KDM3B_HUMAN
ID KDM3B_HUMAN Reviewed; 1761 AA.
AC Q7LBC6; A6H8X7; Q9BVH6; Q9BW93; Q9BZ52; Q9NYF4; Q9UPS0;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 2.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Lysine-specific demethylase 3B;
DE EC=1.14.11.65 {ECO:0000269|PubMed:16603237};
DE AltName: Full=JmjC domain-containing histone demethylation protein 2B;
DE AltName: Full=Jumonji domain-containing protein 1B;
DE AltName: Full=Nuclear protein 5qNCA;
DE AltName: Full=[histone H3]-dimethyl-L-lysine(9) demethylase 3B {ECO:0000305};
GN Name=KDM3B; Synonyms=C5orf7, JHDM2B, JMJD1B, KIAA1082;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), AND TISSUE SPECIFICITY.
RC TISSUE=Bone marrow;
RX PubMed=11087669; DOI=10.1006/geno.2000.6345;
RA Lai F., Godley L.A., Fernald A.A., Orelli B.J., Pamintuan L., Zhao N.,
RA Le Beau M.M.;
RT "cDNA cloning and genomic structure of three genes localized to human
RT chromosome band 5q31 encoding potential nuclear proteins.";
RL Genomics 70:123-130(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, AND VARIANT
RP THR-256.
RX PubMed=11687974; DOI=10.1038/sj.onc.1204850;
RA Hu Z., Gomes I., Horrigan S.K., Kravarusic J., Mar B., Arbieva Z.,
RA Chyna B., Fulton N., Edassery S., Raza A., Westbrook C.A.;
RT "A novel nuclear protein, 5qNCA (LOC51780) is a candidate for the myeloid
RT leukemia tumor suppressor gene on chromosome 5 band q31.";
RL Oncogene 20:6946-6954(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT THR-256.
RC TISSUE=Brain;
RX PubMed=10470851; DOI=10.1093/dnares/6.3.197;
RA Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A.,
RA Kotani H., Nomura N., Ohara O.;
RT "Prediction of the coding sequences of unidentified human genes. XIV. The
RT complete sequences of 100 new cDNA clones from brain which code for large
RT proteins in vitro.";
RL DNA Res. 6:197-205(1999).
RN [4]
RP SEQUENCE REVISION.
RX PubMed=12168954; DOI=10.1093/dnares/9.3.99;
RA Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.;
RT "Construction of expression-ready cDNA clones for KIAA genes: manual
RT curation of 330 KIAA cDNA clones.";
RL DNA Res. 9:99-106(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15372022; DOI=10.1038/nature02919;
RA Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
RA Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
RA She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
RA Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
RA Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M.,
RA Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T.,
RA Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A.,
RA Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R.,
RA Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L.,
RA Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N.,
RA Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J.,
RA Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A.,
RA Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
RT "The DNA sequence and comparative analysis of human chromosome 5.";
RL Nature 431:268-274(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND VARIANT THR-256.
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3), AND VARIANT
RP THR-256.
RC TISSUE=Brain, and Eye;
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 [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=16603237; DOI=10.1016/j.cell.2006.03.027;
RA Yamane K., Toumazou C., Tsukada Y.I., Erdjument-Bromage H., Tempst P.,
RA Wong J., Zhang Y.;
RT "JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription
RT activation by androgen receptor.";
RL Cell 125:483-495(2006).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-798, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.;
RT "Global, in vivo, and site-specific phosphorylation dynamics in signaling
RT networks.";
RL Cell 127:635-648(2006).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-773 AND SER-779, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [13]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-361, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-773; SER-779 AND SER-798, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [16]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-492; SER-560; THR-614;
RP SER-766; SER-773; SER-778; SER-779; SER-1253 AND SER-1259, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [18]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-788, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [19]
RP INVOLVEMENT IN DIJOS, AND VARIANTS DIJOS 45-ARG--SER-1761 DEL;
RP 93-GLU--SER-1761 DEL; ARG-117; GLY-336; 827-GLN--SER-1761 DEL; GLN-943;
RP TRP-943; GLN-1028; VAL-1032; PRO-1509; 1517-ARG--SER-1761 DEL; CYS-1544;
RP LYS-1731 AND ARG-1734.
