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Lysine-specific demethylase 2B (EC 1.14.11.27) (CXXC-type zinc finger protein 2) (F-box and leucine-rich repeat protein 10) (F-box protein FBL10) (F-box/LRR-repeat protein 10) (JmjC domain-containing histone demethylation protein 1B) (Jumonji domain-containing EMSY-interactor methyltransferase motif protein) (Protein JEMMA) (Protein-containing CXXC domain 2) ([Histone-H3]-lysine-36 demethylase 1B)

 KDM2B_HUMAN             Reviewed;        1336 AA.
Q8NHM5; A8MRS1; Q1RLM7; Q8NCI2; Q96HC7; Q96SL0; Q96T03; Q9NS96;
Q9UF75;
16-AUG-2004, integrated into UniProtKB/Swiss-Prot.
01-OCT-2002, sequence version 1.
20-JUN-2018, entry version 158.
RecName: Full=Lysine-specific demethylase 2B;
EC=1.14.11.27 {ECO:0000269|PubMed:16362057};
AltName: Full=CXXC-type zinc finger protein 2;
AltName: Full=F-box and leucine-rich repeat protein 10;
AltName: Full=F-box protein FBL10;
AltName: Full=F-box/LRR-repeat protein 10;
AltName: Full=JmjC domain-containing histone demethylation protein 1B;
AltName: Full=Jumonji domain-containing EMSY-interactor methyltransferase motif protein;
Short=Protein JEMMA;
AltName: Full=Protein-containing CXXC domain 2;
AltName: Full=[Histone-H3]-lysine-36 demethylase 1B;
Name=KDM2B; Synonyms=CXXC2, FBL10, FBXL10, JHDM1B, PCCX2;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Hughes-Davies L.;
"JEMMA (Jumonji domain, EMSY-interactor, methyltransferase motif) is a
novel protein which interacts with EMSY.";
Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4), AND NUCLEOTIDE
SEQUENCE [LARGE SCALE MRNA] OF 504-1336 (ISOFORM 1).
TISSUE=Hippocampus;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16541075; DOI=10.1038/nature04569;
Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y.,
Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C.,
Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M.,
Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L.,
Milosavljevic A., Miner G.R., Montgomery K.T., Morgan M.B.,
Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D.,
Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y., Zhang Z.,
Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z.,
Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H., Draper H.,
Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S., Kelly S.H.,
Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V.,
Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H., Santibanez J.,
Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q., Williams G.A.,
Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V., Bailey M.,
Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E., Burkett C.E.,
Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K.,
Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D.,
Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M.,
Dathorne S.R., David R., Davis C.M., Davy-Carroll L., Deshazo D.R.,
Donlin J.E., D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J.,
Escotto M., Flagg N., Forbes L.D., Gabisi A.M., Garza M., Hamilton C.,
Henderson N., Hernandez O., Hines S., Hogues M.E., Huang M.,
Idlebird D.G., Johnson R., Jolivet A., Jones S., Kagan R., King L.M.,
Leal B., Lebow H., Lee S., LeVan J.M., Lewis L.C., London P.,
Lorensuhewa L.M., Loulseged H., Lovett D.A., Lucier A., Lucier R.L.,
Ma J., Madu R.C., Mapua P., Martindale A.D., Martinez E., Massey E.,
Mawhiney S., Meador M.G., Mendez S., Mercado C., Mercado I.C.,
Merritt C.E., Miner Z.L., Minja E., Mitchell T., Mohabbat F.,
Mohabbat K., Montgomery B., Moore N., Morris S., Munidasa M.,
Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O., Nwokenkwo S.,
Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J.,
Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A.,
Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M.,
Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I.,
Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A.,
Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D.,
Trejos Z.Y., Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I.,
Vera V.A., Villasana D.M., Wang L., Ward-Moore S., Warren J.T.,
Wei X., White F., Williamson A.L., Wleczyk R., Wooden H.S.,
Wooden S.H., Yen J., Yoon L., Yoon V., Zorrilla S.E., Nelson D.,
Kucherlapati R., Weinstock G., Gibbs R.A.;
"The finished DNA sequence of human chromosome 12.";
Nature 440:346-351(2006).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5), AND NUCLEOTIDE
SEQUENCE [LARGE SCALE MRNA] OF 710-1336 (ISOFORM 1).
TISSUE=Brain;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 129-1336 (ISOFORM 3).
TISSUE=Testis;
PubMed=17974005; DOI=10.1186/1471-2164-8-399;
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[6]
NUCLEOTIDE SEQUENCE [MRNA] OF 480-1336 (ISOFORM 2).
TISSUE=Fibroblast;
Fujino T., Hasegawa M., Shibata S., Kishimoto T., Imai S., Takano T.;
Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
[7]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=16362057; DOI=10.1038/nature04433;
Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H.,
Tempst P., Zhang Y.;
"Histone demethylation by a family of JmjC domain-containing
proteins.";
Nature 439:811-816(2006).
