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Reviewed, UniProtKB/Swiss-Prot P56524 (HDAC4_HUMAN)

Last modified January 19, 2010. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Histone deacetylase 4
      Short name=HD4
    EC=3.5.1.98
Gene names
Name: HDAC4
Synonyms: KIAA0288
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1084 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

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. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D. Ref.6

Catalytic activity

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

Subunit structure

Interacts with HDAC7 By similarity. Homodimer. Homodimerization via its N-terminal domain. Interacts with MEF2C, AHRR, and NR2C1. Interacts with a 14-3-3 chaperone protein in a phosphorylation dependent manner. Interacts with BTBD14B By similarity. Interacts with KDM5B. Ref.6 Ref.5 Ref.10 Ref.11 Ref.12

Subcellular location

Nucleus. Cytoplasm. Note: Shuttles between the nucleus and the cytoplasm. Upon muscle cells differentiation, it accumulates in the nuclei of myotubes, suggesting a positive role of nuclear HDAC4 in muscle differentiation. The export to cytoplasm depends on the interaction with a 14-3-3 chaperone protein and is due to its phosphorylation at Ser-246, Ser-467 and Ser-632 by CaMK4. The nuclear localization probably depends on sumoylation. Ref.5 Ref.8

Tissue specificity

Ubiquitous.

Domain

The nuclear export sequence mediates the shuttling between the nucleus and the cytoplasm.

Post-translational modification

Phosphorylated by CaMK4 at Ser-246, Ser-467 and Ser-632. Phosphorylation at other residues is required for the interaction with 14-3-3. Ref.8 Ref.7 Ref.13 Ref.14

Sumoylation on Lys-559 is promoted by the E3 SUMO-protein ligase RANBP2, and prevented by phosphorylation by CaMK4.

Sequence similarities

Belongs to the histone deacetylase family. Type 2 subfamily.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityPolymorphism
   DomainCoiled coil
   Molecular functionChromatin regulator
Hydrolase
Repressor
   PTMIsopeptide bond
Phosphoprotein
Ubl conjugation
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological processB cell differentiation

Traceable author statement. Source: UniProtKB

cardiac muscle hypertrophy in response to stress

Traceable author statement. Source: UniProtKB

chromatin remodeling

Inferred from direct assay. Source: UniProtKB

histone deacetylation

Inferred from direct assay. Source: UniProtKB

inflammatory response

Traceable author statement. Source: UniProtKB

negative regulation of gene-specific transcription from RNA polymerase II promoter

Inferred from direct assay. Source: UniProtKB

negative regulation of glycolysis

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of myotube differentiation

Inferred from mutant phenotype. Source: UniProtKB

negative regulation of transcription factor activity

Inferred from mutant phenotype. Source: UniProtKB

nervous system development

Traceable author statement. Source: UniProtKB

peptidyl-lysine deacetylation

Inferred from direct assay. Source: UniProtKB

positive regulation of cell proliferation

Inferred from mutant phenotype. Source: UniProtKB

positive regulation of gene-specific transcription from RNA polymerase II promoter

Inferred from mutant phenotype. Source: UniProtKB

positive regulation of protein sumoylation

Inferred from direct assay. Source: UniProtKB

positive regulation of transcription factor activity

Inferred from mutant phenotype. Source: UniProtKB

regulation of protein binding

Inferred from mutant phenotype. Source: UniProtKB

response to denervation involved in regulation of muscle adaptation

Inferred from sequence or structural similarity. Source: UniProtKB

response to interleukin-1

Inferred from mutant phenotype. Source: UniProtKB

transcription

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componenthistone deacetylase complex

Inferred from direct assay. Source: UniProtKB

transcriptional repressor complex

Inferred from direct assay. Source: UniProtKB

   Molecular functionhistone deacetylase activity Ref.1

Inferred from direct assay. Source: UniProtKB

histone deacetylase binding

Inferred from physical interaction. Source: UniProtKB

potassium ion binding

Inferred from direct assay. Source: UniProtKB

specific transcriptional repressor activity

Inferred from mutant phenotype. Source: UniProtKB

transcription activator activity

Inferred from sequence or structural similarity. Source: UniProtKB

transcription activator binding

Inferred from physical interaction. Source: UniProtKB

transcription factor binding

Inferred from physical interaction. Source: UniProtKB

transcription repressor binding

Inferred from physical interaction. Source: UniProtKB

zinc ion binding

Inferred from direct assay. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10841084Histone deacetylase 4
PRO_0000114699

