ID Q08BS8_DANRE Unreviewed; 1023 AA.
AC Q08BS8;
DT 31-OCT-2006, integrated into UniProtKB/TrEMBL.
DT 31-OCT-2006, sequence version 1.
DT 27-MAR-2024, entry version 122.
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=hdac4 {ECO:0000313|ZFIN:ZDB-GENE-061013-95};
GN Synonyms=wu:fa96d08 {ECO:0000313|RefSeq:NP_001034447.2}, wu:fc56f08
GN {ECO:0000313|RefSeq:NP_001034447.2}, zgc:152701
GN {ECO:0000313|EMBL:AAI24584.1, ECO:0000313|RefSeq:NP_001034447.2};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000313|EMBL:AAI24584.1};
RN [1] {ECO:0000313|EMBL:AAI24584.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Olfactory epithelium {ECO:0000313|EMBL:AAI24584.1}, and PCR
RC rescue {ECO:0000313|EMBL:AAI65681.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=22676467;
RA DeLaurier A., Nakamura Y., Braasch I., Khanna V., Kato H., Wakitani S.,
RA Postlethwait J.H., Kimmel C.B.;
RT "Histone deacetylase-4 is required during early cranial neural crest
RT development for generation of the zebrafish palatal skeleton.";
RL BMC Dev. Biol. 12:16-16(2012).
RN [3] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=21773810;
RA Zhu K., Wang H., Gul Y., Zhao Y., Wang W., Liu S., Wang M.;
RT "Expression characterization and the promoter activity analysis of
RT zebrafish hdac4.";
RL Fish Physiol. Biochem. 38:585-593(2012).
RN [4] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=24240475;
RA Huang H.T., Kathrein K.L., Barton A., Gitlin Z., Huang Y.H., Ward T.P.,
RA Hofmann O., Dibiase A., Song A., Tyekucheva S., Hide W., Zhou Y., Zon L.I.;
RT "A network of epigenetic regulators guides developmental haematopoiesis in
RT vivo.";
RL Nat. Cell Biol. 15:1516-1525(2013).
RN [5] {ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=23594743; DOI=10.1038/nature12111;
RG Genome Reference Consortium Zebrafish;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Eliott D.,
RA Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Mortimer B.,
RA Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M.,
RA Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M.,
RA Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J.,
RA Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D.,
RA Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K.,
RA Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R.,
RA Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M.,
RA Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D.,
RA Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M.,
RA Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M.,
RA Woodmansey R., Clark G., Cooper J., Cooper J., Tromans A., Grafham D.,
RA Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J.,
RA Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I.,
RA Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G., Osoegawa K., Zhu B.,
RA Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P.,
RA Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R.,
RA Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I.,
RA Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H.,
RA Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [6] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=25603810; DOI=10.1186/1752-0509-8-s5-s6;
RA Lin C., Lin C.N., Wang Y.C., Liu F.Y., Chien Y.W., Chuang Y.J., Lan C.Y.,
RA Hsieh W.P., Chen B.S.;
RT "Robustness analysis on interspecies interaction network for iron and
RT glucose competition between Candida albicans and zebrafish during
RT infection.";
RL BMC Syst. Biol. 8:S6-S6(2014).
RN [7] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=25189256;
RA Li Y., Wang J., Xie Y., Liu S., Tian Y.;
RT "Pattern of change in histone 3 lysine 9 acetylation and histone
RT deacetylases in development of zebrafish embryo.";
RL J. Genet. 93:539-544(2014).
RN [8] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=29633426;
RA Rothschild S.C., Lee H.J., Ingram S.R., Mohammadi D.K., Walsh G.S.,
RA Tombes R.M.;
RT "Calcium signals act through histone deacetylase to mediate pronephric
RT kidney morphogenesis.";
RL Dev. Dyn. 247:807-817(2018).
RN [9] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=29027256;
RA Zhang L., Jin Y., Han Z., Liu H., Shi L., Hua X., Doering J.A., Tang S.,
RA Giesy J.P., Yu H.;
RT "Integrated in silico and in vivo approaches to investigate effects of BDE-
RT 99 mediated by the nuclear receptors on developing zebrafish.";
RL Environ. Toxicol. Chem. 37:780-787(2018).
RN [10] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=30267687; DOI=10.1016/j.isci.2018.08.008;
RA Mitra S., Sharma P., Kaur S., Khursheed M.A., Gupta S., Ahuja R.,
RA Kurup A.J., Chaudhary M., Ramachandran R.;
RT "Histone Deacetylase-Mediated Muller Glia Reprogramming through Her4.1-
RT Lin28a Axis Is Essential for Retina Regeneration in Zebrafish.";
RL IScience 7:68-84(2018).
RN [11] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=30615915;
RA Fellous A., Earley R.L., Silvestre F.;
RT "Identification and expression of mangrove rivulus (Kryptolebias
RT marmoratus) histone deacetylase (HDAC) and lysine acetyltransferase (KAT)
RT genes.";
RL Gene 691:56-69(2019).
