HDA4_CAEEL
ID HDA4_CAEEL Reviewed; 869 AA.
AC O17323; H1ZUW2; Q400M0;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 3.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Histone deacetylase 4;
DE EC=3.5.1.98;
DE AltName: Full=CeHDA-7;
DE AltName: Full=Histone deacetylase 7;
GN Name=hda-4; Synonyms=hda-7; ORFNames=C10E2.3;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B), TISSUE SPECIFICITY, AND INTERACTION
RP WITH MEF-2 (ISOFORM B).
RC STRAIN=Bristol N2;
RX PubMed=12054517; DOI=10.1016/s0006-291x(02)00374-1;
RA Choi K.Y., Ji Y.J., Jee C., Kim do H., Ahnn J.;
RT "Characterization of CeHDA-7, a class II histone deacetylase interacting
RT with MEF-2 in Caenorhabditis elegans.";
RL Biochem. Biophys. Res. Commun. 293:1295-1300(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE SPLICING.
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3] {ECO:0000305}
RP FUNCTION, PHOSPHORYLATION AT SER-251, AND MUTAGENESIS OF 80-GLN--THR-869
RP AND SER-251.
RX PubMed=17170704; DOI=10.1038/sj.emboj.7601479;
RA van der Linden A.M., Nolan K.M., Sengupta P.;
RT "KIN-29 SIK regulates chemoreceptor gene expression via an MEF2
RT transcription factor and a class II HDAC.";
RL EMBO J. 26:358-370(2007).
RN [4] {ECO:0000305}
RP FUNCTION, PHOSPHORYLATION, AND MUTAGENESIS OF SER-416 AND SER-515.
RX PubMed=18832350; DOI=10.1534/genetics.108.094771;
RA van der Linden A.M., Wiener S., You Y.J., Kim K., Avery L., Sengupta P.;
RT "The EGL-4 PKG acts with KIN-29 salt-inducible kinase and protein kinase A
RT to regulate chemoreceptor gene expression and sensory behaviors in
RT Caenorhabditis elegans.";
RL Genetics 180:1475-1491(2008).
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4) (By
CC similarity). Histone deacetylation gives a tag for epigenetic
CC repression and plays an important role in transcriptional regulation,
CC cell cycle progression and developmental events (By similarity).
CC Histone deacetylases act via the formation of large multiprotein
CC complexes (By similarity). Involved in transduction of sensory signals,
CC together with egl-4, kin-29 and mef-2; binding to transcription factor
CC mef-2 enables negative modulation of chemoreceptor gene expression in
CC chemosensory neurons (PubMed:17170704, PubMed:18832350). May be
CC involved in muscle development (By similarity).
CC {ECO:0000250|UniProtKB:P56524, ECO:0000269|PubMed:17170704,
CC ECO:0000269|PubMed:18832350}.
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 -!- SUBUNIT: [Isoform b]: Interacts with mef-2.
CC {ECO:0000269|PubMed:12054517}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a;
CC IsoId=O17323-1; Sequence=Displayed;
CC Name=b;
CC IsoId=O17323-2; Sequence=VSP_044209;
CC -!- TISSUE SPECIFICITY: Expressed in body-wall muscle cells, hypodermal
CC seam cells and neuronal cells including sensory amphid neuronal
CC processes, the nerve ring, ventral nerve cords and motor neuronal
CC commissures. {ECO:0000269|PubMed:12054517}.
CC -!- PTM: Phosphorylated by serine/threonine-protein kinase kin-29 at Ser-
CC 251; the phosphorylation inhibits repression of transcription by mef-2
CC (PubMed:17170704). May be phosphorylated by either cyclic-AMP dependent
CC or cyclic-GMP dependent protein kinases (PubMed:18832350).
CC {ECO:0000269|PubMed:17170704, ECO:0000269|PubMed:18832350}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC subfamily. {ECO:0000305}.
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DR EMBL; FO080490; CCD64116.1; -; Genomic_DNA.
DR EMBL; FO080492; CCD64116.1; JOINED; Genomic_DNA.
DR EMBL; FO080490; CCF23337.1; -; Genomic_DNA.
DR EMBL; FO080492; CCF23337.1; JOINED; Genomic_DNA.
DR PIR; T32425; T32425.
DR RefSeq; NP_001257278.1; NM_001270349.1. [O17323-1]
DR RefSeq; NP_001257279.1; NM_001270350.1. [O17323-2]
DR AlphaFoldDB; O17323; -.
DR SMR; O17323; -.
DR BioGRID; 46606; 2.
DR IntAct; O17323; 1.
DR MINT; O17323; -.
DR STRING; 6239.C10E2.3a; -.
DR EPD; O17323; -.
DR PaxDb; O17323; -.
DR PeptideAtlas; O17323; -.
DR EnsemblMetazoa; C10E2.3a.1; C10E2.3a.1; WBGene00001837. [O17323-1]
DR EnsemblMetazoa; C10E2.3b.1; C10E2.3b.1; WBGene00001837. [O17323-2]
DR GeneID; 181723; -.
DR KEGG; cel:CELE_C10E2.3; -.
DR UCSC; C10E2.3; c. elegans.
DR CTD; 181723; -.
DR WormBase; C10E2.3a; CE42060; WBGene00001837; hda-4. [O17323-1]
DR WormBase; C10E2.3b; CE37192; WBGene00001837; hda-4. [O17323-2]
DR eggNOG; KOG1343; Eukaryota.
