ID G1K2I1_DANRE Unreviewed; 1522 AA.
AC G1K2I1; A0A8M2BEG9;
DT 19-OCT-2011, integrated into UniProtKB/TrEMBL.
DT 20-JUN-2018, sequence version 3.
DT 24-JAN-2024, entry version 85.
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=cb264 {ECO:0000313|RefSeq:XP_005167081.1};
GN Synonyms=jarid1bb {ECO:0000313|RefSeq:XP_005167081.1}, plu1
GN {ECO:0000313|RefSeq:XP_005167081.1}, wu:fc44h11
GN {ECO:0000313|RefSeq:XP_005167081.1}, zgc:85741
GN {ECO:0000313|RefSeq:XP_005167081.1};
GN OrderedLocusNames=kdm5bb {ECO:0000313|Ensembl:ENSDARP00000023794,
GN ECO:0000313|RefSeq:XP_005167081.1,
GN ECO:0000313|ZFIN:ZDB-GENE-030424-1};
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:ENSDARP00000023794};
RN [1] {ECO:0000313|Ensembl:ENSDARP00000023794}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000023794};
RG Ensembl;
RL Submitted (AUG-2011) to UniProtKB.
RN [2] {ECO:0000313|Ensembl:ENSDARP00000023794, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000023794};
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 [3] {ECO:0000313|RefSeq:XP_005167081.1}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:XP_005167081.1};
RG RefSeq;
RL Submitted (SEP-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; BX664742; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; FO704829; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_005167081.1; XM_005167024.4.
DR Ensembl; ENSDART00000005583; ENSDARP00000023794; ENSDARG00000003098.
DR Ensembl; ENSDART00000005583.9; ENSDARP00000023794.9; ENSDARG00000003098.10.
DR GeneID; 415256; -.
DR CTD; 415256; -.
DR ZFIN; ZDB-GENE-030424-1; kdm5bb.
DR OMA; PRCDIGM; -.
DR OrthoDB; 48111at2759; -.
DR TreeFam; TF106476; -.
DR Proteomes; UP000000437; Chromosome 8.
DR Bgee; ENSDARG00000003098; Expressed in tail bud paraxial mesoderm and 58 other cell types or tissues.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0034647; F:histone H3K4me/H3K4me2/H3K4me3 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd16874; ARID_KDM5B; 1.
DR CDD; cd15603; PHD1_KDM5B; 1.
DR CDD; cd15607; PHD2_KDM5B; 1.
DR CDD; cd15687; PHD3_KDM5B; 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); 3.
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; IPR047981; KDM5B_ARID.
DR InterPro; IPR047978; KDM5B_PHD1.
DR InterPro; IPR047979; KDM5B_PHD3.
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:SF3; LYSINE-SPECIFIC DEMETHYLASE 5B; 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; 2.
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; 3.
DR SUPFAM; SSF46774; ARID-like; 1.
DR SUPFAM; SSF51197; Clavaminate synthase-like; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 3.
DR PROSITE; PS51011; ARID; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
DR PROSITE; PS01359; ZF_PHD_1; 2.
DR PROSITE; PS50016; ZF_PHD_2; 3.
