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Histone deacetylase 9 (HD9) (EC 3.5.1.98) (Histone deacetylase 7B) (HD7b) (Histone deacetylase-related protein) (MEF2-interacting transcription repressor MITR)

 HDAC9_MOUSE             Reviewed;         588 AA.
Q99N13; Q4QQN7; Q8R4Y6; Q9EPT2;
18-OCT-2001, integrated into UniProtKB/Swiss-Prot.
20-MAR-2007, sequence version 2.
28-MAR-2018, entry version 147.
RecName: Full=Histone deacetylase 9;
Short=HD9;
EC=3.5.1.98;
AltName: Full=Histone deacetylase 7B;
Short=HD7b;
AltName: Full=Histone deacetylase-related protein;
AltName: Full=MEF2-interacting transcription repressor MITR;
Name=Hdac9; Synonyms=Hdac7b, Hdrp, Mitr;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), HOMODIMERIZATION, INTERACTION
WITH CTBP1; HDAC1; HDAC3; HDAC4 AND HDAC5, AND MUTAGENESIS OF
25-ASP-LEU-26.
STRAIN=NIH Swiss; TISSUE=Embryonic heart;
PubMed=11022042; DOI=10.1074/jbc.M007364200;
Zhang C.L., McKinsey T.A., Lu J.R., Olson E.N.;
"Association of COOH-terminal-binding protein (CtBP) and MEF2-
interacting transcription repressor (MITR) contributes to
transcriptional repression of the MEF2 transcription factor.";
J. Biol. Chem. 276:35-39(2001).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
STRAIN=Swiss Webster / NIH;
Zhou X., Richon V.M., Rifkind R.A., Marks P.A.;
"Cloning of the mouse HDRP cDNA.";
Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=C57BL/6J; TISSUE=Retina;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
FUNCTION, PHOSPHORYLATION AT SER-220 AND SER-450, TISSUE SPECIFICITY,
DEVELOPMENTAL STAGE, AND SUBCELLULAR LOCATION.
PubMed=11390982; DOI=10.1073/pnas.131198498;
Zhang C.L., McKinsey T.A., Olson E.N.;
"The transcriptional corepressor MITR is a signal-responsive inhibitor
of myogenesis.";
Proc. Natl. Acad. Sci. U.S.A. 98:7354-7359(2001).
[5]
PHOSPHORYLATION AT SER-220 AND SER-450, FUNCTION, AND DISRUPTION
PHENOTYPE.
PubMed=12202037; DOI=10.1016/S0092-8674(02)00861-9;
Zhang C.L., McKinsey T.A., Chang S., Antos C.L., Hill J.A.,
Olson E.N.;
"Class II histone deacetylases act as signal-responsive repressors of
cardiac hypertrophy.";
Cell 110:479-488(2002).
[6]
PHOSPHORYLATION AT SER-240, AND SUBCELLULAR LOCATION.
PubMed=15546868; DOI=10.1074/jbc.M411894200;
Deng X., Ewton D.Z., Mercer S.E., Friedman E.;
"Mirk/dyrk1B decreases the nuclear accumulation of class II histone
deacetylases during skeletal muscle differentiation.";
J. Biol. Chem. 280:4894-4905(2005).
[7]
FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DOWN-REGULATION BY
DENERVATION, INTERACTION WITH HDAC1 AND HDAC3, AND SUBCELLULAR
LOCATION.
PubMed=15711539; DOI=10.1038/nn1408;
Mejat A., Ramond F., Bassel-Duby R., Khochbin S., Olson E.N.,
Schaeffer L.;
"Histone deacetylase 9 couples neuronal activity to muscle chromatin
acetylation and gene expression.";
Nat. Neurosci. 8:313-321(2005).
[8]
DOWN-REGULATION BY NEURONAL APOPTOSIS, FUNCTION, AND INTERACTION WITH
HDAC1 AND MAPK10.
PubMed=16611996; DOI=10.1128/MCB.26.9.3550-3564.2006;
Morrison B.E., Majdzadeh N., Zhang X., Lyles A., Bassel-Duby R.,
Olson E.N., D'Mello S.R.;
"Neuroprotection by histone deacetylase-related protein.";
Mol. Cell. Biol. 26:3550-3564(2006).
[9]
INDUCTION BY MEF2, AND DEVELOPMENTAL STAGE.
PubMed=17101791; DOI=10.1128/MCB.01415-06;
Haberland M., Arnold M.A., McAnally J., Phan D., Kim Y., Olson E.N.;
"Regulation of HDAC9 gene expression by MEF2 establishes a negative-
feedback loop in the transcriptional circuitry of muscle
differentiation.";
Mol. Cell. Biol. 27:518-525(2007).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-552, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Brain;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[11]
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 139-158 IN COMPLEX WITH MEF2
AND DNA.
PubMed=15567413; DOI=10.1016/j.jmb.2004.10.033;
Han A., He J., Wu Y., Liu J.O., Chen L.;
"Mechanism of recruitment of class II histone deacetylases by myocyte
enhancer factor-2.";
J. Mol. Biol. 345:91-102(2005).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:11390982, ECO:0000269|PubMed:12202037,
ECO:0000269|PubMed:15711539, ECO:0000269|PubMed:16611996}.
