ID B0S6L0_DANRE Unreviewed; 1578 AA.
AC B0S6L0; A0A8M1NGK0;
DT 08-APR-2008, integrated into UniProtKB/TrEMBL.
DT 08-APR-2008, sequence version 1.
DT 27-MAR-2024, entry version 121.
DE RecName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase {ECO:0000256|ARBA:ARBA00012902};
DE EC=1.14.11.67 {ECO:0000256|ARBA:ARBA00012902};
GN Name=kdm5c {ECO:0000313|Ensembl:ENSDARP00000110667,
GN ECO:0000313|RefSeq:NP_001116706.1,
GN ECO:0000313|ZFIN:ZDB-GENE-060810-94};
GN Synonyms=im:7158173 {ECO:0000313|RefSeq:NP_001116706.1}, jarid1c
GN {ECO:0000313|RefSeq:NP_001116706.1}, si:ch211-218o21.2
GN {ECO:0000313|RefSeq:NP_001116706.1}, wu:fa28h03
GN {ECO:0000313|RefSeq:NP_001116706.1}, wu:fi31b07
GN {ECO:0000313|RefSeq:NP_001116706.1};
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|Ensembl:ENSDARP00000110667};
RN [1] {ECO:0000313|RefSeq:NP_001116706.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
RX PubMed=17320160; DOI=10.1016/j.cell.2007.02.017;
RA Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H.,
RA Whetstine J.R., Bonni A., Roberts T.M., Shi Y.;
RT "The X-linked mental retardation gene SMCX/JARID1C defines a family of
RT histone H3 lysine 4 demethylases.";
RL Cell 128:1077-1088(2007).
RN [2] {ECO:0000313|RefSeq:NP_001116706.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
RX PubMed=20194436; DOI=10.1101/gad.1864410;
RA Tsukada Y., Ishitani T., Nakayama K.I.;
RT "KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions
RT in brain development.";
RL Genes Dev. 24:432-437(2010).
RN [3] {ECO:0000313|Ensembl:ENSDARP00000110667}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000110667};
RG Ensembl;
RL Submitted (FEB-2012) to UniProtKB.
RN [4] {ECO:0000313|RefSeq:NP_001116706.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
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|Ensembl:ENSDARP00000110667, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000110667};
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_001116706.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
RX PubMed=26469318;
RA Elkon R., Milon B., Morrison L., Shah M., Vijayakumar S., Racherla M.,
RA Leitch C.C., Silipino L., Hadi S., Weiss-Gayet M., Barras E., Schmid C.D.,
RA Ait-Lounis A., Barnes A., Song Y., Eisenman D.J., Eliyahu E.,
RA Frolenkov G.I., Strome S.E., Durand B., Zaghloul N.A., Jones S.M.,
RA Reith W., Hertzano R.;
RT "RFX transcription factors are essential for hearing in mice.";
RL Nat. Commun. 6:8549-8549(2015).
RN [7] {ECO:0000313|RefSeq:NP_001116706.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
RX PubMed=30458291;
RA Fellous A., Earley R.L., Silvestre F.;
RT "The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish,
RT Kryptolebias marmoratus, suggest involvement of histone methylation
RT machinery in development and reproduction.";
RL Gene 687:173-187(2019).
RN [8] {ECO:0000313|RefSeq:NP_001116706.1}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:NP_001116706.1};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-
CC [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone
CC H3] + 3 succinate; Xref=Rhea:RHEA:60208, Rhea:RHEA-COMP:15537,
CC Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61961; EC=1.14.11.67;
CC Evidence={ECO:0000256|ARBA:ARBA00000604};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000256|ARBA:ARBA00001954};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000256|ARBA:ARBA00006801}.
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DR EMBL; BX537348; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001116706.1; NM_001123234.1.
DR STRING; 7955.ENSDARP00000110667; -.
DR PaxDb; 7955-ENSDARP00000110667; -.
DR PeptideAtlas; B0S6L0; -.
DR Ensembl; ENSDART00000127053; ENSDARP00000110667; ENSDARG00000006124.
DR Ensembl; ENSDART00000127053.3; ENSDARP00000110667.2; ENSDARG00000006124.12.
DR GeneID; 553406; -.
DR KEGG; dre:553406; -.
DR AGR; ZFIN:ZDB-GENE-060810-94; -.
DR CTD; 8242; -.
DR ZFIN; ZDB-GENE-060810-94; kdm5c.
DR eggNOG; KOG1246; Eukaryota.
DR HOGENOM; CLU_000991_2_2_1; -.
DR OMA; MASGKMM; -.
DR OrthoDB; 48111at2759; -.
DR PhylomeDB; B0S6L0; -.
DR TreeFam; TF106476; -.
DR Reactome; R-DRE-3214842; HDMs demethylate histones.
DR Proteomes; UP000000437; Chromosome 8.
DR Bgee; ENSDARG00000006124; Expressed in testis and 31 other cell types or tissues.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0034647; F:histone H3K4me/H3K4me2/H3K4me3 demethylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0043524; P:negative regulation of neuron apoptotic process; IMP:ZFIN.
DR GO; GO:0006355; P:regulation of DNA-templated transcription; IBA:GO_Central.
DR CDD; cd16875; ARID_KDM5C_5D; 1.
DR CDD; cd15604; PHD1_KDM5C_5D; 1.
DR CDD; cd15608; PHD2_KDM5C_5D; 1.
DR Gene3D; 1.10.150.60; ARID DNA-binding domain; 1.
DR Gene3D; 2.60.120.650; Cupin; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR InterPro; IPR001606; ARID_dom.
DR InterPro; IPR036431; ARID_dom_sf.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR048615; KDM5_C-hel.
