ID A0A3B3I2C1_ORYLA Unreviewed; 1005 AA.
AC A0A3B3I2C1;
DT 05-DEC-2018, integrated into UniProtKB/TrEMBL.
DT 05-DEC-2018, sequence version 1.
DT 27-MAR-2024, entry version 27.
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|Ensembl:ENSORLP00000038186.1};
OS Oryzias latipes (Japanese rice fish) (Japanese killifish).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Ovalentaria; Atherinomorphae; Beloniformes; Adrianichthyidae; Oryziinae;
OC Oryzias.
OX NCBI_TaxID=8090 {ECO:0000313|Ensembl:ENSORLP00000038186.1, ECO:0000313|Proteomes:UP000001038};
RN [1] {ECO:0000313|Ensembl:ENSORLP00000038186.1, ECO:0000313|Proteomes:UP000001038}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Hd-rR {ECO:0000313|Ensembl:ENSORLP00000038186.1,
RC ECO:0000313|Proteomes:UP000001038};
RX PubMed=17554307; DOI=10.1038/nature05846;
RA Kasahara M., Naruse K., Sasaki S., Nakatani Y., Qu W., Ahsan B., Yamada T.,
RA Nagayasu Y., Doi K., Kasai Y., Jindo T., Kobayashi D., Shimada A.,
RA Toyoda A., Kuroki Y., Fujiyama A., Sasaki T., Shimizu A., Asakawa S.,
RA Shimizu N., Hashimoto S., Yang J., Lee Y., Matsushima K., Sugano S.,
RA Sakaizumi M., Narita T., Ohishi K., Haga S., Ohta F., Nomoto H., Nogata K.,
RA Morishita T., Endo T., Shin-I T., Takeda H., Morishita S., Kohara Y.;
RT "The medaka draft genome and insights into vertebrate genome evolution.";
RL Nature 447:714-719(2007).
RN [2] {ECO:0000313|Ensembl:ENSORLP00000038186.1}
RP IDENTIFICATION.
RC STRAIN=Hd-rR {ECO:0000313|Ensembl:ENSORLP00000038186.1};
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|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 AlphaFoldDB; A0A3B3I2C1; -.
DR Ensembl; ENSORLT00000045488.1; ENSORLP00000038186.1; ENSORLG00000029432.1.
DR GeneTree; ENSGT00940000157440; -.
DR Proteomes; UP000001038; Chromosome 2.
DR Bgee; ENSORLG00000029432; Expressed in intestine and 14 other cell types or tissues.
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:0000122; P:negative regulation of transcription by RNA polymerase II; IEA:InterPro.
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 3: Inferred from homology;
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 Reference proteome {ECO:0000313|Proteomes:UP000001038};
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 85..173
FT /note="Histone deacetylase glutamine rich N-terminal"
FT /evidence="ECO:0000259|Pfam:PF12203"
FT DOMAIN 678..989
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 59..86
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 228..333
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 525..558
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 111..179
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 228..248
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 261..300
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 314..333
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 533..550
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 800
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-1"
FT BINDING 670
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 672
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 678
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT BINDING 748
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-2"
FT SITE 973
FT /note="Contributes to catalysis"
FT /evidence="ECO:0000256|PIRSR:PIRSR037911-3"
SQ SEQUENCE 1005 AA; 109294 MW; 577E63A85B86A7C7 CRC64;
MATSYFTFLT CGSEGILGKE PPLEVLKTSA LNHIPTVDIS SALPLRLPPA AIPMDLRVDH
QASPPGQQSP GPLGGTGGQQ GAVAASMREQ QLQQELLTLK QKQQIQRQIL IAEFQRQHEQ
LSRQHEAQLQ EHIKQQQELL ALKHQQELLE HQRKMENHRL EQELEKQQRE QKLQLLKNKE
RGQESAVAST EVKMRLQEFV LNKKKALAQR SLNQAGVPND APYWYRKTQH SSLDQSSPPQ
TGVSTYNHPV LGVYNPRDDF PLRKTASEPN LKLRSRLKQK VSERRSSPLL RRRDSPIATA
KKRSLDMADS ACSSAPGSGP SSPNNSSNSI PNENGVAVAV SNSMEVSLAQ RLCGGAEAGS
VNPLSLYTSP SLPNITLGLP ATATATAASN VTSAQQDGGL QPALSLSPPF HLTPYLAEPA
GGHGAHSPLL QHMVLMEQSP AQSPLVTGVG GLSMSSASMA KLQRPHRPLG RTQSAPLPQG
SAAQAHAQAL ALQQLVVQQQ HQQFLEKHKQ QFQQQLHLNK IMAKPGESPV GRQHQSHPEE
TEEELREHQE GGASPGVIIK QEPLDPQEVQ EEALQQQRER DSQTEQELLF RQQALLLEQQ
RIHQLRNYQA SLEAAGVSVS FPGHRPLSRA QSSPASASSF PISVPLPDPP IKPRFTTGLV
YDSLMQKHQC MCGNTNSHPE HAGRIQSIWS RLQETGLRAQ CECIRGRKAT LEELQTVHSE
AHVLLYGTNP LRQKLDCSIT PMFVRLPCGG VGVDSDTIWN EVHSSSAARL AVGSVVELVF
KVATGELKNG FAVVRPPGHH AEESTPMGFC YFNSVAIAAR LLQQRLSVSK VLIVDWDVHH
GNGTQQAFYD DPNVLYVSVH RYDDGNFFPG SGAPDEVGSG PGVGFNVNVA FTGGLDPPMG
DAEYLAAFRS VVMPIANEFA PDIVLVSSGF DAVEGHPPPL GGYTLTSKCF GYLTKQLMTL
AGGRLVLALE GGHDLTAICD ASEACVAALL GQEVRAAPAA RRRSS
//
