KD5BB_DANRE
ID KD5BB_DANRE Reviewed; 1503 AA.
AC Q6IQX0; B0S5X8; B0S5X9;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Lysine-specific demethylase 5B-B;
DE EC=1.14.11.67 {ECO:0000250|UniProtKB:Q9BY66};
DE AltName: Full=Histone demethylase JARID1B-B;
DE AltName: Full=Jumonji/ARID domain-containing protein 1B-B;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase 5B-B {ECO:0000305};
GN Name=kdm5bb; Synonyms=jarid1b, jarid1bb;
GN ORFNames=si:dkey-193l3.2, zgc:85741;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
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., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., 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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3,
CC thereby playing a central role in histone code. Does not demethylate
CC histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated,
CC dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional
CC corepressor (By similarity). {ECO:0000250}.
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:0000250|UniProtKB:Q9BY66};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00355,
CC ECO:0000255|PROSITE-ProRule:PRU00537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6IQX0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6IQX0-2; Sequence=VSP_035555;
CC -!- DOMAIN: Both the JmjC domain and the JmjN domain are required for
CC enzymatic activity. {ECO:0000250}.
CC -!- DOMAIN: The 2 first PHD-type zinc finger domains are required for
CC transcription repression activity. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAQ14256.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BX322655; CAQ14256.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BX322655; CAQ14257.1; -; Genomic_DNA.
DR EMBL; BX664742; CAQ14257.1; JOINED; Genomic_DNA.
DR EMBL; BX664742; CAQ13548.1; -; Genomic_DNA.
DR EMBL; BX322655; CAQ13548.1; JOINED; Genomic_DNA.
DR EMBL; BC071280; AAH71280.1; -; mRNA.
DR AlphaFoldDB; Q6IQX0; -.
DR SMR; Q6IQX0; -.
DR STRING; 7955.ENSDARP00000023794; -.
DR PaxDb; Q6IQX0; -.
DR PRIDE; Q6IQX0; -.
DR ZFIN; ZDB-GENE-030424-1; kdm5bb.
DR eggNOG; KOG1246; Eukaryota.
DR InParanoid; Q6IQX0; -.
DR PhylomeDB; Q6IQX0; -.
DR BRENDA; 1.14.11.67; 928.
DR Reactome; R-DRE-3214842; HDMs demethylate histones.
DR Reactome; R-DRE-8866911; TFAP2 (AP-2) family regulates transcription of cell cycle factors.
DR PRO; PR:Q6IQX0; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0034720; P:histone H3-K4 demethylation; ISS:UniProtKB.
DR Gene3D; 1.10.150.60; -; 1.
DR Gene3D; 3.30.40.10; -; 3.
DR InterPro; IPR001606; ARID_dom.
DR InterPro; IPR036431; ARID_dom_sf.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
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 Pfam; PF01388; ARID; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF00628; PHD; 2.
DR Pfam; PF08429; PLU-1; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM00501; BRIGHT; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 3.
DR SUPFAM; SSF46774; SSF46774; 1.