RX PubMed=30929739; DOI=10.1016/j.ajhg.2019.02.023;
RA Diets I.J., van der Donk R., Baltrunaite K., Waanders E., Reijnders M.R.F.,
RA Dingemans A.J.M., Pfundt R., Vulto-van Silfhout A.T., Wiel L., Gilissen C.,
RA Thevenon J., Perrin L., Afenjar A., Nava C., Keren B., Bartz S., Peri B.,
RA Beunders G., Verbeek N., van Gassen K., Thiffault I., Cadieux-Dion M.,
RA Huerta-Saenz L., Wagner M., Konstantopoulou V., Vodopiutz J., Griese M.,
RA Boel A., Callewaert B., Brunner H.G., Kleefstra T., Hoogerbrugge N.,
RA de Vries B.B.A., Hwa V., Dauber A., Hehir-Kwa J.Y., Kuiper R.P.,
RA Jongmans M.C.J.;
RT "De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual
RT Disability, Short Stature, and Facial Dysmorphism.";
RL Am. J. Hum. Genet. 104:758-766(2019).
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. {ECO:0000269|PubMed:16603237}.
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:0000269|PubMed:16603237};
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=3;
CC Name=1;
CC IsoId=Q7LBC6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q7LBC6-2; Sequence=VSP_018299, VSP_018300;
CC Name=3;
CC IsoId=Q7LBC6-3; Sequence=VSP_018298;
CC -!- TISSUE SPECIFICITY: Ubiquitous. Highly expressed in placenta, skeletal
CC muscle, kidney, heart and liver. {ECO:0000269|PubMed:11087669,
CC ECO:0000269|PubMed:11687974}.
CC -!- DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the
CC association with nuclear receptors. {ECO:0000250}.
CC -!- DISEASE: Diets-Jongmans syndrome (DIJOS) [MIM:618846]: An autosomal
CC dominant disorder characterized by varying degrees of intellectual
CC disability, developmental delay, short stature, and characteristic
CC facial features such as a wide mouth, a pointed chin, long ears and a
CC low columella. {ECO:0000269|PubMed:30929739}. Note=The disease is
CC caused by variants affecting the gene represented in this entry.
CC -!- MISCELLANEOUS: Its gene is located in the 5q region of the genome which
CC is deleted in del(5q) interstitial deletion, a frequent deletion found
CC in myeloid leukemias and myelodysplasias, suggesting that it may be a
CC good candidate for the del(5q) tumor suppressor gene.
CC -!- SIMILARITY: Belongs to the JHDM2 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA83034.2; 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; AF251039; AAF63765.1; -; mRNA.
DR EMBL; AF338242; AAK13499.1; -; mRNA.
DR EMBL; AB029005; BAA83034.2; ALT_INIT; mRNA.
DR EMBL; AC104116; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC113403; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471062; EAW62141.1; -; Genomic_DNA.
DR EMBL; BC000539; AAH00539.2; -; mRNA.
DR EMBL; BC001202; AAH01202.1; -; mRNA.
DR EMBL; BC146788; AAI46789.1; -; mRNA.
DR CCDS; CCDS34242.1; -. [Q7LBC6-1]
DR RefSeq; NP_057688.2; NM_016604.3. [Q7LBC6-1]
DR PDB; 4C8D; X-ray; 2.18 A; A=1380-1720.
DR PDB; 5R7X; X-ray; 1.44 A; A/B=1380-1728.
DR PDB; 5RAA; X-ray; 1.57 A; A/B=1380-1728.
DR PDB; 5RAB; X-ray; 1.52 A; A/B=1380-1728.
DR PDB; 5RAC; X-ray; 1.73 A; A/B=1380-1728.
DR PDB; 5RAD; X-ray; 1.90 A; A/B=1380-1728.
DR PDB; 5RAE; X-ray; 1.88 A; A/B=1380-1728.
DR PDB; 5RAF; X-ray; 1.62 A; A/B=1380-1728.
DR PDB; 5RAG; X-ray; 1.52 A; A/B=1380-1728.
DR PDB; 5RAH; X-ray; 1.66 A; A/B=1380-1728.
DR PDB; 5RAI; X-ray; 1.54 A; A/B=1380-1728.
