ID E5RQ38_RAT Unreviewed; 1068 AA.
AC E5RQ38; F1MA74;
DT 08-MAR-2011, integrated into UniProtKB/TrEMBL.
DT 08-MAR-2011, sequence version 1.
DT 27-MAR-2024, entry version 101.
DE RecName: Full=Histone deacetylase {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037911};
DE EC=3.5.1.98 {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037911};
GN Name=Hdac9 {ECO:0000313|Ensembl:ENSRNOP00000005521.6,
GN ECO:0000313|RGD:1310748};
GN Synonyms=HDAC9 {ECO:0000313|EMBL:BAJ52888.1}, LOC687001
GN {ECO:0000313|RGD:1310748};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116 {ECO:0000313|EMBL:BAJ52888.1};
RN [1] {ECO:0000313|Ensembl:ENSRNOP00000005521.6, ECO:0000313|Proteomes:UP000002494}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway {ECO:0000313|Ensembl:ENSRNOP00000005521.6,
RC ECO:0000313|Proteomes:UP000002494};
RX PubMed=15057822; DOI=10.1038/nature02426;
RG Rat Genome Sequencing Project Consortium;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2] {ECO:0000313|EMBL:BAJ52888.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Wistar {ECO:0000313|EMBL:BAJ52888.1};
RC TISSUE=Liver {ECO:0000313|EMBL:BAJ52888.1};
RA Osada S., Yura T., Hashizume H., Suzuki E., Imagawa M.;
RT "Promotion of anchorage-independent growth by cytoplasmic and nuclear
RT histone deacetylase 9.";
RL Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|Ensembl:ENSRNOP00000005521.6}
RP IDENTIFICATION.
RC STRAIN=Brown Norway {ECO:0000313|Ensembl:ENSRNOP00000005521.6};
RG Ensembl;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone
CC deacetylation gives a tag for epigenetic repression and plays an
CC important role in transcriptional regulation, cell cycle progression
CC and developmental events. {ECO:0000256|PIRNR:PIRNR037911}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-
CC [histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA-
CC COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:61930; EC=3.5.1.98;
CC Evidence={ECO:0000256|ARBA:ARBA00001028,
CC ECO:0000256|PIRNR:PIRNR037911};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|PIRNR:PIRNR037911}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC subfamily. {ECO:0000256|ARBA:ARBA00007738,
CC ECO:0000256|PIRNR:PIRNR037911}.
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DR EMBL; AB558551; BAJ52888.1; -; mRNA.
DR RefSeq; NP_001186974.1; NM_001200045.1.
DR STRING; 10116.ENSRNOP00000005521; -.
DR PaxDb; 10116-ENSRNOP00000005521; -.
DR Ensembl; ENSRNOT00000005521.8; ENSRNOP00000005521.6; ENSRNOG00000004158.8.
DR GeneID; 687001; -.
DR KEGG; rno:687001; -.
DR AGR; RGD:1310748; -.
DR CTD; 9734; -.
DR RGD; 1310748; Hdac9.
DR eggNOG; KOG1343; Eukaryota.
DR GeneTree; ENSGT00940000160307; -.
DR HOGENOM; CLU_006530_2_0_1; -.
DR OMA; EYLEAFX; -.
DR OrthoDB; 124800at2759; -.
DR TreeFam; TF106174; -.
DR Reactome; R-RNO-350054; Notch-HLH transcription pathway.
DR Proteomes; UP000002494; Chromosome 6.
DR Bgee; ENSRNOG00000004158; Expressed in spleen and 15 other cell types or tissues.
DR GO; GO:0005737; C:cytoplasm; ISO:RGD.
DR GO; GO:0000118; C:histone deacetylase complex; IEA:UniProtKB-UniRule.
DR GO; GO:0035097; C:histone methyltransferase complex; ISO:RGD.
DR GO; GO:0005634; C:nucleus; ISO:RGD.
DR GO; GO:0005667; C:transcription regulator complex; ISO:RGD.
DR GO; GO:0140297; F:DNA-binding transcription factor binding; ISO:RGD.
DR GO; GO:0004407; F:histone deacetylase activity; ISO:RGD.
DR GO; GO:0042826; F:histone deacetylase binding; ISO:RGD.
DR GO; GO:0031078; F:histone H3K14 deacetylase activity; ISO:RGD.
DR GO; GO:0032129; F:histone H3K9 deacetylase activity; ISO:RGD.
DR GO; GO:0034739; F:histone H4K16 deacetylase activity; ISO:RGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0005080; F:protein kinase C binding; ISO:RGD.
DR GO; GO:0033558; F:protein lysine deacetylase activity; ISO:RGD.
DR GO; GO:0061629; F:RNA polymerase II-specific DNA-binding transcription factor binding; ISO:RGD.
DR GO; GO:0003714; F:transcription corepressor activity; ISO:RGD.
DR GO; GO:0032869; P:cellular response to insulin stimulus; ISO:RGD.
DR GO; GO:0042632; P:cholesterol homeostasis; ISO:RGD.
DR GO; GO:0008340; P:determination of adult lifespan; ISO:RGD.
DR GO; GO:0006281; P:DNA repair; ISO:RGD.
DR GO; GO:0007507; P:heart development; ISO:RGD.