DR SUPFAM; SSF57903; SSF57903; 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 2: Evidence at transcript level;
KW Alternative splicing; Chromatin regulator; Dioxygenase; Iron;
KW Metal-binding; Nucleus; Oxidoreductase; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1503
FT /note="Lysine-specific demethylase 5B-B"
FT /id="PRO_0000292415"
FT DOMAIN 15..56
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 80..170
FT /note="ARID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00355"
FT DOMAIN 439..605
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 295..345
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 1168..1216
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 1444..1497
FT /note="PHD-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 202..223
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 268..287
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1362..1381
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1403..1442
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 268..283
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1403..1428
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 485
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 488
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 573
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT VAR_SEQ 175
FT /note="L -> LAPEFAVKLTGFGEPPVLEE (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_035555"
FT CONFLICT 1284
FT /note="Y -> H (in Ref. 2; AAH71280)"
FT /evidence="ECO:0000305"
FT CONFLICT 1293
FT /note="L -> Q (in Ref. 2; AAH71280)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1503 AA; 171098 MW; B6CE3A9BA82F506F CRC64;
MTQQGPAEFT PPPECPVFEP SWEEFKDPFA FINKIRPIAE KTGICKVRPP PDWQPPFACD
VDRLHFTPRI QRLNELEAQT RVKLNFLDQI AKFWDLQGCT LKIPHVERKI LDLYQLNKLV
ADEGGFDLVC RERRWTKIAM TMGFAPGKAV GSHLRAHYER ILYPYNLFQS GTNLLCLQKP
GDEVNDIDKE YKPHDLLQRQ NVPLQPSNTS APARRAKRMK TESGCIKSEE GEGVENKPNL
RRRMGSFVVK TEPKKEIPIQ VKEEPVEIKE LNPEPEKSKP KKKNIPPPPV SMVDLYVCLV
CGKGNDEDRL LLCDGCDDSY HTFCLIPPLT DVPKGDWRCP KCLTQECCKP QEAFGFEQAH
RDYTLKAFGE MADSFKSDYF NMPVHMVPTE LVEKEFWRLV GTIQEDVTVE YGADIASKEF
GSGFPIKGGR FKIAPHDEKY LQCGWNLNNM AMMTPSVLTH VTADICGMTL PWLYVGMCFS
SFCWHIEDHW SYSINYLHWG EPKTWYGAPG FAAEQLEAVM KKLAPELFDS QPDLLHQLVT
IMNPNTLMAH GVPIYRTNQC AGEFVITFPR SYHSGFNQGF NFAEAVNFCT VDWMPLGRQC
VDHYRQLHRY CVFSHDEMVC NMAMKADCLD VVLASAVQKD MQLMIKEERE LREKVRKMGV
AQCELFQYDL LADDERQCVK CRTTCYLSAL TCPCRPGVQV CLYHTHDLCS CPISNYTLNY
RFTLDDLYPM MNAVRQRAEY YDDWASRVTE VMEAKLDKKR NVTVFRTLLE ESNEQSFPEN
DLLRQLRLVT QDAEKCSSVA QQLLNGKRQT RYRTGKAKSP NQLTVEEMRS FVRQLYNLPC
SLTQAPLLKE LLNSIEDFQQ HSEKLLSDEV SADAVSEIES LLEEGSQFDV FLPELPLLRE
RLEQARWLTG VHQAEDPVAN PCGLSLESMR RLIDRGVGLT PHPSIERMMA RLQELLTVSE
ELEENAQALL KARPPESLET LCSMLTQVEG VPAYLPNCLL LQDTVNRAKE WLQEAESLQV
GGQVPVFSSL SDMVLRAHSI PVRLEPLDQL EVQVSEVQSW KETAAKTFLI KSSPFTLLEV
LCPRWEMGSS LKKKKMRKMK GDCVSSGKKK FVKLDSMSDV ERALSDSKDS ASAMFTLAEV
RLKELESLCS LRASNESKLL PTADCASLKV CVCQKPAMGA MLQCELCRDA FHSVCVRGPS
DPLDPEAWLC PLCLRSTKPP LDKIRSLLSS LQRIRVRLPE GDALRYMIER SVSWQRRVRE
VIDSYGLSST SQDGRGASPS QNLYRSTGHS RKLQLCGSPS RCQDWAVSGQ EQTVFYTEQR
CIPLQGLSPE LEELMVEGLV LQVSLPETQQ LYRLLLSGPP TTNTSHAEHK SYLTPPQTET
DAITSAEKKA KRRMNRDEVD IRERGTKLKS KKQRMMGVEK RRERKAASVS ASDMSQSEDS
EEDMTLCPAE SCLQPEGEEV DWVQCDCCNR WFHMICVGVS AELAAEEDYM CVSCSTSHMD
RRK