DR PDB; 5RAJ; X-ray; 1.61 A; A/B=1380-1728.
DR PDB; 5RAK; X-ray; 1.69 A; A/B=1380-1728.
DR PDB; 5RAL; X-ray; 1.68 A; A/B=1380-1728.
DR PDB; 5RAM; X-ray; 2.05 A; A/B=1380-1728.
DR PDB; 5RAN; X-ray; 1.95 A; A/B=1380-1728.
DR PDB; 5RAO; X-ray; 1.59 A; A/B=1380-1728.
DR PDB; 5RAP; X-ray; 1.90 A; A/B=1380-1728.
DR PDB; 5RAQ; X-ray; 1.85 A; A/B=1380-1728.
DR PDB; 5RAR; X-ray; 1.47 A; A/B=1380-1728.
DR PDB; 5RAS; X-ray; 1.58 A; A/B=1380-1728.
DR PDB; 5RAU; X-ray; 1.73 A; A/B=1380-1728.
DR PDB; 5RAV; X-ray; 1.77 A; A/B=1380-1728.
DR PDB; 5RAW; X-ray; 1.55 A; A/B=1380-1728.
DR PDB; 5RAX; X-ray; 2.01 A; A/B=1380-1728.
DR PDB; 5RAY; X-ray; 1.63 A; A/B=1380-1728.
DR PDB; 5RAZ; X-ray; 1.81 A; A/B=1380-1728.
DR PDB; 5RB0; X-ray; 1.95 A; A/B=1380-1728.
DR PDB; 5RB1; X-ray; 1.76 A; A/B=1380-1728.
DR PDB; 5RB2; X-ray; 1.52 A; A/B=1380-1728.
DR PDB; 5RB3; X-ray; 1.53 A; A/B=1380-1728.
DR PDB; 5RB4; X-ray; 1.55 A; A/B=1380-1728.
DR PDB; 5RB5; X-ray; 1.51 A; A/B=1380-1728.
DR PDB; 5RB6; X-ray; 1.63 A; A/B=1380-1728.
DR PDB; 5RB7; X-ray; 1.57 A; A/B=1380-1728.
DR PDB; 6RBJ; X-ray; 2.09 A; A/B=1380-1728.
DR PDBsum; 4C8D; -.
DR PDBsum; 5R7X; -.
DR PDBsum; 5RAA; -.
DR PDBsum; 5RAB; -.
DR PDBsum; 5RAC; -.
DR PDBsum; 5RAD; -.
DR PDBsum; 5RAE; -.
DR PDBsum; 5RAF; -.
DR PDBsum; 5RAG; -.
DR PDBsum; 5RAH; -.
DR PDBsum; 5RAI; -.
DR PDBsum; 5RAJ; -.
DR PDBsum; 5RAK; -.
DR PDBsum; 5RAL; -.
DR PDBsum; 5RAM; -.
DR PDBsum; 5RAN; -.
DR PDBsum; 5RAO; -.
DR PDBsum; 5RAP; -.
DR PDBsum; 5RAQ; -.
DR PDBsum; 5RAR; -.
DR PDBsum; 5RAS; -.
DR PDBsum; 5RAU; -.
DR PDBsum; 5RAV; -.
DR PDBsum; 5RAW; -.
DR PDBsum; 5RAX; -.
DR PDBsum; 5RAY; -.
DR PDBsum; 5RAZ; -.
DR PDBsum; 5RB0; -.
DR PDBsum; 5RB1; -.
DR PDBsum; 5RB2; -.
DR PDBsum; 5RB3; -.
DR PDBsum; 5RB4; -.
DR PDBsum; 5RB5; -.
DR PDBsum; 5RB6; -.
DR PDBsum; 5RB7; -.
DR PDBsum; 6RBJ; -.
DR AlphaFoldDB; Q7LBC6; -.
DR SMR; Q7LBC6; -.
DR BioGRID; 119727; 69.
DR IntAct; Q7LBC6; 28.
DR MINT; Q7LBC6; -.
DR STRING; 9606.ENSP00000326563; -.
DR BindingDB; Q7LBC6; -.
DR ChEMBL; CHEMBL3784906; -.
DR GlyGen; Q7LBC6; 22 sites, 2 O-linked glycans (22 sites).
