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Lysine-specific demethylase 5B-B (EC 1.14.11.-) (Histone demethylase JARID1B-B) (Jumonji/ARID domain-containing protein 1B-B)

 KD5BB_DANRE             Reviewed;        1503 AA.
Q6IQX0; B0S5X8; B0S5X9;
26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
14-OCT-2008, sequence version 2.
25-OCT-2017, entry version 96.
RecName: Full=Lysine-specific demethylase 5B-B;
EC=1.14.11.-;
AltName: Full=Histone demethylase JARID1B-B;
AltName: Full=Jumonji/ARID domain-containing protein 1B-B;
Name=kdm5bb; Synonyms=jarid1b, jarid1bb;
ORFNames=si:dkey-193l3.2, zgc:85741;
Danio rerio (Zebrafish) (Brachydanio rerio).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
Cyprinidae; Danio.
NCBI_TaxID=7955;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Tuebingen;
PubMed=23594743; DOI=10.1038/nature12111;
Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C.,
Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L.,
McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C.,
Koch R., Rauch G.J., White S., Chow W., Kilian B., Quintais L.T.,
Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T.,
Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F.,
Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H.,
Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G.,
Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B.,
Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S.,
Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C.,
Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H.,
Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C.,
Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
Humphries M., Sycamore N., Barker D., Saunders D., Wallis J.,
Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S.,
Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R.,
Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R.,
Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R.,
Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A.,
Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S.,
Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J.,
Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C.,
Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H.,
Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J.,
Stemple D.L.;
"The zebrafish reference genome sequence and its relationship to the
human genome.";
Nature 496:498-503(2013).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Kidney;
NIH - Zebrafish Gene Collection (ZGC) project;
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone
H3, thereby playing a central role in histone code. Does not
demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates
trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as
a transcriptional corepressor (By similarity). {ECO:0000250}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00355, ECO:0000255|PROSITE-ProRule:PRU00537}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q6IQX0-1; Sequence=Displayed;
Note=No experimental confirmation available.;
Name=2;
IsoId=Q6IQX0-2; Sequence=VSP_035555;
Note=No experimental confirmation available.;
-!- DOMAIN: Both the JmjC domain and the JmjN domain are required for
enzymatic activity. {ECO:0000250}.
-!- DOMAIN: The 2 first PHD-type zinc finger domains are required for
transcription repression activity. {ECO:0000250}.
-!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAQ14256.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; BX322655; CAQ14256.1; ALT_SEQ; Genomic_DNA.
EMBL; BX322655; CAQ14257.1; -; Genomic_DNA.
EMBL; BX664742; CAQ14257.1; JOINED; Genomic_DNA.
EMBL; BX664742; CAQ13548.1; -; Genomic_DNA.
EMBL; BX322655; CAQ13548.1; JOINED; Genomic_DNA.
EMBL; BC071280; AAH71280.1; -; mRNA.
UniGene; Dr.35782; -.
ProteinModelPortal; Q6IQX0; -.
SMR; Q6IQX0; -.
STRING; 7955.ENSDARP00000023794; -.
PaxDb; Q6IQX0; -.
PRIDE; Q6IQX0; -.
ZFIN; ZDB-GENE-030424-1; kdm5bb.
eggNOG; KOG1246; Eukaryota.
eggNOG; ENOG410XR9J; LUCA.
HOGENOM; HOG000290719; -.
InParanoid; Q6IQX0; -.
PhylomeDB; Q6IQX0; -.
BRENDA; 1.14.11.B2; 928.
PRO; PR:Q6IQX0; -.
Proteomes; UP000000437; Unplaced.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0034648; F:histone demethylase activity (H3-dimethyl-K4 specific); ISS:UniProtKB.
GO; GO:0034647; F:histone demethylase activity (H3-trimethyl-K4 specific); ISS:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0016706; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors; IEA:InterPro.
GO; GO:0034720; P:histone H3-K4 demethylation; ISS:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 1.10.150.60; -; 1.
Gene3D; 3.30.40.10; -; 3.
InterPro; IPR001606; ARID_dom.
InterPro; IPR036431; ARID_dom_sf.
InterPro; IPR003347; JmjC_dom.
InterPro; IPR003349; JmjN.
InterPro; IPR013637; Lys_sp_deMease-like_dom.
InterPro; IPR019786; Zinc_finger_PHD-type_CS.
InterPro; IPR004198; Znf_C5HC2.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF01388; ARID; 1.
Pfam; PF02373; JmjC; 1.
Pfam; PF02375; JmjN; 1.
Pfam; PF00628; PHD; 2.
Pfam; PF08429; PLU-1; 1.
Pfam; PF02928; zf-C5HC2; 1.
SMART; SM00501; BRIGHT; 1.
SMART; SM00558; JmjC; 1.
SMART; SM00545; JmjN; 1.
SMART; SM00249; PHD; 3.
SUPFAM; SSF46774; SSF46774; 1.
SUPFAM; SSF57903; SSF57903; 3.
PROSITE; PS51011; ARID; 1.
PROSITE; PS51184; JMJC; 1.
PROSITE; PS51183; JMJN; 1.
PROSITE; PS01359; ZF_PHD_1; 2.
PROSITE; PS50016; ZF_PHD_2; 3.
2: Evidence at transcript level;
Alternative splicing; Chromatin regulator; Complete proteome;
Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase;
Reference proteome; Repeat; Transcription; Transcription regulation;
Zinc; Zinc-finger.
CHAIN 1 1503 Lysine-specific demethylase 5B-B.
/FTId=PRO_0000292415.
DOMAIN 15 56 JmjN. {ECO:0000255|PROSITE-
ProRule:PRU00537}.
DOMAIN 80 170 ARID. {ECO:0000255|PROSITE-
ProRule:PRU00355}.
DOMAIN 439 605 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
ZN_FING 295 345 PHD-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
ZN_FING 1168 1216 PHD-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
ZN_FING 1444 1497 PHD-type 3. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
COMPBIAS 286 289 Poly-Pro.
COMPBIAS 1092 1095 Poly-Lys.
METAL 485 485 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 488 488 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 573 573 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
VAR_SEQ 175 175 L -> LAPEFAVKLTGFGEPPVLEE (in isoform 2).
{ECO:0000305}.
/FTId=VSP_035555.
CONFLICT 1284 1284 Y -> H (in Ref. 2; AAH71280).
{ECO:0000305}.
CONFLICT 1293 1293 L -> Q (in Ref. 2; AAH71280).
{ECO:0000305}.
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


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