KDM7B_DANRE
ID KDM7B_DANRE Reviewed; 577 AA.
AC P0CF52;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 1.
DT 03-AUG-2022, entry version 51.
DE RecName: Full=Lysine-specific demethylase 7B;
DE Short=DrKDM7b;
DE EC=1.14.11.-;
DE AltName: Full=JmjC domain-containing histone demethylation protein 1D-B;
GN Name=jhdm1db; Synonyms=kdm7b;
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 FUNCTION, AND TISSUE SPECIFICITY.
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).
CC -!- FUNCTION: Histone demethylase required for brain development.
CC Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2
CC and H3K27me2, respectively) of histone H3 and monomethylated histone H4
CC 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone
CC code (By similarity). {ECO:0000250, ECO:0000269|PubMed:20194436}.
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:0000250}.
CC -!- TISSUE SPECIFICITY: Predominantly expressed in brain.
CC {ECO:0000269|PubMed:20194436}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC Binding to H3K4me3 prevents its access to H3K9me2 (By similarity).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D
CC subfamily. {ECO:0000305}.
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DR EMBL; CU468035; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; P0CF52; -.
DR SMR; P0CF52; -.
DR STRING; 7955.ENSDARP00000050378; -.
DR PaxDb; P0CF52; -.
DR PRIDE; P0CF52; -.
DR ZFIN; ZDB-GENE-050309-32; kdm7ab.
DR eggNOG; KOG1633; Eukaryota.
DR eggNOG; KOG1634; Eukaryota.
DR InParanoid; P0CF52; -.
DR PhylomeDB; P0CF52; -.
DR Reactome; R-DRE-3214842; HDMs demethylate histones.
DR PRO; PR:P0CF52; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; ISS:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; ISS:UniProtKB.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IDA:ZFIN.
DR GO; GO:0071558; F:histone H3-tri/di-methyl-lysine-27 demethylase activity; IDA:ZFIN.
DR GO; GO:0035575; F:histone H4-methyl-lysine-20 demethylase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0071557; P:histone H3-K27 demethylation; IDA:ZFIN.
DR GO; GO:0070544; P:histone H3-K36 demethylation; ISS:UniProtKB.
DR GO; GO:0033169; P:histone H3-K9 demethylation; IDA:ZFIN.
DR GO; GO:0035574; P:histone H4-K20 demethylation; ISS:UniProtKB.
DR GO; GO:0030901; P:midbrain development; IMP:UniProtKB.
DR GO; GO:0006482; P:protein demethylation; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR InterPro; IPR041070; JHD.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR Pfam; PF17811; JHD; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Neurogenesis;
KW Nucleus; Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..577
FT /note="Lysine-specific demethylase 7B"
FT /id="PRO_0000394250"
FT DOMAIN 198..354
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 5..56
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 460..513
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 471..504
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 247
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 250
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 252
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 267
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 322
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
SQ SEQUENCE 577 AA; 67006 MW; 4BB07DB47BE8164D CRC64;
MATAQLYCVC RQPYDVSRFM IECDICKDWF HGSCVEVEEH YAVDIDVYHC PNCDVHHGPS
LMKKRRNWHR HDYTEPDDGS KPVQAGTSVF VRELQARTFP SGDEILQPMH GGQVTQRYLE
RHGFRYPIIV SKREELGLRL PPPDFSIKDV ERYVGGNKVI DVIDVARQAD SKMKLKAFVK
YYYSPQRPKV LNVISLEFSD TKMAELVVVP DIAQKMSWVE NYWPDDSYFP KPFVQKYCLM
GVKDSYTDFH IDFGGTSVWY HVLWGEKIFY LIKPTPANLA LYEEWSSSPN QSEVFFGEKV
DKCYKCVVRQ GTTLLIPTGW IHAVLTSQDC MAFGGNFLHN LNIGMQLRCY EMERRLKTPD
LFKFPYFEAI CWYVAKNLLE TLKESREENC LPPEYLIKGV KALITALRNW LKREVTEPAS
EVPDHIRPNH LIKMLTKEIQ YLENGNCGNK PMKLQESSIC PSTRSAHERG SHARKTARRL
RGHHHHHHRH HHHHHHHHHH NHQHSDGPKA PSHLDIYEQH TQEVLKRLEM GPYEEDASFN
LKVNGKFNKV STASAAAAER SLENDLRLVL CNGQIVR
