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Protein

Histone deacetylase 9

Gene

Hdac9

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: 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

  • histone deacetylase activity Source: UniProtKB
  • histone deacetylase binding Source: MGI
  • protein deacetylase activity Source: MGI
  • protein kinase C binding Source: MGI
  • repressing transcription factor binding Source: BHF-UCL
  • transcription corepressor activity Source: MGI
  • transcription factor binding Source: UniProtKB

GO - Biological processi

  • B cell activation Source: UniProtKB
  • B cell differentiation Source: UniProtKB
  • cellular response to insulin stimulus Source: MGI
  • chromatin organization Source: UniProtKB
  • heart development Source: MGI
  • histone deacetylation Source: MGI
  • histone H3 deacetylation Source: MGI
  • histone H4 deacetylation Source: MGI
  • inflammatory response Source: UniProtKB
  • negative regulation of striated muscle tissue development Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • nervous system development Source: UniProtKB
  • peptidyl-lysine deacetylation Source: MGI
  • positive regulation of cell migration involved in sprouting angiogenesis Source: MGI
  • regulation of skeletal muscle fiber development Source: MGI
  • regulation of striated muscle cell differentiation Source: MGI
  • 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
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1931221. Hdac9.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • histone deacetylase complex Source: UniProtKB
  • histone methyltransferase complex Source: BHF-UCL
  • nucleus Source: UniProtKB
  • transcription factor complex Source: MGI
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)DescriptionActionsGraphical viewLength
Mutagenesisi25 – 26DL → AS: Abolishes binding to CTBP1 and impairs function in transcription repression. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001147111 – 588Histone deacetylase 9Add BLAST588

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei22PhosphoserineBy similarity1
Modified residuei220Phosphoserine2 Publications1
Modified residuei240Phosphoserine; by DYRK1B1 Publication1
Modified residuei450Phosphoserine2 Publications1
Modified residuei552PhosphoserineCombined sources1

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.
PeptideAtlasiQ99N13.
PRIDEiQ99N13.

PTM databases

iPTMnetiQ99N13.
PhosphoSitePlusiQ99N13.

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).1 Publication

Gene expression databases

BgeeiENSMUSG00000004698.
CleanExiMM_HDAC9.

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. Interacts with FOXP3 in the absence of T-cell stimulation (By similarity).By similarity4 Publications

Binary interactionsi

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

GO - Molecular functioni

  • histone deacetylase binding Source: MGI
  • protein kinase C binding Source: MGI
  • repressing transcription factor binding Source: BHF-UCL
  • transcription factor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi219748. 8 interactors.
DIPiDIP-41905N.
IntActiQ99N13. 5 interactors.
MINTiMINT-146908.
STRINGi10090.ENSMUSP00000106443.

Structurei

Secondary structure

1588
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi143 – 153Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TQEX-ray2.70X/Y139-158[»]
ProteinModelPortaliQ99N13.
SMRiQ99N13.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ99N13.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni23 – 27Interaction with CTBP11 Publication5
Regioni136 – 154Interaction with MEF2Add BLAST19
Regioni175 – 343Interaction with MAPK101 PublicationAdd BLAST169
Regioni218 – 261Interaction with ETV6By similarityAdd BLAST44

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1343. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000232065.
HOVERGENiHBG057100.
InParanoidiQ99N13.
KOiK11409.
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. AlignAdd to basket

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

        10         20         30         40         50
MHSMISSVDV KSEVPMGLEP ISPLDLRTDL RMMMPVVDPV VREKQLQQEL
60 70 80 90 100
LLIQQQQQIQ KQLLIAEFQK QHENLTRQHQ AQLQEHIKEL LAIKQQQELL
110 120 130 140 150
EKEQKLEQQR QEQEVERHRR EQQLPPLRGK DRGRERAVAS TEVKQKLQEF
160 170 180 190 200
LLSKSATKDT PTNGKNHSVG RHPKLWYTAA HHTSLDQSSP PLSGTSPSYK
210 220 230 240 250
YTLPGAQDSK DDFPLRKTAS EPNLKVRSRL KQKVAERRSS PLLRRKDGNL
260 270 280 290 300
VTSFKKRVFE VAESSVSSSS PGSGPSSPNN GPAGNVTENE ASALPPTPHP
310 320 330 340 350
EQLVPQQRIL IHEDSMNLLS LYTSPSLPNI TLGLPAVPSP LNASNSLKDK
360 370 380 390 400
QKCETQMLRQ GVPLPSQYGS SIAASSSHVH VAMEGKPNSS HQALLQHLLL
410 420 430 440 450
KEQMRQQKLL VAGGVPLHPQ SPLATKERIS PGIRGTHKLP RHRPLNRTQS
460 470 480 490 500
APLPQSTLAQ LVIQQQHQQF LEKQKQYQQQ IHMNKLLSKS IEQLKQPGSH
510 520 530 540 550
LEEAEEELQG DQSMEDRAAS KDNSARSDSS ACVEDTLGQV GAVKVKEEPV
560 570 580
DSDEDAQIQE MECGEQAAFM QQVIGKDLAP GFVIKVII
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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti120R → K in AAK15027 (Ref. 2) Curated1
Sequence conflicti120R → K in AAL86358 (Ref. 2) Curated1
Sequence conflicti136R → K in AAK15027 (Ref. 2) Curated1
Sequence conflicti136R → K in AAL86358 (Ref. 2) Curated1
Sequence conflicti388N → T in AAH98187 (PubMed:15489334).Curated1
Sequence conflicti523N → T in AAG48332 (PubMed:11022042).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_029173177 – 178Missing in isoform 3. 1 Publication2
Alternative sequenceiVSP_023769219 – 262Missing in isoform 2. 1 PublicationAdd BLAST44

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TQEX-ray2.70X/Y139-158[»]
ProteinModelPortaliQ99N13.
SMRiQ99N13.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi219748. 8 interactors.
DIPiDIP-41905N.
IntActiQ99N13. 5 interactors.
MINTiMINT-146908.
STRINGi10090.ENSMUSP00000106443.

PTM databases

iPTMnetiQ99N13.
PhosphoSitePlusiQ99N13.

Proteomic databases

PaxDbiQ99N13.
PeptideAtlasiQ99N13.
PRIDEiQ99N13.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi9734.
MGIiMGI:1931221. Hdac9.

Phylogenomic databases

eggNOGiKOG1343. Eukaryota.
COG0123. LUCA.
HOGENOMiHOG000232065.
HOVERGENiHBG057100.
InParanoidiQ99N13.
KOiK11409.
PhylomeDBiQ99N13.
TreeFamiTF106174.

Miscellaneous databases

EvolutionaryTraceiQ99N13.
PROiQ99N13.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000004698.
CleanExiMM_HDAC9.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 139 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

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 one 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.