KDM4B_MOUSE
ID KDM4B_MOUSE Reviewed; 1086 AA.
AC Q91VY5; Q3UR22; Q6ZQ30; Q99K42;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Lysine-specific demethylase 4B;
DE EC=1.14.11.66 {ECO:0000250|UniProtKB:O94953};
DE AltName: Full=JmjC domain-containing histone demethylation protein 3B;
DE AltName: Full=Jumonji domain-containing protein 2B;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(9) demethylase 4B {ECO:0000305};
GN Name=Kdm4b; Synonyms=Jhdm3b, Jmjd2b;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Embryonic tail, and Spinal ganglion;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Mammary tumor;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP FUNCTION, AND DEVELOPMENTAL STAGE.
RX PubMed=27023172; DOI=10.1038/tp.2016.31;
RA Fujiwara K., Fujita Y., Kasai A., Onaka Y., Hashimoto H., Okada H.,
RA Yamashita T.;
RT "Deletion of JMJD2B in neurons leads to defective spine maturation,
RT hyperactive behavior and memory deficits in mouse.";
RL Transl. Psychiatry 6:e766-e766(2016).
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of
CC histone H3, thereby playing a role in histone code. Does not
CC demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-
CC 20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker
CC activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue
CC generates formaldehyde and succinate (By similarity). Plays a critical
CC role in the development of the central nervous system (CNS).
CC {ECO:0000250|UniProtKB:O94953, ECO:0000269|PubMed:27023172}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-
CC [histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L-
CC lysyl(9)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60200, Rhea:RHEA-
CC COMP:15538, Rhea:RHEA-COMP:15542, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, ChEBI:CHEBI:61961;
CC EC=1.14.11.66; Evidence={ECO:0000250|UniProtKB:O94953};
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:PRU00537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q91VY5-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q91VY5-2; Sequence=VSP_018309, VSP_018310;
CC -!- DEVELOPMENTAL STAGE: Expression is especially strong in the hippocampus
CC and throughout the CNS from embryonic periods through adulthood.
CC {ECO:0000269|PubMed:27023172}.
CC -!- DOMAIN: The 2 Tudor domains recognize and bind methylated histones.
CC Double Tudor domain has an interdigitated structure and the unusual
CC fold is required for its ability to bind methylated histone tails (By
CC similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JHDM3 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC98043.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK129233; BAC98043.1; ALT_INIT; mRNA.
DR EMBL; AK141879; BAE24866.1; -; mRNA.
DR EMBL; BC005480; AAH05480.1; -; mRNA.
DR EMBL; BC007145; AAH07145.1; -; mRNA.
DR CCDS; CCDS28904.1; -. [Q91VY5-1]
DR RefSeq; NP_742144.1; NM_172132.2. [Q91VY5-1]
DR AlphaFoldDB; Q91VY5; -.
DR SMR; Q91VY5; -.
DR BioGRID; 228758; 8.
DR IntAct; Q91VY5; 2.
DR STRING; 10090.ENSMUSP00000025036; -.
DR iPTMnet; Q91VY5; -.
DR PhosphoSitePlus; Q91VY5; -.
DR EPD; Q91VY5; -.
DR MaxQB; Q91VY5; -.
DR PaxDb; Q91VY5; -.
DR PeptideAtlas; Q91VY5; -.
DR PRIDE; Q91VY5; -.
DR ProteomicsDB; 264989; -. [Q91VY5-1]
DR ProteomicsDB; 264990; -. [Q91VY5-2]
DR Antibodypedia; 11548; 550 antibodies from 36 providers.
DR DNASU; 193796; -.
DR Ensembl; ENSMUST00000025036; ENSMUSP00000025036; ENSMUSG00000024201. [Q91VY5-1]
DR GeneID; 193796; -.
DR KEGG; mmu:193796; -.
DR UCSC; uc008dbu.2; mouse. [Q91VY5-2]
DR UCSC; uc008dbv.2; mouse. [Q91VY5-1]
DR CTD; 23030; -.
DR MGI; MGI:2442355; Kdm4b.
DR VEuPathDB; HostDB:ENSMUSG00000024201; -.
DR eggNOG; KOG0958; Eukaryota.
DR GeneTree; ENSGT00940000159248; -.
DR InParanoid; Q91VY5; -.
DR OMA; DSWMCSR; -.
DR OrthoDB; 1186832at2759; -.
DR PhylomeDB; Q91VY5; -.
DR TreeFam; TF106449; -.
DR BRENDA; 1.14.11.66; 3474.
DR BRENDA; 1.14.11.69; 3474.
DR Reactome; R-MMU-3214842; HDMs demethylate histones.
DR Reactome; R-MMU-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-MMU-9018519; Estrogen-dependent gene expression.
DR BioGRID-ORCS; 193796; 1 hit in 77 CRISPR screens.
DR ChiTaRS; Kdm4b; mouse.