Regions

Region118 – 313196Interaction with MEF2A
Region655 – 1084430Histone deacetylase
Coiled coil67 – 177111 Potential
Motif1051 – 108434Nuclear export signal By similarity

Sites

Active site8031 By similarity

Amino acid modifications

Modified residue2461Phosphoserine; by CaMK4 Ref.7
Modified residue3501Phosphoserine Ref.14
Modified residue4671Phosphoserine; by CaMK4 Ref.7
Modified residue5651Phosphoserine Ref.13
Modified residue6321Phosphoserine; by CaMK4 Ref.7 Ref.13
Modified residue6331Phosphoserine Ref.13
Cross-link559Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.11

Natural variations

Natural variant7271P → R in a breast cancer sample; somatic mutation. Ref.15
VAR_036042

Experimental info

Mutagenesis2461S → A: Reduces phosphorylation and its subsequent nuclear export. Ref.7
Mutagenesis4671S → A: Reduces phosphorylation and its subsequent nuclear export. Ref.8 Ref.7
Mutagenesis5591K → R: Abolishes sumoylation and reduces the histone deacetylase activity. Ref.11
Mutagenesis6321S → A: Reduces phosphorylation and its subsequent nuclear export. Ref.8 Ref.7
Mutagenesis8031H → L: Abolishes histone deacetylase activity. Ref.6
Mutagenesis10561V → A: Reduces CaMK-dependent nuclear export. Ref.9
Mutagenesis10621L → A: Reduces CaMK-dependent nuclear export. Ref.9
Sequence conflict3731A → T in AAD29046. Ref.1
Sequence conflict3731A → T in BAA22957. Ref.2

Secondary structure

............................................................................... 1084
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56524-1 [UniParc].

Last modified September 22, 2009. Version 3.
Checksum: BB7FD37652D12398

FASTA1,084119,040
        10         20         30         40         50         60 
MSSQSHPDGL SGRDQPVELL NPARVNHMPS TVDVATALPL QVAPSAVPMD LRLDHQFSLP 

        70         80         90        100        110        120 
VAEPALREQQ LQQELLALKQ KQQIQRQILI AEFQRQHEQL SRQHEAQLHE HIKQQQEMLA 

       130        140        150        160        170        180 
MKHQQELLEH QRKLERHRQE QELEKQHREQ KLQQLKNKEK GKESAVASTE VKMKLQEFVL 

       190        200        210        220        230        240 
NKKKALAHRN LNHCISSDPR YWYGKTQHSS LDQSSPPQSG VSTSYNHPVL GMYDAKDDFP 

       250        260        270        280        290        300 
LRKTASEPNL KLRSRLKQKV AERRSSPLLR RKDGPVVTAL KKRPLDVTDS ACSSAPGSGP 

       310        320        330        340        350        360 
SSPNNSSGSV SAENGIAPAV PSIPAETSLA HRLVAREGSA APLPLYTSPS LPNITLGLPA 

       370        380        390        400        410        420 
TGPSAGTAGQ QDAERLTLPA LQQRLSLFPG THLTPYLSTS PLERDGGAAH SPLLQHMVLL 

       430        440        450        460        470        480 
EQPPAQAPLV TGLGALPLHA QSLVGADRVS PSIHKLRQHR PLGRTQSAPL PQNAQALQHL 

       490        500        510        520        530        540 
VIQQQHQQFL EKHKQQFQQQ QLQMNKIIPK PSEPARQPES HPEETEEELR EHQALLDEPY 

       550        560        570        580        590        600 
LDRLPGQKEA HAQAGVQVKQ EPIESDEEEA EPPREVEPGQ RQPSEQELLF RQQALLLEQQ 

       610        620        630        640        650        660 
RIHQLRNYQA SMEAAGIPVS FGGHRPLSRA QSSPASATFP VSVQEPPTKP RFTTGLVYDT 

       670        680        690        700        710        720 
LMLKHQCTCG SSSSHPEHAG RIQSIWSRLQ ETGLRGKCEC IRGRKATLEE LQTVHSEAHT 

