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Reviewed, UniProtKB/Swiss-Prot O15379 (HDAC3_HUMAN)

Last modified June 16, 2009. Version 98. 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 · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Histone deacetylase 3
      Short name=HD3
    EC=3.5.1.98
Alternative name(s):
    RPD3-2
    SMAP45
Gene names
Name: HDAC3
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length428 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
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. Probably participates in the regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1 repression activity. Required to repress transcription of the POU1F1 transcription factor.

Catalytic activity

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

Subunit structure

Interacts with HDAC7 and HDAC9. Forms a heterologous complex at least with YY1. Interacts with DAXX, HDAC10 and DACH1. Found in a complex with NCOR1 and NCOR2. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Interacts with BCOR, MJD2A/JHDM3A, NRIP1, PRDM6 and SRY. Interacts with BTBD14B. Interacts with GLIS2 By similarity. Interacts with CBFA2T3.

Subcellular location

Nucleus.

Tissue specificity

Widely expressed.

Post-translational modification

Sumoylated in vitro. Ref.14

Sequence similarities

Belongs to the histone deacetylase family. Type 1 subfamily.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O15379-1)

Also known as: RPD3-2B;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: O15379-2)

Also known as: RPD3-2A;

The sequence of this isoform differs from the canonical sequence as follows:
     1-15: MAKTVAYFYDPDVGN → MIVFKPYQASQHDMCR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 428428Histone deacetylase 3
PRO_0000114696

Regions

Region3 – 316314Histone deacetylase

Sites

Active site1351 By similarity

Natural variations

Alternative sequence1 – 1515MAKTV…PDVGN → MIVFKPYQASQHDMCR in isoform 2.
VSP_002079
Natural variant4111N → S: dbSNP rs34901743.
VAR_033988

Experimental info

Sequence conflict3591R → L in AAC52038. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (RPD3-2B) [UniParc].

Last modified July 15, 1998. Version 2.
Checksum: 94485C1EBDCF5AD0

FASTA42848,848
        10         20         30         40         50         60 
MAKTVAYFYD PDVGNFHYGA GHPMKPHRLA LTHSLVLHYG LYKKMIVFKP YQASQHDMCR 

        70         80         90        100        110        120 
FHSEDYIDFL QRVSPTNMQG FTKSLNAFNV GDDCPVFPGL FEFCSRYTGA SLQGATQLNN 

       130        140        150        160        170        180 
KICDIAINWA GGLHHAKKFE ASGFCYVNDI VIGILELLKY HPRVLYIDID IHHGDGVQEA 

       190        200        210        220        230        240 
FYLTDRVMTV SFHKYGNYFF PGTGDMYEVG AESGRYYCLN VPLRDGIDDQ SYKHLFQPVI 

       250        260        270        280        290        300 
NQVVDFYQPT CIVLQCGADS LGCDRLGCFN LSIRGHGECV EYVKSFNIPL LVLGGGGYTV 

       310        320        330        340        350        360 
RNVARCWTYE TSLLVEEAIS EELPYSEYFE YFAPDFTLHP DVSTRIENQN SRQYLDQIRQ 

       370        380        390        400        410        420 
TIFENLKMLN HAPSVQIHDV PADLLTYDRT DEADAEERGP EENYSRPEAP NEFYDGDHDN 


DKESDVEI 

« Hide

Isoform 2 (RPD3-2A).

Checksum: 0B654598513D284B
Show »

FASTA42949,111

References

« Hide 'large scale' references
[1]"Differential display cloning of a novel human histone deacetylase (HDAC3) cDNA from PHA-activated immune cells."
Dangond F., Hafler D.A., Tong J.K., Randall J., Kojima R., Utku N., Gullans S.R.
Biochem. Biophys. Res. Commun. 242:648-652(1998) [PubMed: 9464271] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
Tissue: Spleen and T-cell.
[2]"Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family."
Yang W.-M., Yao Y.-L., Sun J.-M., Davie J.R., Seto E.
J. Biol. Chem. 272:28001-28007(1997) [PubMed: 9346952] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
Tissue: Fibroblast.
[3]"Characterization of a human RPD3 ortholog, HDAC3."
Emiliani S., Fischle W., van Lint C., Al-Abed Y., Verdin E.
Proc. Natl. Acad. Sci. U.S.A. 95:2795-2800(1998) [PubMed: 9501169] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[4]"Genomic organization and chromosomal localization of the human histone deacetylase 3 gene."
Mahlknecht U., Emiliani S., Najfeld V., Young S., Verdin E.
Genomics 56:197-202(1999) [PubMed: 10051405] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Skin.
[6]Lynch E.D., Lee M.K., King M.-C.
Submitted (MAR-1998) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE OF 95-353 AND 407-428.
[7]"Receptor-interacting protein 140 directly recruits histone deacetylases for gene silencing."
Wei L.-N., Hu X., Chandra D., Seto E., Farooqui M.
J. Biol. Chem. 275:40782-40787(2000) [PubMed: 11006275] [Abstract]
Cited for: INTERACTION WITH NRIP1.
[8]"Sequestration and inhibition of Daxx-mediated transcriptional repression by PML."
Li H., Leo C., Zhu J., Wu X., O'Neil J., Park E.-J., Chen J.D.
Mol. Cell. Biol. 20:1784-1796(2000) [PubMed: 10669754] [Abstract]
Cited for: INTERACTION WITH DAXX.
[9]"Identification of a transcriptional repressor related to the noncatalytic domain of histone deacetylases 4 and 5."
Zhou X., Richon V.M., Rifkind R.A., Marks P.A.
Proc. Natl. Acad. Sci. U.S.A. 97:1056-1061(2000) [PubMed: 10655483] [Abstract]
Cited for: INTERACTION WITH HDAC9.
[10]"The histone deacetylase-3 complex contains nuclear receptor corepressors."
Wen Y.-D., Perissi V., Staszewski L.M., Yang W.-M., Krones A., Glass C.K., Rosenfeld M.G., Seto E.
Proc. Natl. Acad. Sci. U.S.A. 97:7202-7207(2000) [PubMed: 10860984] [Abstract]
Cited for: IDENTIFICATION IN A COMPLEX WITH NCOR1 AND NCOR2.
[11]"Human HDAC7 histone deacetylase activity is associated with HDAC3 in vivo."
Fischle W., Dequiedt F., Fillion M., Hendzel M.J., Voelter W., Verdin E.
J. Biol. Chem. 276:35826-35835(2001) [PubMed: 11466315] [Abstract]
Cited for: INTERACTION WITH HDAC7.
[12]"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: 11533236] [Abstract]
Cited for: INTERACTION WITH CBFA2T3.
[13]"Identification of HDAC10, a novel class II human histone deacetylase containing a leucine-rich domain."
Tong J.J., Liu J., Bertos N.R., Yang X.-J.
Nucleic Acids Res. 30:1114-1123(2002) [PubMed: 11861901] [Abstract]
Cited for: INTERACTION WITH HDAC10.
[14]"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: SUMOYLATION.
[15]"A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness."
Guenther M.G., Lane W.S., Fischle W., Verdin E., Lazar M.A., Shiekhattar R.
Genes Dev. 14:1048-1057(2000) [PubMed: 10809664] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, COMPONENT OF THE N-COR COMPLEX WITH NCOR2 AND TBL1X.
[16]"Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3."
Li J., Wang J., Wang J., Nawaz Z., Liu J.M., Qin J., Wong J.
EMBO J. 19:4342-4350(2000) [PubMed: 10944117] [Abstract]
Cited for: COMPONENT OF THE N-COR COMPLEX WITH NCOR2 AND HDAC3.
[17]"BCoR, a novel corepressor involved in BCL-6 repression."
Huynh K.D., Fischle W., Verdin E., Bardwell V.J.
Genes Dev. 14:1810-1823(2000) [PubMed: 10898795] [Abstract]
Cited for: INTERACTION WITH BCOR.
[18]"The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2."
Zhang J., Kalkum M., Chait B.T., Roeder R.G.
Mol. Cell 9:611-623(2002) [PubMed: 11931768] [Abstract]
Cited for: COMPONENT OF THE N-COR COMPLEX WITH NCOR1; NCOR2; GPS2; TBL1R AND TBL1X.
[19]"Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1."
Yoon H.-G., Chan D.W., Huang Z.-Q., Li J., Fondell J.D., Qin J., Wong J.
EMBO J. 22:1336-1346(2003) [PubMed: 12628926] [Abstract]
Cited for: COMPONENT OF THE N-COR COMPLEX WITH TBL1R; TBL1X AND CORO2A.
[20]"DACH1 inhibits transforming growth factor-beta signaling through binding Smad4."
Wu K., Yang Y., Wang C., Davoli M.A., D'Amico M., Li A., Cveklova K., Kozmik Z., Lisanti M.P., Russell R.G., Cvekl A., Pestell R.G.
J. Biol. Chem. 278:51673-51684(2003) [PubMed: 14525983] [Abstract]
Cited for: INTERACTION WITH DACH1.
[21]"Regulation of human SRY subcellular distribution by its acetylation/deacetylation."
Thevenet L., Mejean C., Moniot B., Bonneaud N., Galeotti N., Aldrian-Herrada G., Poulat F., Berta P., Benkirane M., Boizet-Bonhoure B.
EMBO J. 23:3336-3345(2004) [PubMed: 15297880] [Abstract]
Cited for: INTERACTION WITH SRY.
[22]"Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein."
Gray S.G., Iglesias A.H., Lizcano F., Villanueva R., Camelo S., Jingu H., Teh B.T., Koibuchi N., Chin W.W., Kokkotou E., Dangond F.
J. Biol. Chem. 280:28507-28518(2005) [PubMed: 15927959] [Abstract]
Cited for: INTERACTION WITH JMJD2A.
+Additional computationally mapped references.

Cross-references

Sequence databases

U66914 mRNA. Translation: AAC52038.1.
U75697 mRNA. Translation: AAB88241.1.
U75696 mRNA. Translation: AAB88240.1.
AF005482 mRNA. Translation: AAB87752.1.
AF039703 mRNA. Translation: AAC98927.1.
AF059650 Genomic DNA. Translation: AAC26509.1.
BC000614 mRNA. Translation: AAH00614.1.
AF053138, AF053137 Genomic DNA. Translation: AAC08351.1.
AF053139 Genomic DNA. Translation: AAC08352.1.
IPIIPI00006187.
IPI00217965.
PIRJC5834.
RefSeqNP_003874.2.
UniGeneHs.519632

3D structure databases

HSSPHSSP built from PDB template 1C3P based on UniProtKB O67135.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP:24253N.
IntActO15379. 12 interactions.

PTM databases

PhosphoSiteO15379.

Proteomic databases

PRIDEO15379.

Genome annotation databases

EnsemblENSG00000171720. Homo sapiens. [Contig view]
GeneID8841.
KEGGhsa:8841.

Organism-specific databases

GeneCardsGC05M140980.
H-InvDBHIX0005255.
HGNCHGNC:4854. HDAC3.
HPACAB005583.
MIM605166. gene.
PharmGKBPA29228.
GenAtlasSearch...

Phylogenomic databases

HOGENOMO15379.
HOVERGENO15379.
OMAO15379. NNMQGFT.

Enzyme and pathway databases

Pathway_Interaction_DBretinoic_acid_pathway. Retinoic acid receptors-mediated signaling.
hdac_classi_pathway. Signaling events mediated by HDAC Class I.
hdac_classii_pathway. Signaling events mediated by HDAC Class II.
ReactomeREACT_11061. Signalling by NGF.

Gene expression databases

ArrayExpressO15379.
BgeeO15379.
CleanExHS_HDAC3.
GermOnlineENSG00000171720. Homo sapiens.

Family and domain databases

InterProIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
[Graphical view]
Gene3DG3DSA:3.40.800.20. His_deacetylse. 1 hit.
PANTHERPTHR10625. His_deacetylse. 1 hit.
PTHR10625:SF28. His_deacetylse_1. 1 hit.
PfamPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSPR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNetSearch...

Other Resources

BindingDBO15379.
DrugBankDB02546. Vorinostat.
NextBio33190.
PMAP-CutDBO15379.
SOURCESearch...

Entry information

Entry nameHDAC3_HUMAN
AccessionPrimary (citable) accession number: O15379
Secondary accession number(s): O43268, Q9UEI5, Q9UEV0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: July 15, 1998
Last modified: June 16, 2009
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

Relevant documents

Human chromosome 5

Human chromosome 5: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

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

SIMILARITY comments

Index of protein domains and families

Forthcoming format changes

Announcement of forthcoming format changes

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