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:G1K2I1};
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 15..56
FT /note="JmjN"
FT /evidence="ECO:0000259|PROSITE:PS51183"
FT DOMAIN 80..170
FT /note="ARID"
FT /evidence="ECO:0000259|PROSITE:PS51011"
FT DOMAIN 314..364
FT /note="PHD-type"
FT /evidence="ECO:0000259|PROSITE:PS50016"
FT DOMAIN 458..624
FT /note="JmjC"
FT /evidence="ECO:0000259|PROSITE:PS51184"
FT DOMAIN 1187..1235
FT /note="PHD-type"
FT /evidence="ECO:0000259|PROSITE:PS50016"
FT DOMAIN 1463..1516
FT /note="PHD-type"
FT /evidence="ECO:0000259|PROSITE:PS50016"
FT REGION 221..242
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 287..306
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1381..1400
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1422..1461
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 964..991
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 287..302
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1422..1447
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1522 AA; 173142 MW; F61669B7DCE46377 CRC64;
MTQQGPAEFT PPPECPVFEP SWEEFKDPFA FINKIRPIAE KTGICKVRPP PDWQPPFACD
VDRLHFTPRI QRLNELEAQT RVKLNFLDQI AKFWDLQGCT LKIPHVERKI LDLYQLNKLV
ADEGGFDLVC RERRWTKIAM TMGFAPGKAV GSHLRAHYER ILYPYNLFQS GTNLLAPEFA
VKLTGFGEPP VLEECLQKPG DEVNDIDKEY KPHDLLQRQN VPLQPSNTSA PARRAKRMKT
ESGCIKSEEG EGVENKPNLR RRMGSFVVKT EQKKEIPIQV KEEPVEIKEL NPEPEKSKPK
KKNIPPPPVS MVDLYVCLVC GKGNDEDRLL LCDGCDDSYH TFCLIPPLTD VPKGDWRCPK
CLTQECCKPQ EAFGFEQAHR DYTLKAFGEM ADSFKSDYFN MPVHMVPTEL VEKEFWRLVG
TIQEDVTVEY GADIASKEFG SGFPIKGGRF KIAPHDEKYL QCGWNLNNMA MMTPSVLTHV
TADICGMTLP WLYVGMCFSS FCWHIEDHWS YSINYLHWGE PKTWYGAPGF AAEQLEAVMK
KLAPELFDSQ PDLLHQLVTI MNPNTLMAHG VPIYRTNQCA GEFVITFPRS YHSGFNQGFN
FAEAVNFCTV DWMPLGRQCV DHYRQLHRYC VFSHDEMVCN MAMKADCLDV VLASAVQKDM
QLMIKEEREL REKVRKMGVA QCELFQYDLL ADDERQCVKC RTTCYLSALT CPCRPGVQVC
LYHTHDLCSC PISNYTLNYR FTLDDLYPMM NAVRQRAEYY DDWASRVTEV MEAKLDKKRN
VTVFRTLLEE SNEQSFPEND LLRQLRLVTQ DAEKCSSVAQ QLLNGKRQTR YRTGKAKSPN
QLTVEEMRSF VRQLYNLPCS LTQAPLLKEL LNSIEDFQQH SEKLLSDEVS ADAVSEIESL
LEEGSQFDVF LPELPLLRER LEQARWLTGV HQAEDPVANP CGLSLESMRR LIDRGVGLTP
HPSIERMMAR LQELLTVSEE LEENAQALLK ARPPESLETL CSMLTQVEGV PAYLPNCLLL
QDTVNRAKEW LQEAESLQVG GQVPVFSSLS DMVLRAHSIP VRLEPLDQLE VQVSEVQSWK
ETAAKTFLIK SSPFTLLEVL CPRWEMGSSL KKKKMRKMKG DCVSSGKKKF VKLDSMSDVE
RALSDSKDSA SAMFTLAEVR LKELESLCSL RASNESKLLP TADCASLKVC VCQKPAMGAM
LQCELCRDAF HSVCVRGPSD PLDPEAWLCP LCLRSTKPPL DKIRSLLSSL QRIRVRLPEG
DALRYMIERS VSWQRRVREV IDSYGLSSTS QDGRGASPSQ NLYRSTGHSR KLQLCGSPSR
CQDWAVSGQE QTVFYTEQRC IPLQGLSPEL EELMVEGLVL QVSLPETQQL YRLLLSGPPT
TNTSHAEHKS YLTPPQTETD AITSAEKKAK RRMNRDEVDI RERGTKLKSK KQRMMGVEKR
RERKAASVSA SDMSQSEDSE EDMTLCPAES CLQPEGEEVD WVQCDCCNRW FHMICVGVSA
ELAAEEDYMC VSCSTSHMDR RK
//