       730        740        750        760        770        780 
LLYGTNPLNR QKLDSKKLLG SLASVFVRLP CGGVGVDSDT IWNEVHSAGA ARLAVGCVVE 

       790        800        810        820        830        840 
LVFKVATGEL KNGFAVVRPP GHHAEESTPM GFCYFNSVAV AAKLLQQRLS VSKILIVDWD 

       850        860        870        880        890        900 
VHHGNGTQQA FYSDPSVLYM SLHRYDDGNF FPGSGAPDEV GTGPGVGFNV NMAFTGGLDP 

       910        920        930        940        950        960 
PMGDAEYLAA FRTVVMPIAS EFAPDVVLVS SGFDAVEGHP TPLGGYNLSA RCFGYLTKQL 

       970        980        990       1000       1010       1020 
MGLAGGRIVL ALEGGHDLTA ICDASEACVS ALLGNELDPL PEKVLQQRPN ANAVRSMEKV 

      1030       1040       1050       1060       1070       1080 
MEIHSKYWRC LQRTTSTAGR SLIEAQTCEN EEAETVTAMA SLSVGVKPAE KRPDEEPMEE 


EPPL 

« Hide

References

« Hide 'large scale' references
[1]"Three proteins define a class of human histone deacetylases related to yeast Hda1p."
Grozinger C.M., Hassig C.A., Schreiber S.L.
Proc. Natl. Acad. Sci. U.S.A. 96:4868-4873(1999) [PubMed: 10220385] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Leukemia.
[2]"Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins."
Ohara O., Nagase T., Ishikawa K., Nakajima D., Ohira M., Seki N., Nomura N.
DNA Res. 4:53-59(1997) [PubMed: 9179496] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[3]Ohara O., Nagase T., Ishikawa K., Nakajima D., Ohira M., Seki N., Nomura N.
Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO N-TERMINUS.
[4]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed: 15815621] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"HDAC4 deacetylase associates with and represses the MEF2 transcription factor."
Miska E.A., Karlsson C., Langley E., Nielsen S.J., Pines J., Kouzarides T.
EMBO J. 18:5099-5107(1999) [PubMed: 10487761] [Abstract]
Cited for: SUBCELLULAR LOCATION, INTERACTION WITH MEF2A.
[6]"HDAC4, a human histone deacetylase related to yeast HDA1, is a transcriptional corepressor."
Wang A.H., Bertos N.R., Vezmar M., Pelletier N., Crosato M., Heng H.H., Th'ng J., Han J., Yang X.-J.
Mol. Cell. Biol. 19:7816-7827(1999) [PubMed: 10523670] [Abstract]
Cited for: FUNCTION, INTERACTION WITH MEF2C AND MEF2D, MUTAGENESIS OF HIS-803.
[7]"Regulation of histone deacetylase 4 by binding of 14-3-3 proteins."
Wang A.H., Kruhlak M.J., Wu J., Bertos N.R., Vezmar M., Posner B.I., Bazett-Jones D.P., Yang X.-J.
Mol. Cell. Biol. 20:6904-6912(2000) [PubMed: 10958686] [Abstract]
Cited for: PHOSPHORYLATION AT SER-246; SER-467 AND SER-632, MUTAGENESIS OF SER-246; SER-467 AND SER-632.
[8]"The modular nature of histone deacetylase HDAC4 confers phosphorylation-dependent intracellular trafficking."
Zhao X., Ito A., Kane C.D., Liao T.-S., Bolger T.A., Lemrow S.M., Means A.R., Yao T.-P.
J. Biol. Chem. 276:35042-35048(2001) [PubMed: 11470791] [Abstract]
Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION, MUTAGENESIS OF SER-467 AND SER-632.
[9]"Identification of a signal-responsive nuclear export sequence in class II histone deacetylases."
McKinsey T.A., Zhang C.-L., Olson E.N.
Mol. Cell. Biol. 21:6312-6321(2001) [PubMed: 11509672] [Abstract]
Cited for: NUCLEAR EXPORT SIGNAL, MUTAGENESIS OF VAL-1056 AND LEU-1062.
[10]"The orphan nuclear receptor TR2 interacts directly with both class I and class II histone deacetylases."
Franco P.J., Farooqui M., Seto E., Wei L.-N.
Mol. Endocrinol. 15:1318-1328(2001) [PubMed: 11463856] [Abstract]
Cited for: INTERACTION WITH NR2C1.
[11]"The SUMO E3 ligase RanBP2 promotes modification of the HDAC4 deacetylase."
Kirsh O., Seeler J.-S., Pichler A., Gast A., Mueller S., Miska E., Mathieu M., Harel-Bellan A., Kouzarides T., Melchior F., Dejean A.
EMBO J. 21:2682-2691(2002) [PubMed: 12032081] [Abstract]
Cited for: HOMODIMERIZATION, SUMOYLATION AT LYS-559, MUTAGENESIS OF LYS-559.
[12]"Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases."
Barrett A., Santangelo S., Tan K., Catchpole S., Roberts K., Spencer-Dene B., Hall D., Scibetta A., Burchell J., Verdin E., Freemont P., Taylor-Papadimitriou J.
Int. J. Cancer 121:265-275(2007) [PubMed: 17373667] [Abstract]
Cited for: INTERACTION WITH KDM5B.
[13]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-565; SER-632 AND SER-633, MASS SPECTROMETRY.
[14]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-350, MASS SPECTROMETRY.
Tissue: T-cell.
[15]"The consensus coding sequences of human breast and colorectal cancers."
Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. expand/collapse author list , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E.
Science 314:268-274(2006) [PubMed: 16959974] [Abstract]
Cited for: VARIANT [LARGE SCALE ANALYSIS] ARG-727.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF132607 mRNA. Translation: AAD29046.1.
AB006626 mRNA. Translation: BAA22957.2. Different initiation.
AC017028 Genomic DNA. No translation available.
IPIIPI00010088.
RefSeqNP_006028.2.
UniGeneHs.20516