DR InterPro; IPR013637; Lys_sp_deMease-like_dom.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR004198; Znf_C5HC2.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR10694; LYSINE-SPECIFIC DEMETHYLASE; 1.
DR PANTHER; PTHR10694:SF43; LYSINE-SPECIFIC DEMETHYLASE 5C; 1.
DR Pfam; PF01388; ARID; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF21323; KDM5_C-hel; 1.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF08429; PLU-1; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM01014; ARID; 1.
DR SMART; SM00501; BRIGHT; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 2.
DR SUPFAM; SSF46774; ARID-like; 1.
DR SUPFAM; SSF51197; Clavaminate synthase-like; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 2.
DR PROSITE; PS51011; ARID; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator {ECO:0000256|ARBA:ARBA00022853};
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Dioxygenase {ECO:0000256|ARBA:ARBA00022964};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002};
KW Proteomics identification {ECO:0007829|PeptideAtlas:B0S6L0};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
KW Zinc {ECO:0000256|ARBA:ARBA00022833};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|PROSITE-
KW ProRule:PRU00146}.
FT DOMAIN 14..55
FT /note="JmjN"
FT /evidence="ECO:0000259|PROSITE:PS51183"
FT DOMAIN 79..169
FT /note="ARID"
FT /evidence="ECO:0000259|PROSITE:PS51011"
FT DOMAIN 358..408
FT /note="PHD-type"
FT /evidence="ECO:0000259|PROSITE:PS50016"
FT DOMAIN 502..668
FT /note="JmjC"
FT /evidence="ECO:0000259|PROSITE:PS51184"
FT REGION 173..339
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1206..1245
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1413..1444
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1520..1578
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 1365..1392
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 178..194
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 270..284
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 317..339
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1225..1245
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1424..1440
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1539..1556
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1557..1572
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1578 AA; 178661 MW; F8A0A73BF097FAEA CRC64;
MMDVGEEFVP PPECPVFEPS WEEFADPLGY IAKIRPIAEK SGICKIRPPP DWQPPFAVEV
DNFHFTPRIQ RLNELEAETR VKLNYLDRIA KFWEIQGSSL KIPNLERRIL DLFSLAKIVT
EEGGFESVSK ERRWARVAQK LGYPPGKNIG SLLRSHYERI VYPFELFQSG ASLPPRKPRQ
YDSDEVDREY KPHSIPLRQS VPPSKMSSYG RRANRLQPEG PEDPTHHPLT TGSQHISSPE
PTEEDIEKNP ELKKLQIYGA GPKMMGLGLV PRDKTRKKDD LPQTVIVRDS AVKDEPAETA
VTKSDPDIPP PPPNLIIKED VDDDKSHIDK PNDPSDEPCT KMTMRLRRNL NNPQFVDSFV
CRMCGRGDED EKLMLCDGCD DNYHTFCLIP PLTDPPKGNW RCPKCVAEEC KKPSEAFGFE
QATREYTLQS FGEMADTFKA DYFNMPVHMV PTELVEKEFW RLVSSIEEDV TVEYGADIHS
KEFGSGFPVN NGKRQLSEEE EEYARSGWNL NVMPVLEQSL LCHINADISG MKVPWLYVGM
VFSAFCWHIE DHWSYSINYL HWGEPKTWYG VPCSAAEKLE EVMKKLTPEL FEFQPDLLHQ
LVTIMNPNIL MSHGVPVVRT NQCAGEFVIT FPRAYHSGFN QGYNFAEAVN FCTADWLPTG
RSCIEHYRQL RRYCVFSQEE LTCKMAACPE KLDLNLAAAT HREMFIIVQE ERKLRKSLLE
RGIKEAEREA FELLPDDERQ CDKCKTTCFL SALACSNCPE RLVCLYHAQD LCSCPSEKLY
LRYRYTLDEL LAMLHRLKVR AESFDSWANR VKEALEQDEG NKIDIKDLEV LKEEAADKKF
PNNELLQRLN TVFVDIEKCE SCSTELLSNS QSSRMTLKEL KTLVDTMQNL PCVIKQQDEV
QLILQKIEEF DSRAQVLVDS TKSEWKQDSP LPVATEIQAL LEEGASLPVI APACELLSGL
LEQGRWLGEV RRTLGPEGSE VTLTVLRNLM ESGCNVPQSV SVETAMAELQ ELLTIAERWE
EKAQICLEDR QKHHLSTLEA IVNEAQLIPV QLPNILSLQA CLSRARAWVT DLEEIQNGEH
YPCLDDLEGL VAIGRDLPVK MEELKQLELQ VASAHSWREK ASKTFLKKNS QHSLLEVLCP
CVEKSKKMED NSMVTEADSD VNVLGLTAQD LRDPGAIVMA FKEGERLEKE ALLRLQQVNL
AKPSIENGVS TDQDSIKTEK KQSNSMETDV PLNSDSPVLQ NGGSSHSLTS SQTVCICGGP
PRPLLHRCHL CKDWFHGGCV SFPPLLATSD THLTKPLCWW DWNTRFLCPR CQRSRRPRLE
TILALLVALQ RLPVRLPEGE ALQCLTERAI NWQGRAKQAL DTPEVQEALD RLQQVEDEMV
SIKEEEPEEK KKWNGDAVIV LSDSEEAEDG VIDLTEDGNS PKKNERNAVN GTQSGCENGI
GRKSSAHEVT GVESLLSLVP SLKGPVVELN TSVRAQLEEL QLEGDLLEVT LDQTHAIYRI
LQASSQPPQD TLRTLIQIEL QEQRSSGRGN KSKDSKRKRK SQKTEGEPKS TEASDCKKTK
ALNLSPPTDT HTDVVMFS
//