DR PRO; PR:Q91VY5; -.
DR Proteomes; UP000000589; Chromosome 17.
DR RNAct; Q91VY5; protein.
DR Bgee; ENSMUSG00000024201; Expressed in embryonic brain and 266 other tissues.
DR ExpressionAtlas; Q91VY5; baseline and differential.
DR Genevisible; Q91VY5; MM.
DR GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0005634; C:nucleus; ISO:MGI.
DR GO; GO:0005721; C:pericentric heterochromatin; IDA:MGI.
DR GO; GO:0032452; F:histone demethylase activity; IDA:MGI.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; ISO:MGI.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IDA:MGI.
DR GO; GO:0140684; F:histone H3-tri/dimethyl-lysine-9 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0007420; P:brain development; IMP:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0070544; P:histone H3-K36 demethylation; IDA:MGI.
DR GO; GO:0033169; P:histone H3-K9 demethylation; IDA:MGI.
DR GO; GO:1900113; P:negative regulation of histone H3-K9 trimethylation; IDA:MGI.
DR CDD; cd04508; TUDOR; 1.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR034732; EPHD.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR040477; KDM4_Tudor_2.
DR InterPro; IPR002999; Tudor.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF18104; Tudor_2; 2.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 2.
DR SMART; SM00333; TUDOR; 2.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51805; EPHD; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
PE 2: Evidence at transcript level;
KW Acetylation; Alternative splicing; Chromatin regulator; Dioxygenase; Iron;
KW Metal-binding; Nucleus; Oxidoreductase; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1086
FT /note="Lysine-specific demethylase 4B"
FT /id="PRO_0000183176"
FT DOMAIN 15..57
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 146..309
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 905..962
FT /note="Tudor 1"
FT DOMAIN 963..1019
FT /note="Tudor 2"
FT ZN_FING 719..777
FT /note="PHD-type 1"
FT ZN_FING 782..815
FT /note="C2HC pre-PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 838..895
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 379..536
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 557..624
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1024..1043
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 379..395
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 453..470
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 485..533
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 133
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 189
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 191
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 199
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 207
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 235
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 241
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 242
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 277
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 307
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 309
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT MOD_RES 599
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O94953"
FT VAR_SEQ 593..599
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_018309"
FT VAR_SEQ 940..997
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_018310"
FT CONFLICT 40
FT /note="A -> T (in Ref. 1; BAE24866)"
FT /evidence="ECO:0000305"
FT CONFLICT 576
FT /note="M -> L (in Ref. 2; AAH05480)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1086 AA; 121604 MW; 5418B6CBF5E14DAA CRC64;
MGSEDHSAQN PSCKIMTFRP TMDEFRDFNR YVAYIESQGA HRAGLAKIIP PKEWKPRQTY
DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR LANSEKYCTP RHQDFDDLER
KYWKNLTFVS PIYGADISGS LYDDDVAQWN IGNLRTILDM VERECGTIIE GVNTPYLYFG
MWKTTFAWHT EDMDLYSINY LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR
HKMTLISPII LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY
GKVATQCTCR KDMVKISMDV FVRILQPERY EQWKQGRDLT VLDHTRPTAL SSPELSSWSA
SRTSIKAKLL RRQISVKESR PWRKAEEERR REPTRRPGPA SHRRRSQPKK SKPEESRSPG
EATAGVSTLD EARGCSRGEA MPEDEEEEEL LPSQGHEAEG VEEDGRGKPR PTKARNKKKT
PSPSSPPLLS APPALFPTEE VLRPPPQPKS PGPAMGPMAA EGGPPPTPLN VVPPGAPVEE
AEVRPRPIIP MLYVLPRTSS TDGDREHSAH AQLAPMELGP EEENQAQAGD SQGTTPFSKL
KVEIKKSRRH PLGRPPTRSP LSVVKQEASS DEEAFLFSGE DDVTDPEALR SLLSLQWKNK
AASFQAERKF NAAAALSEPY CAICTLFYPY SQSVQTERDS AVQPPSKSGQ RTRPLIPEMC
FTSSGENTEP LPANSYVGED GTSPLISCAH CCLQVHASCY GVRPELAKEG WTCSRCAAHA
WTAECCLCNL RGGALQRTTE HRWIHVICAI AVPEVRFLNV IERNPVDVSA IPEQRWKLKC
IYCRKRMKRV SGACIQCSYE HCSTSFHVTC AHAAGVLMEP DDWPYVVSIT CLKHRASGAG
GQLLRTVSLG QIVITKNRNG LYYRCRVIGT TAQTFYEVNF DDGSYSDNLY PESITSRDCL
RLGPPPEGEL VELRWTDGNL YRARFISMAT SLIYQVEFED GSQLTVKRGD IFTLEEELPK
RVRSRLSLST GTPQEPSFSG DDVKAAKRPR VASVLATTTE DTGRSPEYLS FMESLLQAQG
RPGAPF
