ProteinModelPortaliQ9Z2V5.
SMRiQ9Z2V5. Positions 1043-1144.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 403317Histone deacetylase 1Add
BLAST
Regioni481 – 799319Histone deacetylase 2Add
BLAST
Regioni1088 – 10903Ubiquitin bindingBy similarity
Regioni1116 – 11238Ubiquitin bindingBy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi455 – 4606Poly-Glu

Sequence similaritiesi

Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1065 – 112662UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062809.
HOGENOMiHOG000004769.
HOVERGENiHBG051894.
InParanoidiQ9Z2V5.
KOiK11407.
OMAiLQENWVC.
OrthoDBiEOG7992PT.
TreeFamiTF106173.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
3.40.800.20. 2 hits.
InterProiIPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 2 hits.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PRINTSiPR01270. HDASUPER.
SMARTiSM00290. ZnF_UBP. 1 hit.
[Graphical view]
PROSITEiPS50271. ZF_UBP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Z2V5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTSTGQDSST RQRKSRHNPQ SPLQESSATL KRGGKKCAVP HSSPNLAEVK
60 70 80 90 100
KKGKMKKLSQ PAEEDLVVGL QGLDLNPETR VPVGTGLVFD EQLNDFHCLW
110 120 130 140 150
DDSFPESPER LHAIREQLIL EGLLGRCVSF QARFAEKEEL MLVHSLEYID
160 170 180 190 200
LMETTQYMNE GELRVLAETY DSVYLHPNSY SCACLATGSV LRLVDALMGA
210 220 230 240 250
EIRNGMAVIR PPGHHAQHNL MDGYCMFNHL AVAARYAQKK HRIQRVLIVD
260 270 280 290 300
WDVHHGQGTQ FIFDQDPSVL YFSIHRYEHG RFWPHLKASN WSTIGFGQGQ
310 320 330 340 350
GYTINVPWNQ TGMRDADYIA AFLHILLPVA SEFQPQLVLV AAGFDALHGD
360 370 380 390 400
PKGEMAATPA GFAHLTHLLM GLAGGKLILS LEGGYNLRAL AKGVSASLHT
410 420 430 440 450
LLGDPCPMLE SCVVPCASAQ TSIYCTLEAL EPFWEVLERS VETQEEDEVE
460 470 480 490 500
EAVLEEEEEE GGWEATALPM DTWPLLQNRT GLVYDEKMMS HCNLWDNHHP
510 520 530 540 550
ETPQRILRIM CHLEEVGLAA RCLILPARPA LDSELLTCHS AEYVEHLRTT
560 570 580 590 600
EKMKTRDLHR EGANFDSIYI CPSTFACAKL ATGAACRLVE AVLSGEVLNG
610 620 630 640 650
IAVVRPPGHH AEPNAACGFC FFNSVAVAAR HAQIIAGRAL RILIVDWDVH
660 670 680 690 700
HGNGTQHIFE DDPSVLYVSL HRYDRGTFFP MGDEGASSQV GRDAGIGFTV
710 720 730 740 750
NVPWNGPRMG DADYLAAWHR LVLPIAYEFN PELVLISAGF DAAQGDPLGG
760 770 780 790 800
CQVTPEGYAH LTHLLMGLAG GRIILILEGG YNLASISESM AACTHSLLGD
810 820 830 840 850
PPPQLTLLRP PQSGALVSIS EVIQVHRKYW RSLRLMKMED KEECSSSRLV
860 870 880 890 900
IKKLPPTASP VSAKEMTTPK GKVPEESVRK TIAALPGKES TLGQAKSKMA
910 920 930 940 950
KAVLAQGQSS EQAAKGTTLD LATSKETVGG ATTDLWASAA APENFPNQTT
960 970 980 990 1000
SVEALGETEP TPPASHTNKQ TTGASPLQGV TAQQSLQLGV LSTLELSREA
1010 1020 1030 1040 1050
EEAHDSEEGL LGEAAGGQDM NSLMLTQGFG DFNTQDVFYA VTPLSWCPHL
1060 1070 1080 1090 1100
MAVCPIPAAG LDVSQPCKTC GTVQENWVCL TCYQVYCSRY VNAHMVCHHE
1110 1120 1130 1140
ASEHPLVLSC VDLSTWCYVC QAYVHHEDLQ DVKNAAHQNK FGEDMPHSH
Length:1,149
Mass (Da):125,787
Last modified:July 27, 2011 - v3
Checksum:iD5F73BA3F79AF520
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti133 – 1331R → W in AAD09835. (PubMed:9891014)Curated
Sequence conflicti394 – 3941V → I in AAD09835. (PubMed:9891014)Curated
Sequence conflicti421 – 4211T → I in AAD09835. (PubMed:9891014)Curated
Sequence conflicti532 – 5321D → G in AAD09835. (PubMed:9891014)Curated
Sequence conflicti836 – 8361M → S in AAD09835. (PubMed:9891014)Curated
Sequence conflicti851 – 8511I → V in AAD09835. (PubMed:9891014)Curated
Sequence conflicti1126 – 11272HE → QD in AAD09835. (PubMed:9891014)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF006603 mRNA. Translation: AAD09835.2.
AL670169 Genomic DNA. Translation: CAM17240.1.
CCDSiCCDS40845.1.
PIRiT13964.
RefSeqiNP_001123888.1. NM_001130416.1.
NP_034543.3. NM_010413.3.
XP_006527630.1. XM_006527567.1.
UniGeneiMm.29854.

