ID KDM3B_MOUSE Reviewed; 1762 AA. AC Q6ZPY7; B9EKS2; Q2VPQ5; Q5U5V7; Q6P9K3; Q8CCE2; Q8K2A5; Q9CU57; DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot. DT 29-SEP-2021, sequence version 3. DT 24-JAN-2024, entry version 121. DE RecName: Full=Lysine-specific demethylase 3B; DE EC=1.14.11.65 {ECO:0000250|UniProtKB:Q7LBC6}; DE AltName: Full=JmjC domain-containing histone demethylation protein 2B; DE AltName: Full=Jumonji domain-containing protein 1B; DE AltName: Full=[histone H3]-dimethyl-L-lysine(9) demethylase 3B {ECO:0000305}; GN Name=Kdm3b; Synonyms=Jhdm2b, Jmjd1b, Kiaa1082; 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] (ISOFORM 2). RC TISSUE=Embryonic tail; RX PubMed=14621295; DOI=10.1093/dnares/10.4.167; RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., RA Saga Y., Nagase T., Ohara O., Koga H.; RT "Prediction of the coding sequences of mouse homologues of KIAA gene: III. RT The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs RT identified by screening of terminal sequences of cDNA clones randomly RT sampled from size-fractionated libraries."; RL DNA Res. 10:167-180(2003). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=C57BL/6J; RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112; RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S., RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., RA Eichler E.E., Ponting C.P.; RT "Lineage-specific biology revealed by a finished genome assembly of the RT mouse."; RL PLoS Biol. 7:E1000112-E1000112(2009). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). RC STRAIN=C57BL/6J, and Czech II; TISSUE=Brain, Eye, and 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 [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1319-1762 (ISOFORM 1). RC STRAIN=C57BL/6J; TISSUE=Testis, and Thymus; 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 [5] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-547; SER-557 AND SER-561, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Brain, Heart, Kidney, Lung, Spleen, and Testis; RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001; RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R., RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.; RT "A tissue-specific atlas of mouse protein phosphorylation and expression."; RL Cell 143:1174-1189(2010). CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of CC histone H3, thereby playing a central role in histone code. CC Demethylation of Lys residue generates formaldehyde and succinate May CC have tumor suppressor activity (By similarity). {ECO:0000250}. CC -!- CATALYTIC ACTIVITY: CC Reaction=2 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] CC + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl(9)-[histone H3] + 2 CC succinate; Xref=Rhea:RHEA:60188, Rhea:RHEA-COMP:15541, Rhea:RHEA- CC COMP:15546, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, CC ChEBI:CHEBI:16842, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031, CC ChEBI:CHEBI:61976; EC=1.14.11.65; CC Evidence={ECO:0000250|UniProtKB:Q7LBC6}; 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 -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=2; CC Name=1; CC IsoId=Q6ZPY7-1; Sequence=Displayed; CC Name=2; CC IsoId=Q6ZPY7-3; Sequence=VSP_061228, VSP_061229, VSP_061230; CC -!- DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the CC association with nuclear receptors. {ECO:0000250}. CC -!- SIMILARITY: Belongs to the JHDM2 histone demethylase family. CC {ECO:0000305}. CC -!- SEQUENCE CAUTION: CC Sequence=AAH38376.1; Type=Frameshift; Evidence={ECO:0000305}; CC Sequence=BAC98091.