DR iPTMnet; Q7LBC6; -.
DR PhosphoSitePlus; Q7LBC6; -.
DR BioMuta; KDM3B; -.
DR DMDM; 308153456; -.
DR EPD; Q7LBC6; -.
DR jPOST; Q7LBC6; -.
DR MassIVE; Q7LBC6; -.
DR MaxQB; Q7LBC6; -.
DR PaxDb; Q7LBC6; -.
DR PeptideAtlas; Q7LBC6; -.
DR PRIDE; Q7LBC6; -.
DR ProteomicsDB; 68846; -. [Q7LBC6-1]
DR ProteomicsDB; 68847; -. [Q7LBC6-2]
DR ProteomicsDB; 68848; -. [Q7LBC6-3]
DR Antibodypedia; 14936; 361 antibodies from 38 providers.
DR DNASU; 51780; -.
DR Ensembl; ENST00000314358.10; ENSP00000326563.5; ENSG00000120733.14. [Q7LBC6-1]
DR Ensembl; ENST00000542866.2; ENSP00000439462.2; ENSG00000120733.14. [Q7LBC6-3]
DR GeneID; 51780; -.
DR KEGG; hsa:51780; -.
DR MANE-Select; ENST00000314358.10; ENSP00000326563.5; NM_016604.4; NP_057688.3.
DR UCSC; uc003lcy.1; human. [Q7LBC6-1]
DR CTD; 51780; -.
DR DisGeNET; 51780; -.
DR GeneCards; KDM3B; -.
DR HGNC; HGNC:1337; KDM3B.
DR HPA; ENSG00000120733; Low tissue specificity.
DR MalaCards; KDM3B; -.
DR MIM; 609373; gene.
DR MIM; 618846; phenotype.
DR neXtProt; NX_Q7LBC6; -.
DR OpenTargets; ENSG00000120733; -.
DR PharmGKB; PA25918; -.
DR VEuPathDB; HostDB:ENSG00000120733; -.
DR eggNOG; KOG1356; Eukaryota.
DR GeneTree; ENSGT00940000158095; -.
DR HOGENOM; CLU_002991_0_0_1; -.
DR InParanoid; Q7LBC6; -.
DR OMA; VGAGICK; -.
DR OrthoDB; 1185631at2759; -.
DR PhylomeDB; Q7LBC6; -.
DR TreeFam; TF324723; -.
DR BioCyc; MetaCyc:ENSG00000120733-MON; -.
DR BRENDA; 1.14.11.65; 2681.
DR PathwayCommons; Q7LBC6; -.
DR Reactome; R-HSA-3214842; HDMs demethylate histones.
DR SignaLink; Q7LBC6; -.
DR SIGNOR; Q7LBC6; -.
DR BioGRID-ORCS; 51780; 36 hits in 1103 CRISPR screens.
DR ChiTaRS; KDM3B; human.
DR GeneWiki; JMJD1B; -.
DR GenomeRNAi; 51780; -.
DR Pharos; Q7LBC6; Tbio.
DR PRO; PR:Q7LBC6; -.
DR Proteomes; UP000005640; Chromosome 5.
DR RNAct; Q7LBC6; protein.
DR Bgee; ENSG00000120733; Expressed in ventricular zone and 211 other tissues.
DR ExpressionAtlas; Q7LBC6; baseline and differential.
DR Genevisible; Q7LBC6; HS.
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; IDA:HPA.
DR GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR GO; GO:0140683; F:histone H3-di/monomethyl-lysine-9 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IBA:GO_Central.
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:0033169; P:histone H3-K9 demethylation; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR InterPro; IPR045109; JHDM2-like.
DR InterPro; IPR003347; JmjC_dom.
DR PANTHER; PTHR12549; PTHR12549; 1.
DR Pfam; PF02373; JmjC; 1.