DR GeneTree; ENSGT00940000169192; -.
DR InParanoid; O17323; -.
DR OMA; QKVIAIH; -.
DR OrthoDB; 1484694at2759; -.
DR Reactome; R-CEL-3108214; SUMOylation of DNA damage response and repair proteins.
DR Reactome; R-CEL-4551638; SUMOylation of chromatin organization proteins.
DR Reactome; R-CEL-8951936; RUNX3 regulates p14-ARF.
DR PRO; PR:O17323; -.
DR Proteomes; UP000001940; Chromosome X.
DR Bgee; WBGene00001837; Expressed in pharyngeal muscle cell (C elegans) and 3 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:WormBase.
DR GO; GO:0000118; C:histone deacetylase complex; ISS:WormBase.
DR GO; GO:0005634; C:nucleus; IDA:WormBase.
DR GO; GO:0005516; F:calmodulin binding; ISS:WormBase.
DR GO; GO:0004407; F:histone deacetylase activity; ISS:WormBase.
DR GO; GO:0003714; F:transcription corepressor activity; ISS:WormBase.
DR GO; GO:0008134; F:transcription factor binding; IPI:WormBase.
DR GO; GO:0006915; P:apoptotic process; ISS:WormBase.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:WormBase.
DR GO; GO:0006325; P:chromatin organization; ISS:WormBase.
DR GO; GO:0016575; P:histone deacetylation; ISS:WormBase.
DR GO; GO:0035556; P:intracellular signal transduction; ISS:WormBase.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:WormBase.
DR GO; GO:0007168; P:receptor guanylyl cyclase signaling pathway; IMP:UniProtKB.
DR GO; GO:0045664; P:regulation of neuron differentiation; IMP:WormBase.
DR GO; GO:0007165; P:signal transduction; IMP:UniProtKB.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Hydrolase; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..869
FT /note="Histone deacetylase 4"
FT /id="PRO_0000114742"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 128..167
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 180..218
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 460..802
FT /note="Histone deacetylase"
FT COMPBIAS 128..146
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 153..167
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 608
FT /evidence="ECO:0000250"
FT MOD_RES 251
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:17170704"
FT VAR_SEQ 1..53
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000303|PubMed:12054517"
FT /id="VSP_044209"
FT MUTAGEN 80..869
FT /note="Missing: In oy59; Suppresses reduced chemoreceptor
FT gene expression phenotype in a Ser/Thr kinase kin-29 mutant
FT background."
FT /evidence="ECO:0000269|PubMed:17170704"
FT MUTAGEN 251
FT /note="S->A: Abolishes phosphorylation; causes significant
FT down-regulation of chemoreceptor str-1 expression."
FT /evidence="ECO:0000269|PubMed:17170704"
FT MUTAGEN 416
FT /note="S->A: Localizes to cytoplasm; does not affect
FT chemoreceptor str-1 expression; when associated with A-
FT 515."
FT /evidence="ECO:0000269|PubMed:18832350"
FT MUTAGEN 515
FT /note="S->A: Localizes to cytoplasm; does not affect
FT chemoreceptor str-1 expression; when associated with A-
FT 416."
FT /evidence="ECO:0000269|PubMed:18832350"
SQ SEQUENCE 869 AA; 94411 MW; 0F186275170F82C3 CRC64;
MEEASSSTGS AGGAGPSVPN LPSTSEAAIG QTNLEPESIA LLQSQLQEYR QKQMDLIGHF
QRAQQELSVQ HMHNLYAALQ QQQQLQNLQT ERSAVNPLLI SQQHSTEDQN SGPAAPLSLA
NSLTNLLSSS NGNLSVPQTP TKEHHPTAPT SNRKCDLPRS NSTTISQLTK DRLKNMIANR
SKGESNSQSN LMSNSVTANG NGHDNGRKLK NSNSQVNVSS PHFEPYRLPT SLANAHNLQQ
ASEFQLRKVN SEPNLKMRIR AKLLSKGSSP VQHVQQNNSQ FNFTHPQLKR SDSETSQNVP
LDFMQSSSQT NLPHLMLPSP SLPNLAAAGA FHGLNLPVGQ DLNAFMAVAN LSPFLSLPSL
LNKKLELGGL TDEGDRNGLI GSSSTSSLAS NVSMGSHQYQ SLLKQQIRDL VLRRKSLVRE
DPEGEGLAEL YNGLLPQAKL QQLQALAAES GFLAKQEPTC TTGLGYDQAM VRHECCCGNN
ASHVENGGRI QSIWSKLIEH GHVQKCEKVT AKKASLEQLQ LVHSQTYTTF FAVSPTACLK
IDANSLPLKR FLQLPCGGIG VDSDTYFNDA STQTAARLAA GTLIELSSQV AEGRLKNGFA
CIRPPGHHAE HEQAMGFCFF NNVAVAVKVL QTKYPAQCAK IAIIDWDVHH GNGTQLSFEN
DPNVLYMSLH RHDKGNFFPG TGSVTEVGKN DAKGLTVNVP FSGDVMRDPE YLAAWRTVIE
PVMASFCPDF IIVSAGFDAC HGHPNALGGY EVTPEMFGYM TKSLLNYASG KVVLALEGGY
DLKSISEAAQ QCVQALIGES DDAGRLSSVA LESLPNPSAV ETLQKVIAIH KSYWPALHGQ
EAAINTTEMQ WRNLKLQVQM QQQQQQQQT