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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; AK129281; BAC98091.1; ALT_INIT; mRNA. DR EMBL; GL456180; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; BC031981; AAH31981.1; -; mRNA. DR EMBL; BC038376; AAH38376.1; ALT_FRAME; mRNA. DR EMBL; BC060727; AAH60727.1; -; mRNA. DR EMBL; BC108415; AAI08416.1; -; mRNA. DR EMBL; BC151084; AAI51085.1; -; mRNA. DR EMBL; AK018027; BAB31043.1; -; mRNA. DR EMBL; AK033343; BAC28239.1; -; mRNA. DR CCDS; CCDS37761.1; -. [Q6ZPY7-1] DR RefSeq; NP_001074725.1; NM_001081256.1. [Q6ZPY7-1] DR AlphaFoldDB; Q6ZPY7; -. DR SMR; Q6ZPY7; -. DR BioGRID; 234928; 1. DR STRING; 10090.ENSMUSP00000037628; -. DR GlyGen; Q6ZPY7; 1 site, 1 O-linked glycan (1 site). DR iPTMnet; Q6ZPY7; -. DR PhosphoSitePlus; Q6ZPY7; -. DR SwissPalm; Q6ZPY7; -. DR EPD; Q6ZPY7; -. DR jPOST; Q6ZPY7; -. DR MaxQB; Q6ZPY7; -. DR PaxDb; 10090-ENSMUSP00000037628; -. DR PeptideAtlas; Q6ZPY7; -. DR ProteomicsDB; 264985; -. [Q6ZPY7-1] DR ProteomicsDB; 336542; -. DR Pumba; Q6ZPY7; -. DR Antibodypedia; 14936; 396 antibodies from 38 providers. DR Ensembl; ENSMUST00000043775.9; ENSMUSP00000037628.8; ENSMUSG00000038773.12. [Q6ZPY7-1] DR GeneID; 277250; -. DR KEGG; mmu:277250; -. DR UCSC; uc008elq.1; mouse. DR AGR; MGI:1923356; -. DR CTD; 51780; -. DR MGI; MGI:1923356; Kdm3b. DR VEuPathDB; HostDB:ENSMUSG00000038773; -. DR eggNOG; KOG1356; Eukaryota. DR GeneTree; ENSGT00940000158095; -. DR HOGENOM; CLU_002991_0_0_1; -. DR InParanoid; Q6ZPY7; -. DR OMA; ENSWVSA; -. DR OrthoDB; 3473445at2759; -. DR PhylomeDB; Q6ZPY7; -. DR TreeFam; TF324723; -. DR BRENDA; 1.14.11.65; 3474. DR BRENDA; 1.14.11.66; 3474. DR Reactome; R-MMU-3214842; HDMs demethylate histones. DR BioGRID-ORCS; 277250; 11 hits in 82 CRISPR screens. DR ChiTaRS; Kdm3b; mouse. DR PRO; PR:Q6ZPY7; -. DR Proteomes; UP000000589; Chromosome 18. DR RNAct; Q6ZPY7; Protein. DR Bgee; ENSMUSG00000038773; Expressed in embryonic post-anal tail and 264 other cell types or tissues. DR GO; GO:0000785; C:chromatin; IBA:GO_Central. DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central. DR GO; GO:0005654; C:nucleoplasm; ISO:MGI. DR GO; GO:0016209; F:antioxidant activity; ISO:MGI. DR GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central. DR GO; GO:0032454; F:histone H3K9 demethylase activity; IBA:GO_Central. DR GO; GO:0140683; F:histone H3K9me/H3K9me2 demethylase activity; IEA:UniProtKB-EC. 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:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central. DR Gene3D; 2.60.120.650; Cupin; 1. DR InterPro; IPR045109; JHDM2-like. DR InterPro; IPR003347; JmjC_dom. DR PANTHER; PTHR12549; JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN; 1. DR PANTHER; PTHR12549:SF8; LYSINE-SPECIFIC DEMETHYLASE 3B; 1. DR Pfam; PF02373; JmjC; 1. DR SMART; SM00558; JmjC; 1. DR SUPFAM; SSF51197; Clavaminate synthase-like; 1. DR PROSITE; PS51184; JMJC; 1. PE 1: Evidence at protein level; KW Acetylation; Alternative splicing; Chromatin regulator; Dioxygenase; Iron; KW Isopeptide bond; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; KW Reference proteome; Transcription; Transcription regulation; KW Ubl conjugation; Zinc; Zinc-finger. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT CHAIN 2..1762 FT /note="Lysine-specific demethylase 3B" FT /id="PRO_0000234374" FT DOMAIN 1499..1722 FT /note="JmjC" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538" FT ZN_FING 1032..1057 FT /note="C6-type" FT /evidence="ECO:0000255" FT REGION 253..350 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 426..468 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 574..613 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 713..763 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 806..853 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 1146..1217 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 1285..1306 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOTIF 1294..1298 FT /note="LXXLL motif" FT COMPBIAS 274..313 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 809..830 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1146..1168 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 1561 