DR SMART; SM00558; JmjC; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Chromatin regulator;
KW Dioxygenase; Disease variant; Dwarfism; Intellectual disability; 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:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT CHAIN 2..1761
FT /note="Lysine-specific demethylase 3B"
FT /id="PRO_0000234373"
FT DOMAIN 1498..1721
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 1031..1056
FT /note="C6-type"
FT /evidence="ECO:0000255"
FT REGION 253..346
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 370..394
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 438..496
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 572..603
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 714..762
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 805..828
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1142..1220
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1293..1297
FT /note="LXXLL motif"
FT COMPBIAS 273..312
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 449..496
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 808..828
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1142..1166
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1178..1192
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1560
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 1562
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 1689
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:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT MOD_RES 361
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 492
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 546
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q6ZPY7"
FT MOD_RES 556
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q6ZPY7"
FT MOD_RES 560
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 614
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 766
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 773
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163"
FT MOD_RES 778
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 779
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163"
FT MOD_RES 798
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17081983,
FT ECO:0007744|PubMed:20068231"
FT MOD_RES 1253
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 1259
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT CROSSLNK 788
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VAR_SEQ 1..1002
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_018298"
FT VAR_SEQ 1..344
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11087669"
FT /id="VSP_018299"
FT VAR_SEQ 345..349
FT /note="TFVPQ -> MGAME (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11087669"
FT /id="VSP_018300"
FT VARIANT 45..1761
FT /note="Missing (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_083997"
FT VARIANT 93..1761
FT /note="Missing (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_083998"
FT VARIANT 117
FT /note="W -> R (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_083999"
FT VARIANT 256
FT /note="A -> T (in dbSNP:rs6865472)"
FT /evidence="ECO:0000269|PubMed:10470851,
FT ECO:0000269|PubMed:11687974, ECO:0000269|PubMed:15489334,
FT ECO:0000269|Ref.6"
FT /id="VAR_026221"
FT VARIANT 336
FT /note="D -> G (in DIJOS; unknown pathological
FT significance)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084000"
FT VARIANT 827..1761
FT /note="Missing (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084001"
FT VARIANT 943
FT /note="R -> Q (in DIJOS; dbSNP:rs1334033128)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084002"
FT VARIANT 943
FT /note="R -> W (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084003"
FT VARIANT 1028
FT /note="R -> Q (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084004"
FT VARIANT 1032
FT /note="D -> V (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084005"
FT VARIANT 1201
FT /note="S -> N (in dbSNP:rs7706614)"
FT /id="VAR_026222"
FT VARIANT 1509
FT /note="L -> P (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084006"
FT VARIANT 1517..1761
FT /note="Missing (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084007"
FT VARIANT 1544
FT /note="Y -> C (in DIJOS; unknown pathological
FT significance)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084008"
FT VARIANT 1731
FT /note="E -> K (in DIJOS; unknown pathological
FT significance)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084009"
FT VARIANT 1734
FT /note="L -> R (in DIJOS)"