-!- CATALYTIC ACTIVITY: Hydrolysis of an N(6)-acetyl-lysine residue of
a histone to yield a deacetylated histone.
-!- SUBUNIT: 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).
{ECO:0000250|UniProtKB:Q9UKV0, ECO:0000269|PubMed:11022042,
ECO:0000269|PubMed:15567413, ECO:0000269|PubMed:15711539,
ECO:0000269|PubMed:16611996}.
-!- INTERACTION:
P60335:Pcbp1; NbExp=6; IntAct=EBI-645361, EBI-309059;
Q3TKT4:Smarca4; NbExp=3; IntAct=EBI-645361, EBI-1210244;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11390982,
ECO:0000269|PubMed:15546868, ECO:0000269|PubMed:15711539}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q99N13-1; Sequence=Displayed;
Name=2; Synonyms=Hdrpa;
IsoId=Q99N13-2; Sequence=VSP_023769;
Note=No experimental confirmation available.;
Name=3;
IsoId=Q99N13-3; Sequence=VSP_029173;
-!- TISSUE SPECIFICITY: Expressed at high levels in heart, brain and
spleen. Expressed in skeletal muscle.
{ECO:0000269|PubMed:11390982, ECO:0000269|PubMed:15711539}.
-!- DEVELOPMENTAL STAGE: 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. {ECO:0000269|PubMed:11390982,
ECO:0000269|PubMed:15711539, ECO:0000269|PubMed:17101791}.
-!- INDUCTION: 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).
{ECO:0000269|PubMed:17101791}.
-!- PTM: Sumoylated. {ECO:0000250}.
-!- PTM: 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.
{ECO:0000269|PubMed:11390982, ECO:0000269|PubMed:12202037,
ECO:0000269|PubMed:15546868}.
-!- DISRUPTION PHENOTYPE: Mice do not present any abnormality at early
age but develop cardiac hypertrophy by eight months of age.
{ECO:0000269|PubMed:12202037}.
-!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AF324492; AAG48332.1; -; mRNA.
EMBL; AF235053; AAK15027.1; -; mRNA.
EMBL; AF279371; AAL86358.1; -; mRNA.
EMBL; BC098187; AAH98187.1; -; mRNA.
CCDS; CCDS36432.1; -. [Q99N13-1]
RefSeq; NP_077038.2; NM_024124.3.
UniGene; Mm.310551; -.
UniGene; Mm.483009; -.
PDB; 1TQE; X-ray; 2.70 A; X/Y=139-158.
PDBsum; 1TQE; -.
ProteinModelPortal; Q99N13; -.
SMR; Q99N13; -.
BioGrid; 219748; 9.
DIP; DIP-41905N; -.
ELM; Q99N13; -.
IntAct; Q99N13; 7.
STRING; 10090.ENSMUSP00000106443; -.
ChEMBL; CHEMBL3832944; -.
iPTMnet; Q99N13; -.
PhosphoSitePlus; Q99N13; -.
PaxDb; Q99N13; -.
PeptideAtlas; Q99N13; -.
PRIDE; Q99N13; -.
GeneID; 79221; -.
KEGG; mmu:79221; -.
UCSC; uc007nja.1; mouse. [Q99N13-3]
UCSC; uc007njb.1; mouse. [Q99N13-2]
UCSC; uc007njc.2; mouse. [Q99N13-1]
CTD; 9734; -.
MGI; MGI:1931221; Hdac9.
eggNOG; KOG1343; Eukaryota.
eggNOG; COG0123; LUCA.
HOGENOM; HOG000232065; -.
HOVERGEN; HBG057100; -.
InParanoid; Q99N13; -.
KO; K11409; -.
PhylomeDB; Q99N13; -.
TreeFam; TF106174; -.
EvolutionaryTrace; Q99N13; -.
PRO; PR:Q99N13; -.
Proteomes; UP000000589; Unplaced.
CleanEx; MM_HDAC9; -.
GO; GO:0005737; C:cytoplasm; ISO:MGI.
GO; GO:0000118; C:histone deacetylase complex; TAS:UniProtKB.
GO; GO:0035097; C:histone methyltransferase complex; IDA:BHF-UCL.
GO; GO:0005634; C:nucleus; ISO:MGI.
GO; GO:0005667; C:transcription factor complex; ISO:MGI.
GO; GO:0004407; F:histone deacetylase activity; TAS:UniProtKB.
GO; GO:0042826; F:histone deacetylase binding; ISO:MGI.
GO; GO:0033558; F:protein deacetylase activity; ISO:MGI.
GO; GO:0005080; F:protein kinase C binding; ISO:MGI.
GO; GO:0070491; F:repressing transcription factor binding; IPI:BHF-UCL.
GO; GO:0003714; F:transcription corepressor activity; IDA:MGI.
GO; GO:0008134; F:transcription factor binding; ISO:MGI.
GO; GO:0042113; P:B cell activation; TAS:UniProtKB.
