KDM4B_DROME
ID KDM4B_DROME Reviewed; 590 AA.
AC Q9V6L0;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 3.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Probable lysine-specific demethylase 4B;
DE EC=1.14.11.66 {ECO:0000250|UniProtKB:O94953};
DE AltName: Full=Probable JmjC domain-containing histone demethylation protein 3B;
DE AltName: Full=Probable [histone H3]-trimethyl-L-lysine(9) demethylase 4B {ECO:0000305};
GN Name=Kdm4B; ORFNames=CG33182;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
CC -!- FUNCTION: Probable histone demethylase that specifically demethylates
CC 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central
CC role in histone code. Demethylation of Lys residue generates
CC formaldehyde and succinate (By similarity). {ECO:0000250}.
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 -!- SIMILARITY: Belongs to the JHDM3 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; AE013599; AAF58413.3; -; Genomic_DNA.
DR RefSeq; NP_001163137.1; NM_001169666.2.
DR RefSeq; NP_001163138.1; NM_001169667.2.
DR RefSeq; NP_001163139.1; NM_001169668.2.
DR RefSeq; NP_788344.2; NM_176164.4.
DR AlphaFoldDB; Q9V6L0; -.
DR SMR; Q9V6L0; -.
DR BioGRID; 77204; 5.
DR STRING; 7227.FBpp0302636; -.
DR PaxDb; Q9V6L0; -.
DR PRIDE; Q9V6L0; -.
DR EnsemblMetazoa; FBtr0087770; FBpp0086883; FBgn0053182.
DR EnsemblMetazoa; FBtr0302052; FBpp0291262; FBgn0053182.
DR EnsemblMetazoa; FBtr0302053; FBpp0291263; FBgn0053182.
DR EnsemblMetazoa; FBtr0302054; FBpp0291264; FBgn0053182.
DR GeneID; 318918; -.
DR KEGG; dme:Dmel_CG33182; -.
DR UCSC; CG33182-RA; d. melanogaster.
DR CTD; 23030; -.
DR FlyBase; FBgn0053182; Kdm4B.
DR VEuPathDB; VectorBase:FBgn0053182; -.
DR eggNOG; KOG0958; Eukaryota.
DR GeneTree; ENSGT00940000154930; -.
DR HOGENOM; CLU_001442_6_2_1; -.
DR InParanoid; Q9V6L0; -.
DR OMA; NWRDDIV; -.
DR PhylomeDB; Q9V6L0; -.
DR BRENDA; 1.14.11.66; 1994.
DR BRENDA; 1.14.11.67; 1994.
DR BRENDA; 1.14.11.69; 1994.
DR BioGRID-ORCS; 318918; 0 hits in 3 CRISPR screens.
DR ChiTaRS; Kdm4B; fly.
DR GenomeRNAi; 318918; -.
DR PRO; PR:Q9V6L0; -.
DR Proteomes; UP000000803; Chromosome 2R.
DR Bgee; FBgn0053182; Expressed in central nervous system and 12 other tissues.
DR ExpressionAtlas; Q9V6L0; baseline.
DR Genevisible; Q9V6L0; DM.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; IDA:FlyBase.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IDA:FlyBase.
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:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0016577; P:histone demethylation; ISS:UniProtKB.
DR GO; GO:0070544; P:histone H3-K36 demethylation; IMP:FlyBase.
DR GO; GO:0033169; P:histone H3-K9 demethylation; IDA:FlyBase.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
PE 3: Inferred from homology;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..590
FT /note="Probable lysine-specific demethylase 4B"
FT /id="PRO_0000234380"
FT DOMAIN 9..51
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 140..306
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT REGION 372..395
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 417..590
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 372..387
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 457..483
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 500..517
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 534..590
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 130
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 186
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 188
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 196
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250"
FT BINDING 204
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 232
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 238
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 239
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 274
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 304
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 306
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
SQ SEQUENCE 590 AA; 66437 MW; E7B8C1CB3FA88F75 CRC64;
MKMSEVPRIK VFRPTWEEFK DFPKYVAYME SQGAHKAGLA KVVPPPEWVP RRSGYADLDA
LNVTIPAPIC QVVTGKQGYY QQINIQKKPL TVKQFSELAS TERYATPKHF DFEDLERKYW
KNITYVAPIY GADVSGSITD TDQDSWNINR LGTILDYVNK DYNIQIDGVN TAYLYFGMWK
TTFAWHTEDM DLYSINYLHF GAPKTWYVVP PECGRKLEKV ANQYFPASYK NCNAYLRHKM
TLISPQILKQ HDVPVSKITQ EAGEIMITFP FGYHAGFNHG FNCAESTNFA MERWIEYGKR
AVQCTCSNDM VKISMDTFVK RFQSDRYDLW MEGRDVGRHP EDPPNAVLSA APLPPHLDVL
LCDKKMKKQC NPTKAKSFKE RNPDLDLDEI QQNPNVPDDV KAMLKESVLT LDTGDLATDE
ADFPNEDAMS LQSPANLKTK QELLEYIDDG TEDDDEEEDF KRRKQKRRYD ADYDDDWLAS
KRKTNSRNNR GRSPRTKDDR SISPASSTSS TSRGARRGKA SGTPRKTPAR RKKDSITTSP
AVSSAATAVK TPTSAVVAGT TSIATTTTPP ADGGGGESSS LGSHCTTASP