FT /evidence="ECO:0000269|PubMed:30929739"
FT /id="VAR_084010"
FT CONFLICT 569
FT /note="C -> R (in Ref. 1; AAF63765)"
FT /evidence="ECO:0000305"
FT STRAND 1381..1385
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1386..1388
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1390..1394
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1401..1410
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1415..1417
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1420..1423
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1426..1429
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1431..1438
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1441..1447
FT /evidence="ECO:0007829|PDB:5R7X"
FT TURN 1448..1450
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1453..1458
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1459..1463
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1466..1468
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1469..1471
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1483..1485
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1487..1489
FT /evidence="ECO:0007829|PDB:5R7X"
FT TURN 1491..1493
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1494..1497
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1499..1506
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1512..1515
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1524..1526
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1539..1543
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1550..1553
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1556..1560
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1563..1574
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1577..1579
FT /evidence="ECO:0007829|PDB:5R7X"
FT TURN 1580..1582
FT /evidence="ECO:0007829|PDB:5RAH"
FT HELIX 1583..1592
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1597..1604
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1610..1616
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1619..1621
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1622..1635
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1646..1649
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1656..1666
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1671..1676
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1680..1683
FT /evidence="ECO:0007829|PDB:5R7X"
FT STRAND 1689..1704
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1707..1713
FT /evidence="ECO:0007829|PDB:5R7X"
FT HELIX 1718..1724
FT /evidence="ECO:0007829|PDB:5R7X"
SQ SEQUENCE 1761 AA; 191581 MW; FB900FCBF0675CD8 CRC64;
MADAAASPVG KRLLLLFADT AASASASAPA AAAASGDPGP ALRTRAWRAG TVRAMSGAVP
QDLAIFVEFD GCNWKQHSWV KVHAEEVIVL LLEGSLVWAP REDPVLLQGI RVSIAQWPAL
TFTPLVDKLG LGSVVPVEYL LDRELRFLSD ANGLHLFQMG TDSQNQILLE HAALRETVNA
LISDQKLQEI FSRGPYSVQG HRVKIYQPEG EEGWLYGVVS HQDSITRLME VSVTESGEIK
SVDPRLIHVM LMDNSAPQSE GGTLKAVKSS KGKKKRESIE GKDGRRRKSA SDSGCDPASK
KLKGDRGEVD SNGSDGGEAS RGPWKGGNAS GEPGLDQRAK QPPSTFVPQI NRNIRFATYT
KENGRTLVVQ DEPVGGDTPA SFTPYSTATG QTPLAPEVGG AENKEAGKTL EQVGQGIVAS
AAVVTTASST PNTVRISDTG LAAGTVPEKQ KGSRSQASGE NSRNSILASS GFGAPLPSSS
QPLTFGSGRS QSNGVLATEN KPLGFSFGCS SAQEAQKDTD LSKNLFFQCM SQTLPTSNYF
TTVSESLADD SSSRDSFKQS LESLSSGLCK GRSVLGTDTK PGSKAGSSVD RKVPAESMPT
LTPAFPRSLL NARTPENHEN LFLQPPKLSR EEPSNPFLAF VEKVEHSPFS SFASQASGSS
SSATTVTSKV APSWPESHSS ADSASLAKKK PLFITTDSSK LVSGVLGSAL TSGGPSLSAM
GNGRSSSPTS SLTQPIEMPT LSSSPTEERP TVGPGQQDNP LLKTFSNVFG RHSGGFLSSP
ADFSQENKAP FEAVKRFSLD ERSLACRQDS DSSTNSDLSD LSDSEEQLQA KTGLKGIPEH
LMGKLGPNGE RSAELLLGKS KGKQAPKGRP RTAPLKVGQS VLKDVSKVKK LKQSGEPFLQ
DGSCINVAPH LHKCRECRLE RYRKFKEQEQ DDSTVACRFF HFRRLIFTRK GVLRVEGFLS
PQQSDPDAMN LWIPSSSLAE GIDLETSKYI LANVGDQFCQ LVMSEKEAMM MVEPHQKVAW
KRAVRGVREM CDVCETTLFN IHWVCRKCGF GVCLDCYRLR KSRPRSETEE MGDEEVFSWL
KCAKGQSHEP ENLMPTQIIP GTALYNIGDM VHAARGKWGI KANCPCISRQ NKSVLRPAVT
NGMSQLPSIN PSASSGNETT FSGGGGPAPV TTPEPDHVPK ADSTDIRSEE PLKTDSSASN
SNSELKAIRP PCPDTAPPSS ALHWLADLAT QKAKEETKEA GSLRSVLNKE SHSPFGLDSF
NSTAKVSPLT PKLFNSLLLG PTASNNKTEG SSLRDLLHSG PGKLPQTPLD TGIPFPPVFS
TSSAGVKSKA SLPNFLDHII ASVVENKKTS DASKRACNLT DTQKEVKEMV MGLNVLDPHT
SHSWLCDGRL LCLHDPSNKN NWKIFRECWK QGQPVLVSGV HKKLKSELWK PEAFSQEFGD
QDVDLVNCRN CAIISDVKVR DFWDGFEIIC KRLRSEDGQP MVLKLKDWPP GEDFRDMMPT
RFEDLMENLP LPEYTKRDGR LNLASRLPSY FVRPDLGPKM YNAYGLITAE DRRVGTTNLH
LDVSDAVNVM VYVGIPIGEG AHDEEVLKTI DEGDADEVTK QRIHDGKEKP GALWHIYAAK
DAEKIRELLR KVGEEQGQEN PPDHDPIHDQ SWYLDQTLRK RLYEEYGVQG WAIVQFLGDA
VFIPAGAPHQ VHNLYSCIKV AEDFVSPEHV KHCFRLTQEF RHLSNTHTNH EDKLQVKNII
YHAVKDAVGT LKAHESKLAR S