Genome annotation databases

EnsembliENSMUST00000033501; ENSMUSP00000033501; ENSMUSG00000031161.
ENSMUST00000115642; ENSMUSP00000111306; ENSMUSG00000031161.
GeneIDi15185.
KEGGimmu:15185.
UCSCiuc009snh.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF006603 mRNA. Translation: AAD09835.2.
AL670169 Genomic DNA. Translation: CAM17240.1.
CCDSiCCDS40845.1.
PIRiT13964.
RefSeqiNP_001123888.1. NM_001130416.1.
NP_034543.3. NM_010413.3.
XP_006527630.1. XM_006527567.1.
UniGeneiMm.29854.

3D structure databases

ProteinModelPortaliQ9Z2V5.
SMRiQ9Z2V5. Positions 1043-1144.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200263. 16 interactions.
IntActiQ9Z2V5. 8 interactions.
MINTiMINT-220628.

Chemistry

BindingDBiQ9Z2V5.
ChEMBLiCHEMBL2878.

PTM databases

PhosphoSiteiQ9Z2V5.

Proteomic databases

MaxQBiQ9Z2V5.
PaxDbiQ9Z2V5.
PRIDEiQ9Z2V5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000033501; ENSMUSP00000033501; ENSMUSG00000031161.
ENSMUST00000115642; ENSMUSP00000111306; ENSMUSG00000031161.
GeneIDi15185.
KEGGimmu:15185.
UCSCiuc009snh.2. mouse.

Organism-specific databases

CTDi10013.
MGIiMGI:1333752. Hdac6.

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062809.
HOGENOMiHOG000004769.
HOVERGENiHBG051894.
InParanoidiQ9Z2V5.
KOiK11407.
OMAiLQENWVC.
OrthoDBiEOG7992PT.
TreeFamiTF106173.

Enzyme and pathway databases

ReactomeiREACT_225256. HSF1 activation.

Miscellaneous databases

NextBioi287707.
PROiQ9Z2V5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z2V5.
CleanExiMM_HDAC6.
ExpressionAtlasiQ9Z2V5. baseline and differential.
GenevestigatoriQ9Z2V5.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
3.40.800.20. 2 hits.
InterProiIPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 2 hits.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PRINTSiPR01270. HDASUPER.
SMARTiSM00290. ZnF_UBP. 1 hit.
[Graphical view]
PROSITEiPS50271. ZF_UBP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of a new family of higher eukaryotic histone deacetylases. Coordinate expression of differentiation-dependent chromatin modifiers."
    Verdel A., Khochbin S.
    J. Biol. Chem. 274:2440-2445(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: C57BL/6J.
    Tissue: Fetus.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "ETO, a target of t(8;21) in acute leukemia, makes distinct contacts with multiple histone deacetylases and binds mSin3A through its oligomerization domain."
    Amann J.M., Nip J., Strom D.K., Lutterbach B., Harada H., Lenny N., Downing J.R., Meyers S., Hiebert S.W.
    Mol. Cell. Biol. 21:6470-6483(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CBFA2T3.
  4. "Microtubule deacetylases, SirT2 and HDAC6, in the nervous system."
    Southwood C.M., Peppi M., Dryden S., Tainsky M.A., Gow A.
    Neurochem. Res. 32:187-195(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  5. "CYLD negatively regulates cell-cycle progression by inactivating HDAC6 and increasing the levels of acetylated tubulin."
    Wickstrom S.A., Masoumi K.C., Khochbin S., Fassler R., Massoumi R.
    EMBO J. 29:131-144(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CYLD AND MICROTUBULES, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  6. "Zmynd15 encodes a histone deacetylase-dependent transcriptional repressor essential for spermiogenesis and male fertility."
    Yan W., Si Y., Slaymaker S., Li J., Zheng H., Young D.L., Aslanian A., Saunders L., Verdin E., Charo I.F.
    J. Biol. Chem. 285:31418-31426(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ZMYND15.
  7. "SIRT2 interferes with autophagy-mediated degradation of protein aggregates in neuronal cells under proteasome inhibition."
    Gal J., Bang Y., Choi H.J.
    Neurochem. Int. 61:992-1000(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN AUTOPHAGY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiHDAC6_MOUSE
AccessioniPrimary (citable) accession number: Q9Z2V5
Secondary accession number(s): B1AUA6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: July 27, 2011
Last modified: February 4, 2015
This is version 126 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.