GO; GO:0030183; P:B cell differentiation; TAS:UniProtKB.
GO; GO:0032869; P:cellular response to insulin stimulus; ISO:MGI.
GO; GO:0006325; P:chromatin organization; TAS:UniProtKB.
GO; GO:0007507; P:heart development; IGI:MGI.
GO; GO:0016575; P:histone deacetylation; ISO:MGI.
GO; GO:0070932; P:histone H3 deacetylation; ISO:MGI.
GO; GO:0070933; P:histone H4 deacetylation; ISO:MGI.
GO; GO:0006954; P:inflammatory response; TAS:UniProtKB.
GO; GO:0045843; P:negative regulation of striated muscle tissue development; TAS:UniProtKB.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:MGI.
GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:MGI.
GO; GO:0007399; P:nervous system development; TAS:UniProtKB.
GO; GO:0034983; P:peptidyl-lysine deacetylation; ISO:MGI.
GO; GO:0090050; P:positive regulation of cell migration involved in sprouting angiogenesis; ISO:MGI.
GO; GO:0048742; P:regulation of skeletal muscle fiber development; IGI:MGI.
GO; GO:0051153; P:regulation of striated muscle cell differentiation; IGI:MGI.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR024643; Hist_deacetylase_Gln_rich_N.
Pfam; PF12203; HDAC4_Gln; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chromatin regulator;
Complete proteome; Hydrolase; Nucleus; Phosphoprotein;
Reference proteome; Repressor; Transcription;
Transcription regulation; Ubl conjugation.
CHAIN 1 588 Histone deacetylase 9.
/FTId=PRO_0000114711.
REGION 23 27 Interaction with CTBP1.
{ECO:0000269|PubMed:11022042}.
REGION 136 154 Interaction with MEF2.
REGION 175 343 Interaction with MAPK10.
{ECO:0000269|PubMed:16611996}.
REGION 218 261 Interaction with ETV6. {ECO:0000250}.
MOD_RES 22 22 Phosphoserine.
{ECO:0000250|UniProtKB:Q9UKV0}.
MOD_RES 220 220 Phosphoserine.
{ECO:0000269|PubMed:11390982,
ECO:0000269|PubMed:12202037}.
MOD_RES 240 240 Phosphoserine; by DYRK1B.
{ECO:0000269|PubMed:15546868}.
MOD_RES 450 450 Phosphoserine.
{ECO:0000269|PubMed:11390982,
ECO:0000269|PubMed:12202037}.
MOD_RES 552 552 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
VAR_SEQ 177 178 Missing (in isoform 3).
{ECO:0000303|PubMed:11022042}.
/FTId=VSP_029173.
VAR_SEQ 219 262 Missing (in isoform 2).
{ECO:0000303|Ref.2}.
/FTId=VSP_023769.
MUTAGEN 25 26 DL->AS: Abolishes binding to CTBP1 and
impairs function in transcription
repression.
{ECO:0000269|PubMed:11022042}.
CONFLICT 120 120 R -> K (in Ref. 2; AAK15027/AAL86358).
{ECO:0000305}.
CONFLICT 136 136 R -> K (in Ref. 2; AAK15027/AAL86358).
{ECO:0000305}.
CONFLICT 388 388 N -> T (in Ref. 3; AAH98187).
{ECO:0000305}.
CONFLICT 523 523 N -> T (in Ref. 1; AAG48332).
{ECO:0000305}.
HELIX 143 153 {ECO:0000244|PDB:1TQE}.
SEQUENCE 588 AA; 65687 MW; 4ED7FA9F02BD4621 CRC64;
MHSMISSVDV KSEVPMGLEP ISPLDLRTDL RMMMPVVDPV VREKQLQQEL LLIQQQQQIQ
KQLLIAEFQK QHENLTRQHQ AQLQEHIKEL LAIKQQQELL EKEQKLEQQR QEQEVERHRR
EQQLPPLRGK DRGRERAVAS TEVKQKLQEF LLSKSATKDT PTNGKNHSVG RHPKLWYTAA
HHTSLDQSSP PLSGTSPSYK YTLPGAQDSK DDFPLRKTAS EPNLKVRSRL KQKVAERRSS
PLLRRKDGNL VTSFKKRVFE VAESSVSSSS PGSGPSSPNN GPAGNVTENE ASALPPTPHP
EQLVPQQRIL IHEDSMNLLS LYTSPSLPNI TLGLPAVPSP LNASNSLKDK QKCETQMLRQ
GVPLPSQYGS SIAASSSHVH VAMEGKPNSS HQALLQHLLL KEQMRQQKLL VAGGVPLHPQ
SPLATKERIS PGIRGTHKLP RHRPLNRTQS APLPQSTLAQ LVIQQQHQQF LEKQKQYQQQ
IHMNKLLSKS IEQLKQPGSH LEEAEEELQG DQSMEDRAAS KDNSARSDSS ACVEDTLGQV
GAVKVKEEPV DSDEDAQIQE MECGEQAAFM QQVIGKDLAP GFVIKVII


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