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538" FT BINDING 1563 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538" FT BINDING 1690 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538" FT MOD_RES 2 FT /note="N-acetylalanine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 493 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 547 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:21183079" FT MOD_RES 557 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:21183079" FT MOD_RES 561 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:21183079" FT MOD_RES 615 FT /note="Phosphothreonine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 767 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 774 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 779 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 799 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 1254 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT MOD_RES 1260 FT /note="Phosphoserine" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT CROSSLNK 789 FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with FT G-Cter in SUMO2)" FT /evidence="ECO:0000250|UniProtKB:Q7LBC6" FT VAR_SEQ 262..461 FT /note="Missing (in isoform 2)" FT /evidence="ECO:0000303|PubMed:14621295" FT /id="VSP_061228" FT VAR_SEQ 1270..1324 FT /note="LTPKLFNSLLLGPTASNSKTEGSSLRDLLHSGPGKLPQTPLDTGIPFPPVFS FT SSS -> HVTSDLAHPRRWGCSPSRTLHEHRSLQDPGRAHCFSQEAPGLGNVYLVKNRF FT VVK (in isoform 2)" FT /evidence="ECO:0000303|PubMed:14621295" FT /id="VSP_061229" FT VAR_SEQ 1325..1762 FT /note="Missing (in isoform 2)" FT /evidence="ECO:0000303|PubMed:14621295" FT /id="VSP_061230" FT CONFLICT 1326 FT /note="V -> G (in Ref. 3; AAH31981)" FT /evidence="ECO:0000305" FT CONFLICT 1569..1570 FT /note="NV -> SL (in Ref. 4; BAB31043)" FT /evidence="ECO:0000305" FT CONFLICT 1745 FT /note="V -> G (in Ref. 4; BAB31043)" FT /evidence="ECO:0000305" SQ SEQUENCE 1762 AA; 191460 MW; EB0D535476236CDF CRC64; MADAAASPVG KRLLLLFADP TASASASAPT AAAVVSGDPG PALRTRAWRA GTVRAMSGAV PQDLAIFVEF DGCNWKQHSW VKVHAEDVLA LLLEGSLVWA PRKDPVLLQG TRVPVAQWPA LTFTPLVDKL GLGSVVPVEY LVDRELRFLS DANGMHLFQM GTDVQNQILL EHAALRETVN ALISDQKLQE IFSRGPYSVQ GHRVKVYQPE GEEVWLCGVV SRQDSVTRLM EVSITETGEV KSVDPRLTHV MLMDSSTPQS EGGTIKAVKS SKGKKKRESI EGRDGRRRKS ASDSGCDPAT KKLKGDRGEV DSNGSDGGEA SRGPWKGGNA SGEPGLEQRA KQPPSTFVPQ INRNIRFATY TKENGRTLVV QDEPVGGDTP VPFTPYASAT GQTPLAPEVG GAENKEAGKT LEQVSQGMVA SAAVVTTASS TPTTVRISDT GLASGTGPEK QKGSWSQASG ENSRNSSLAS SGFGVSLSSL SQPLTFGSGR SQSNGVLATD NKPLGFSFSC SSASESQKDS DLSKNLFFQC MSQNVPSTNY LSRVSESVAD DSSSRDSFTQ SLESLTSGLC KGRSVLGADT QPGPKAGSSV DRKVPAESMP TLTPAFPRSL LNTRTPENHE NLFLQPPKLS REEPSNPFLA FVEKVEHSPF SSFVSQASGS SSSATSVTSK ATASWPESHS SAESAPLAKK KPLFITTDSS KLVSGVLGSA LSTGSPSLSA VGNGRSSSPT NSLTQPIEMP TLSSSPTEER PTVGPGQQDN PLLKTFSTVF GRHSGSFLSA PAEFAQENKA PFEAVKRFSL DERSLACRQD SDSSTNSDLS DLSDSEEQLQ AKSGLKGIPE HLMGKLGPNG ERSAELLLGK GKGKQAPKGR PRTAPLKVGQ SVLKDVSKVR KLKQSGEPFL QDGSCINVAP HLHKCRECRL ERYRKFKEQE QDDSTVACRF FHFRRLVFTR KGVLRVEGFL SPQQSDPDAM NLWIPSSSLA EGIDLETSKY ILANVGDQFC QLVMSEKEAM MMVEPHQKVA WKRAVRGVRE MCDVCETTLF NIHWVCRKCG FGVCLDCYRL RKSRPRSETE EMGDEEVFSW LKCAKGQSHE PENLMPTQII PGTALYNIGD MVHAARGKWG IKANCPCISR QSKSVLRPAV TNGISQLPSV TPSASSGNET TFSSGGGAAA VTNPEPDQVP KGAGTDGRSE EPLKAEGSAS NSNSELKAIR PPCPDTAPPS SALHWLADLA TQKAKEETKD AGSLRSVLNK ESHSPFGLDS FNSTAKVSPL TPKLFNSLLL GPTASNSKTE GSSLRDLLHS GPGKLPQTPL DTGIPFPPVF SSSSAVAKSK ASLPDFLDHI IASVVENKKT SDPSKRSCNL TDTQKEVKEM AMGLNVLDPH TSHSWLCDGR LLCLHDPSNK NNWKIFRECW KQGQPVLVSG VHKKLKSELW KPEAFSQEFG DQDVDLVNCR NCAIISDVKV RDFWDGFEII CKRLRSEDGQ PMVLKLKDWP PGEDFRDMMP TRFEDLMENL PLPEYTKRDG RLNLASRLPS YFVRPDLGPK MYNAYGLITA EDRRVGTTNL HLDVSDAVNV MVYVGIPVGE GAHDEEVLKT IDEGDADEVT KQRIHDGKEK PGALWHIYAA KDAEKIRELL RKVGEEQGQE NPPDHDPIHD QSWYLDQILR KRLFEEYGVQ GWAIVQFLGD AVFIPAGAPH QVHNLYSCIK VAEDFVSPEH VKHCFRLTQE FRHLSNTHTN HEDKLQVKNI IYHAVKDAVG TLKAHESKLA RS //