RN [12] {ECO:0000313|RefSeq:NP_001034447.2}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=30643696;
RA DeLaurier A., Alvarez C.L., Wiggins K.J.;
RT "hdac4 mediates perichondral ossification and pharyngeal skeleton
RT development in the zebrafish.";
RL PeerJ 7:e6167-e6167(2019).
RN [13] {ECO:0000313|RefSeq:NP_001034447.2}
RP IDENTIFICATION.
RG RefSeq;
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|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; BC124583; AAI24584.1; -; mRNA.
DR EMBL; BC165681; AAI65681.1; -; mRNA.
DR RefSeq; NP_001034447.2; NM_001039358.2.
DR GeneID; 568877; -.
DR KEGG; dre:568877; -.
DR AGR; ZFIN:ZDB-GENE-061013-95; -.
DR CTD; 9759; -.
DR ZFIN; ZDB-GENE-061013-95; hdac4.
DR OrthoDB; 124800at2759; -.
DR Proteomes; UP000000437; Chromosome 9.
DR GO; GO:0000118; C:histone deacetylase complex; IEA:UniProtKB-UniRule.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0048701; P:embryonic cranial skeleton morphogenesis; IMP:ZFIN.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IEA:InterPro.
DR GO; GO:0001755; P:neural crest cell migration; IMP:ZFIN.
DR GO; GO:0036073; P:perichondral ossification; IMP:ZFIN.
DR GO; GO:0072114; P:pronephros morphogenesis; IMP:ZFIN.
DR GO; GO:0090299; P:regulation of neural crest formation; IMP:ZFIN.
DR GO; GO:0050896; P:response to stimulus; IEA:UniProt.
DR CDD; cd10162; ClassIIa_HDAC4_Gln-rich-N; 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:SF11; HISTONE DEACETYLASE; 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 1: Evidence at protein level;
KW Chromatin regulator {ECO:0000256|PIRNR:PIRNR037911};
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Hydrolase {ECO:0000256|PIRNR:PIRNR037911};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR037911-2};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242};
KW Proteomics identification {ECO:0007829|PeptideAtlas:Q08BS8};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437};
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 33..122
FT /note="Histone deacetylase glutamine rich N-terminal"
FT /evidence="ECO:0000259|Pfam:PF12203"
FT DOMAIN 620..931
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 175..287
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 472..526
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1004..1023
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 60..128
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 175..195
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 205..248
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 262..287
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 474..499
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 512..526
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1007..1023
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 742
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-1"
FT BINDING 612
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 614
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 620
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 690
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT SITE 915
FT /note="Contributes to catalysis"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-3"
SQ SEQUENCE 1023 AA; 113241 MW; 1636BF7564839C8E CRC64;
MVDVSVALPL QVPPSAIPMD LRVDHQFALA PTDPAQREHQ LQQELLALKQ KQQIQRQLLI
EEFQRQHEQL SRQHEAQLQE HVKHQQDLLA LKHQQELLEH QRKLGRHRQE QEMEKQQREQ
KLQLLKNKER GQESAVASTE VKMRLQEFVL NKKKALAQRS LNHCLPSDPR YWYGKTQHSS
LDQSSPPQTG ISTYNHPVLG MYDPKDDFPL RKTASEPNLK LRSRLKQKVS ERRSSPLLRR
KDGPITTAKK RSLDMAESAC SSAPGSGPSS PNNSSNNITN ENGIAGSISN SAVEPSLAHR
LTGREGPVSQ LSLYTSPSLP NITLGLPATG PSSVASGQQD GDRMAVPGLQ PGIPITTPFM
PGAHLPSYLA ASSLERESGS AHNTLLQHMV LLEQSAAQNS LVAGLSGVPL QSHSIHKLRQ
HRPLGRTQSA PLPQNSQALQ QLVVQQQHQQ FLEKHKQQFQ QQQLHISKMM VKPSEPNRQH
ESHPEETEEE LREHQGLGDP ADPLPHGVTI KQEPPDEQDE DFQQRERQAE EELLFRQQAL
LLEQQRIHQL RNYQASMEAA GLSVSFPVHR PLSRAQSSPA SATFPIVVQE PPAKPRFTTG
LVYDTLMQKH QCMCGNSNIH PEHAGRIQSI WSRLQETGLR GQCECIRGRK ATLEELQTVH
SEAHVLLYGT NPLRQKLDSS VTPMFVRLPC GGIGVDSDTI WNEVHSSSAA RLAVGSVVDL
VFKVASGELR NGFAVVRPPG HHAEESTPMG FCYFNSVAIA AKLLQQRLNV SKILIVDWDV
HHGNGTQQAF YSDPNVLYLS LHRYDDGNFF PGSGAPDEVG IGPGVGFNVN MAFTGGLEPP
MGDADYLAAF RSVVMPIANE FSPDVVLVSS GFDAVEGHPP PLGGYKLTAK CFGYLTKQLM
GLAGGRLVLA LEGGHDLTAI CDASEACVSA LLGNELDPIP EDILQQRPNA NAIQSMEKVL
EVQSKYWRSL QRSVSTLGYS LREAQRCENE EAETVTAMAS LSVANKHMGK RPEEEPMEEE
PPL
//