DR GO; GO:0001818; P:negative regulation of cytokine production; ISO:RGD.
DR GO; GO:0045892; P:negative regulation of DNA-templated transcription; ISO:RGD.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0030182; P:neuron differentiation; IEP:RGD.
DR GO; GO:0090050; P:positive regulation of cell migration involved in sprouting angiogenesis; ISO:RGD.
DR GO; GO:0048742; P:regulation of skeletal muscle fiber development; ISO:RGD.
DR GO; GO:1902809; P:regulation of skeletal muscle fiber differentiation; ISO:RGD.
DR GO; GO:0001975; P:response to amphetamine; IEP:RGD.
DR CDD; cd10163; ClassIIa_HDAC9_Gln-rich-N; 1.
DR CDD; cd11681; HDAC_classIIa; 1.
DR Gene3D; 6.10.250.1550; -; 1.
DR Gene3D; 3.40.800.20; Histone deacetylase domain; 1.
DR InterPro; IPR046949; HDAC4/5/7/9.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR024643; Hist_deacetylase_Gln_rich_N.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR PANTHER; PTHR45364:SF12; HISTONE DEACETYLASE 9; 1.
DR PANTHER; PTHR45364; HISTONE DEACETYLASE 9-RELATED; 1.
DR Pfam; PF12203; HDAC4_Gln; 1.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037911; HDAC_II_euk; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; Arginase/deacetylase; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator {ECO:0000256|PIRNR:PIRNR037911};
KW Hydrolase {ECO:0000256|PIRNR:PIRNR037911};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR037911-2};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242};
KW Reference proteome {ECO:0000313|Proteomes:UP000002494};
KW Repressor {ECO:0000256|PIRNR:PIRNR037911};
KW Transcription {ECO:0000256|PIRNR:PIRNR037911};
KW Transcription regulation {ECO:0000256|PIRNR:PIRNR037911};
KW Zinc {ECO:0000256|PIRSR:PIRSR037911-2}.
FT DOMAIN 37..127
FT /note="Histone deacetylase glutamine rich N-terminal"
FT /evidence="ECO:0000259|Pfam:PF12203"
FT DOMAIN 656..974
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 113..173
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 186..245
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 267..304
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 497..554
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1049..1068
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 113..145
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 149..170
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 186..206
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 213..245
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 267..295
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 499..526
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 785
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-1"
FT BINDING 648
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 650
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 656
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 733
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT SITE 958
FT /note="Contributes to catalysis"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-3"
SQ SEQUENCE 1068 AA; 116979 MW; 0ADAE2EF3E292714 CRC64;
MHSMISSVDV KSEVPMGLEP ISPLDLRTDL RMMMPVVDPV VREKQLQQEL LLIQQQQQIQ
KQLLIAEFQK QHENLTRQHQ AQLQEHIKLQ QELLAIKQQQ ELLEKEQKLE QQRQEQEVER
HRREQQLPPL RGKDRGRERA VASTEVKQKL QEFLLSKSAT KDTPTNGKNH SVGRHPKLWY
TAAHHTSLDQ SSPPLSGTSP SYKYTLPGAQ DTKDDFPLRK TASEPNLKVR SRLKQKVAER
RSSPLLRRKD GNLVTSFKKR VFEVAESSVS SSSPGSGPSS PNNGPAGNVT ENEASVLPPT
PHPEQLVPQQ RILIHEDSMN LLSLYTSPSL PNITLGLPAV PSPLSASNSL KDKQKCETQM
LRQGVPLPGQ YGSGIAASSS HAHVAMEGKP NSSHQALLQH LLLKEQMRQQ KLLVAGGVPL
HPQSPLATKE RISPGIRGTH KLPRHRPLNR TQSAPLPQST LAQLVIQQQH QQFLEKQKQY
QQQIHMNKLL SKSIEQLKQP GSHLEEAEEE LQGDQAMEER ATSKDSGTGK DSSACVEDTL
GQVGAVKVKE EPVDSDEDAQ MQEMECGEQA AFMQQTPLLE SSHTRALSVH QARLAAAGID
GLEKHGLLSR THSSPAPSMS PHPAADCPRQ PASATGIAYD CLMLKHQCIC GNSTTHPEHA
GRIQSIWSRL QETGLLNKCE RIQGRKASLE EIQLVHSEHH SLLYGTSPLD GQKLDPRTLL
GDDSRKFFSS LPCGGLGVDS DTIWNELHSS GAARMAVGCV IELASKVASG ELKNGFAVVR
PPGHHAEESA AMGFCFFNSV AITAKYLRDQ LNISKILIVD LDVHHGNGTQ QAFYADPSIL
YISLHRYDEG NFFPGSGAPN EVGVGLGEGY NVNIAWTGGL DPPMGDVEYL EAFRTVVMPV
AREFDPDMVL VSAGFDALEG HTPPLGGYKV TAKCFGHLTK QLMTLANGRV ALALEGGHDL
TAICDASEAC INALLGNEPG SLEEDVLHQS VNTNAAASLQ KTIEIQSKYW KSIKMVAVAR
GCALPASQLQ EETETVSALA SLTVDVEQPF AQEDGRTAGE PMEEEPAL
//