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2H8NX-ray2.60A/B/C/D62-153[»]
2O94X-ray3.00A/B/C/D62-153[»]
2VQJX-ray2.10A648-1057[»]
2VQMX-ray1.80A648-1057[»]
2VQOX-ray2.15A/B648-1057[»]
2VQQX-ray1.90A/B648-1057[»]
2VQVX-ray3.30A/B648-1057[»]
2VQWX-ray3.00G648-1057[»]
ModBaseSearch...

Protein-protein interaction databases

IntActP56524. 11 interactions.
STRINGP56524.

PTM databases

PhosphoSiteP56524.

Proteomic databases

PRIDEP56524.

Genome annotation databases

EnsemblENST00000345617; ENSP00000264606; ENSG00000068024; Homo sapiens. [Genome view]
GeneID9759.
KEGGhsa:9759.

Organism-specific databases

CTD9759.
GeneCardsGC02M239707.
H-InvDBHIX0021592.
HGNCHGNC:14063. HDAC4.
HPACAB004431.
MIM605314. gene.
PharmGKBPA29229.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG06150.
HOGENOMHBG716007.
HOVERGENP56524.
InParanoidP56524.
OMARVNHMPS.
PhylomeDBP56524.

Enzyme and pathway databases

Pathway_Interaction_DBhdac_classi_pathway. Signaling events mediated by HDAC Class I.
hdac_classii_pathway. Signaling events mediated by HDAC Class II.
hdac_classiii_pathway. Signaling events mediated by HDAC Class III.
ranbp2pathway. Sumoylation by RanBP2 regulates transcriptional repression.

Gene expression databases

ArrayExpressP56524.
BgeeP56524.
CleanExHS_HDAC4.
GenevestigatorP56524.
GermOnlineENSG00000068024. Homo sapiens.

Family and domain databases

InterProIPR019154. Arb2_domain.
IPR000286. His_deacetylse.
IPR017320. Histone_deAcase_II_euk.
[Graphical view]
Gene3DG3DSA:3.40.800.20. His_deacetylse. 1 hit.
PANTHERPTHR10625. His_deacetylse. 1 hit.
PfamPF09757. Arb2. 1 hit.
PF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFPIRSF037911. HDAC_II_euk. 1 hit.
PRINTSPR01270. HDASUPER.
ProtoNetSearch...

Other Resources

NextBio36731.
SOURCESearch...

Entry information

Entry nameHDAC4_HUMAN
AccessionPrimary (citable) accession number: P56524
Secondary accession number(s): Q9UND6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 22, 2009
Last modified: January 19, 2010
This is version 105 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

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Human chromosome 2: entries, gene names and cross-references to MIM

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List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents