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Q99N13

- HDAC9_MOUSE

UniProt

Q99N13 - HDAC9_MOUSE

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Protein
Histone deacetylase 9
Gene
Hdac9, Hdac7b, Hdrp, Mitr
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Devoided of intrinsic deacetylase activity, promotes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) by recruiting HDAC1 and HDAC3. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Represses MEF2-dependent transcription, inhibits skeletal myogenesis and may be involved in heart development. Protects neurons from apoptosis, both by inhibiting JUN phosphorylation by MAPK10 and by repressing JUN transcription via HDAC1 recruitment to JUN promoter.4 Publications

Catalytic activityi

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

GO - Molecular functioni

  1. histone deacetylase activity Source: UniProtKB
  2. protein binding Source: IntAct
  3. repressing transcription factor binding Source: BHF-UCL
  4. transcription corepressor activity Source: MGI
  5. transcription factor binding Source: UniProtKB

GO - Biological processi

  1. B cell activation Source: UniProtKB
  2. B cell differentiation Source: UniProtKB
  3. cellular response to insulin stimulus Source: Ensembl
  4. chromatin modification Source: UniProtKB
  5. heart development Source: MGI
  6. histone H3 deacetylation Source: Ensembl
  7. histone H4 deacetylation Source: Ensembl
  8. inflammatory response Source: UniProtKB
  9. negative regulation of striated muscle tissue development Source: UniProtKB
  10. negative regulation of transcription from RNA polymerase II promoter Source: MGI
  11. negative regulation of transcription, DNA-templated Source: UniProtKB
  12. nervous system development Source: UniProtKB
  13. peptidyl-lysine deacetylation Source: Ensembl
  14. positive regulation of cell migration involved in sprouting angiogenesis Source: Ensembl
  15. regulation of skeletal muscle fiber development Source: MGI
  16. regulation of striated muscle cell differentiation Source: MGI
  17. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 9 (EC:3.5.1.98)
Short name:
HD9
Alternative name(s):
Histone deacetylase 7B
Short name:
HD7b
Histone deacetylase-related protein
MEF2-interacting transcription repressor MITR
Gene namesi
Name:Hdac9
Synonyms:Hdac7b, Hdrp, Mitr
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 12

Organism-specific databases

MGIiMGI:1931221. Hdac9.

Subcellular locationi

Nucleus 3 Publications

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. histone deacetylase complex Source: UniProtKB
  3. histone methyltransferase complex Source: BHF-UCL
  4. nucleus Source: UniProtKB
  5. transcription factor complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Mice do not present any abnormality at early age but develop cardiac hypertrophy by eight months of age.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi25 – 262DL → AS: Abolishes binding to CTBP1 and impairs function in transcription repression. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 588588Histone deacetylase 9
PRO_0000114711Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei22 – 221Phosphoserine By similarity
Modified residuei220 – 2201Phosphoserine2 Publications
Modified residuei240 – 2401Phosphoserine; by DYRK1B1 Publication
Modified residuei450 – 4501Phosphoserine2 Publications

Post-translational modificationi

Sumoylated By similarity.
Phosphorylated on Ser-220 and Ser-450; which promotes 14-3-3-binding, impairs interaction with MEF2, and antagonizes antimyogenic activity. Phosphorylated on Ser-240 by DYRK1B; which impairs nuclear accumulation. Phosphorylated by the PKC kinases PKN1 and PKN2, impairing nuclear import.3 Publications

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ99N13.
PRIDEiQ99N13.

PTM databases

PhosphoSiteiQ99N13.

Expressioni

Tissue specificityi

Expressed at high levels in heart, brain and spleen. Expressed in skeletal muscle.2 Publications

Developmental stagei

At E10.5, expressed in heart, skeletal muscle and neural lineages. At E11.5, expressed in heart, dorsal root ganglia and neural tube. At E12.5, expressed in heart, skeletal muscle, dorsal root ganglia, neural tube and retina. Strongly up-regulated in muscle between E14 and E19 as a result of motor innervation.3 Publications

Inductioni

By MEF2 during muscle differentiation. Down-regulated by muscle denervation. Down-regulated by trichostatin A or sodium butyrate, and during neuronal apoptosis (at protein level).3 Publications

Gene expression databases

BgeeiQ99N13.
CleanExiMM_HDAC9.
GenevestigatoriQ99N13.

Interactioni

Subunit structurei

Homodimer. Interacts with ETV6 By similarity. Interacts with MEF2, HDAC1, HDAC3, HDAC4, HDAC5, CTBP1 and MAPK10. The phosphorylated form interacts with 14-3-3.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Pcbp1P603356EBI-645361,EBI-309059

Protein-protein interaction databases

BioGridi219748. 5 interactions.
DIPiDIP-41905N.
IntActiQ99N13. 5 interactions.
MINTiMINT-146908.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi143 – 15311

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TQEX-ray2.70X/Y139-158[»]
ProteinModelPortaliQ99N13.
SMRiQ99N13. Positions 37-101.

Miscellaneous databases

EvolutionaryTraceiQ99N13.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni23 – 275Interaction with CTBP1
Regioni136 – 15419Interaction with MEF2
Add
BLAST
Regioni175 – 343169Interaction with MAPK10
Add
BLAST
Regioni218 – 26144Interaction with ETV6 By similarity
Add
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062809.
HOGENOMiHOG000232065.
HOVERGENiHBG057100.
KOiK11409.
OrthoDBiEOG7RFTH5.
PhylomeDBiQ99N13.
TreeFamiTF106174.

Family and domain databases

InterProiIPR000286. His_deacetylse.
IPR024643. Hist_deacetylase_Gln_rich_N.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF12203. HDAC4_Gln. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q99N13-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MHSMISSVDV KSEVPMGLEP ISPLDLRTDL RMMMPVVDPV VREKQLQQEL    50
LLIQQQQQIQ KQLLIAEFQK QHENLTRQHQ AQLQEHIKEL LAIKQQQELL 100
EKEQKLEQQR QEQEVERHRR EQQLPPLRGK DRGRERAVAS TEVKQKLQEF 150
LLSKSATKDT PTNGKNHSVG RHPKLWYTAA HHTSLDQSSP PLSGTSPSYK 200
YTLPGAQDSK DDFPLRKTAS EPNLKVRSRL KQKVAERRSS PLLRRKDGNL 250
VTSFKKRVFE VAESSVSSSS PGSGPSSPNN GPAGNVTENE ASALPPTPHP 300
EQLVPQQRIL IHEDSMNLLS LYTSPSLPNI TLGLPAVPSP LNASNSLKDK 350
QKCETQMLRQ GVPLPSQYGS SIAASSSHVH VAMEGKPNSS HQALLQHLLL 400
KEQMRQQKLL VAGGVPLHPQ SPLATKERIS PGIRGTHKLP RHRPLNRTQS 450
APLPQSTLAQ LVIQQQHQQF LEKQKQYQQQ IHMNKLLSKS IEQLKQPGSH 500
LEEAEEELQG DQSMEDRAAS KDNSARSDSS ACVEDTLGQV GAVKVKEEPV 550
DSDEDAQIQE MECGEQAAFM QQVIGKDLAP GFVIKVII 588
Length:588
Mass (Da):65,687
Last modified:March 20, 2007 - v2
Checksum:i4ED7FA9F02BD4621
GO
Isoform 2 (identifier: Q99N13-2) [UniParc]FASTAAdd to Basket

Also known as: Hdrpa

The sequence of this isoform differs from the canonical sequence as follows:
     219-262: Missing.

Note: No experimental confirmation available.

Show »
Length:544
Mass (Da):60,609
Checksum:i60B1203BC91D87D0
GO
Isoform 3 (identifier: Q99N13-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     177-178: Missing.

Show »
Length:586
Mass (Da):65,422
Checksum:iE92E1B8ED6AD5C99
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei177 – 1782Missing in isoform 3.
VSP_029173
Alternative sequencei219 – 26244Missing in isoform 2.
VSP_023769Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti120 – 1201R → K in AAK15027. 1 Publication
Sequence conflicti120 – 1201R → K in AAL86358. 1 Publication
Sequence conflicti136 – 1361R → K in AAK15027. 1 Publication
Sequence conflicti136 – 1361R → K in AAL86358. 1 Publication
Sequence conflicti388 – 3881N → T in AAH98187. 1 Publication
Sequence conflicti523 – 5231N → T in AAG48332. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF324492 mRNA. Translation: AAG48332.1.
AF235053 mRNA. Translation: AAK15027.1.
AF279371 mRNA. Translation: AAL86358.1.
BC098187 mRNA. Translation: AAH98187.1.
CCDSiCCDS36432.1. [Q99N13-1]
RefSeqiNP_077038.2. NM_024124.3.
UniGeneiMm.310551.
Mm.483009.

Genome annotation databases

EnsembliENSMUST00000110819; ENSMUSP00000106443; ENSMUSG00000004698.
GeneIDi79221.
KEGGimmu:79221.
UCSCiuc007nja.1. mouse. [Q99N13-3]
uc007njb.1. mouse. [Q99N13-2]
uc007njc.2. mouse. [Q99N13-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF324492 mRNA. Translation: AAG48332.1 .
AF235053 mRNA. Translation: AAK15027.1 .
AF279371 mRNA. Translation: AAL86358.1 .
BC098187 mRNA. Translation: AAH98187.1 .
CCDSi CCDS36432.1. [Q99N13-1 ]
RefSeqi NP_077038.2. NM_024124.3.
UniGenei Mm.310551.
Mm.483009.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1TQE X-ray 2.70 X/Y 139-158 [» ]
ProteinModelPortali Q99N13.
SMRi Q99N13. Positions 37-101.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 219748. 5 interactions.
DIPi DIP-41905N.
IntActi Q99N13. 5 interactions.
MINTi MINT-146908.

Chemistry

BindingDBi Q99N13.

PTM databases

PhosphoSitei Q99N13.

Proteomic databases

PaxDbi Q99N13.
PRIDEi Q99N13.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000110819 ; ENSMUSP00000106443 ; ENSMUSG00000004698 .
GeneIDi 79221.
KEGGi mmu:79221.
UCSCi uc007nja.1. mouse. [Q99N13-3 ]
uc007njb.1. mouse. [Q99N13-2 ]
uc007njc.2. mouse. [Q99N13-1 ]

Organism-specific databases

CTDi 9734.
MGIi MGI:1931221. Hdac9.

Phylogenomic databases

eggNOGi COG0123.
GeneTreei ENSGT00530000062809.
HOGENOMi HOG000232065.
HOVERGENi HBG057100.
KOi K11409.
OrthoDBi EOG7RFTH5.
PhylomeDBi Q99N13.
TreeFami TF106174.

Miscellaneous databases

ChiTaRSi HDAC9. mouse.
EvolutionaryTracei Q99N13.
NextBioi 349885.
PROi Q99N13.
SOURCEi Search...

Gene expression databases

Bgeei Q99N13.
CleanExi MM_HDAC9.
Genevestigatori Q99N13.

Family and domain databases

InterProi IPR000286. His_deacetylse.
IPR024643. Hist_deacetylase_Gln_rich_N.
[Graphical view ]
PANTHERi PTHR10625. PTHR10625. 1 hit.
Pfami PF12203. HDAC4_Gln. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Association of COOH-terminal-binding protein (CtBP) and MEF2-interacting transcription repressor (MITR) contributes to transcriptional repression of the MEF2 transcription factor."
    Zhang C.L., McKinsey T.A., Lu J.R., Olson E.N.
    J. Biol. Chem. 276:35-39(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), HOMODIMERIZATION, INTERACTION WITH CTBP1; HDAC1; HDAC3; HDAC4 AND HDAC5, MUTAGENESIS OF 25-ASP-LEU-26.
    Strain: NIH Swiss.
    Tissue: Embryonic heart.
  2. "Cloning of the mouse HDRP cDNA."
    Zhou X., Richon V.M., Rifkind R.A., Marks P.A.
    Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    Strain: Swiss Webster / NIH.
  3. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6.
    Tissue: Retina.
  4. "The transcriptional corepressor MITR is a signal-responsive inhibitor of myogenesis."
    Zhang C.L., McKinsey T.A., Olson E.N.
    Proc. Natl. Acad. Sci. U.S.A. 98:7354-7359(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PHOSPHORYLATION AT SER-220 AND SER-450, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION.
  5. "Class II histone deacetylases act as signal-responsive repressors of cardiac hypertrophy."
    Zhang C.L., McKinsey T.A., Chang S., Antos C.L., Hill J.A., Olson E.N.
    Cell 110:479-488(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-220 AND SER-450, FUNCTION, DISRUPTION PHENOTYPE.
  6. "Mirk/dyrk1B decreases the nuclear accumulation of class II histone deacetylases during skeletal muscle differentiation."
    Deng X., Ewton D.Z., Mercer S.E., Friedman E.
    J. Biol. Chem. 280:4894-4905(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-240, SUBCELLULAR LOCATION.
  7. "Histone deacetylase 9 couples neuronal activity to muscle chromatin acetylation and gene expression."
    Mejat A., Ramond F., Bassel-Duby R., Khochbin S., Olson E.N., Schaeffer L.
    Nat. Neurosci. 8:313-321(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DOWN-REGULATION BY DENERVATION, INTERACTION WITH HDAC1 AND HDAC3, SUBCELLULAR LOCATION.
  8. Cited for: DOWN-REGULATION BY NEURONAL APOPTOSIS, FUNCTION, INTERACTION WITH HDAC1 AND MAPK10.
  9. "Regulation of HDAC9 gene expression by MEF2 establishes a negative-feedback loop in the transcriptional circuitry of muscle differentiation."
    Haberland M., Arnold M.A., McAnally J., Phan D., Kim Y., Olson E.N.
    Mol. Cell. Biol. 27:518-525(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY MEF2, DEVELOPMENTAL STAGE.
  10. "Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2."
    Han A., He J., Wu Y., Liu J.O., Chen L.
    J. Mol. Biol. 345:91-102(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 139-158 IN COMPLEX WITH MEF2 AND DNA.

Entry informationi

Entry nameiHDAC9_MOUSE
AccessioniPrimary (citable) accession number: Q99N13
Secondary accession number(s): Q4QQN7, Q8R4Y6, Q9EPT2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: March 20, 2007
Last modified: July 9, 2014
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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