[8]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=17994099; DOI=10.1038/nature06255;
Frescas D., Guardavaccaro D., Bassermann F., Koyama-Nasu R.,
Pagano M.;
"JHDM1B/FBXL10 is a nucleolar protein that represses transcription of
ribosomal RNA genes.";
Nature 450:309-313(2007).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19413330; DOI=10.1021/ac9004309;
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
Mohammed S.;
"Lys-N and trypsin cover complementary parts of the phosphoproteome in
a refined SCX-based approach.";
Anal. Chem. 81:4493-4501(2009).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-493; SER-975 AND
SER-979, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Leukemic T-cell;
PubMed=19690332; DOI=10.1126/scisignal.2000007;
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
Rodionov V., Han D.K.;
"Quantitative phosphoproteomic analysis of T cell receptor signaling
reveals system-wide modulation of protein-protein interactions.";
Sci. Signal. 2:RA46-RA46(2009).
[12]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
Mann M.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-474; SER-477; THR-493
AND SER-497, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-57; SER-474; SER-951;
SER-975; SER-979; SER-1018 AND SER-1031, AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[15]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[16]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-890, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25218447; DOI=10.1038/nsmb.2890;
Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M.,
Vertegaal A.C.;
"Uncovering global SUMOylation signaling networks in a site-specific
manner.";
Nat. Struct. Mol. Biol. 21:927-936(2014).
[17]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-890, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
Vertegaal A.C.;
"SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
Cell Rep. 10:1778-1791(2015).
[18]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-890, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25755297; DOI=10.1074/mcp.O114.044792;
Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V.,
Vertegaal A.C.;
"System-wide analysis of SUMOylation dynamics in response to
replication stress reveals novel small ubiquitin-like modified target
proteins and acceptor lysines relevant for genome stability.";
Mol. Cell. Proteomics 14:1419-1434(2015).
[19]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-857 AND LYS-890, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=28112733; DOI=10.1038/nsmb.3366;
Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
Nielsen M.L.;
"Site-specific mapping of the human SUMO proteome reveals co-
modification with phosphorylation.";
Nat. Struct. Mol. Biol. 24:325-336(2017).
-!- FUNCTION: Histone demethylase that demethylates 'Lys-4' and 'Lys-
36' of histone H3, thereby playing a central role in histone code.
Preferentially demethylates trimethylated H3 'Lys-4' and
dimethylated H3 'Lys-36' residue while it has weak or no activity
for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the
transcribed region of ribosomal RNA and represses the
transcription of ribosomal RNA genes which inhibits cell growth
and proliferation. May also serve as a substrate-recognition
component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin
ligase complex. {ECO:0000269|PubMed:16362057,
ECO:0000269|PubMed:17994099}.
-!- CATALYTIC ACTIVITY: Protein N(6),N(6)-dimethyl-L-lysine + 2 2-
oxoglutarate + 2 O(2) = protein L-lysine + 2 succinate + 2
formaldehyde + 2 CO(2). {ECO:0000269|PubMed:16362057}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBUNIT: Directly interacts with SKP1 and CUL1. {ECO:0000250}.
-!- INTERACTION:
Q6W2J9:BCOR; NbExp=4; IntAct=EBI-3955564, EBI-950027;
P63208:SKP1; NbExp=2; IntAct=EBI-3955564, EBI-307486;
-!- SUBCELLULAR LOCATION: Nucleus, nucleolus
{ECO:0000269|PubMed:17994099}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=5;
Name=1;
IsoId=Q8NHM5-1; Sequence=Displayed;
Name=2;
IsoId=Q8NHM5-2; Sequence=VSP_011340, VSP_011341;
Name=3;
IsoId=Q8NHM5-3; Sequence=VSP_017475, VSP_017476;
Note=No experimental confirmation available.;
Name=4;
IsoId=Q8NHM5-4; Sequence=VSP_043146, VSP_043147, VSP_043148;
Note=No experimental confirmation available.;
Name=5;
IsoId=Q8NHM5-5; Sequence=VSP_057394, VSP_057395, VSP_057396;
Note=No experimental confirmation available.;
-!- DOMAIN: The JmjC domain mediates demethylation activity (By
similarity). It is also required for repression of ribosomal RNA
genes. {ECO:0000250}.
-!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAH08735.2; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=BAB55112.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=BAB55301.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Sequence=BAC11159.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; AJ459424; CAD30700.1; -; mRNA.
EMBL; AK027440; BAB55112.1; ALT_INIT; mRNA.
EMBL; AK027692; BAB55301.1; ALT_INIT; mRNA.
EMBL; AK074718; BAC11159.1; ALT_INIT; mRNA.
EMBL; AK127328; BAG54483.1; -; mRNA.
EMBL; AC048337; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AC073650; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AC145422; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; KC877509; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC008735; AAH08735.2; ALT_INIT; mRNA.
EMBL; BC115379; AAI15380.1; -; mRNA.
EMBL; AL133572; CAB63721.2; -; mRNA.
EMBL; AB031230; BAA97672.1; -; mRNA.
CCDS; CCDS41849.1; -. [Q8NHM5-4]
CCDS; CCDS41850.1; -. [Q8NHM5-1]
PIR; T43477; T43477.
RefSeq; NP_001005366.1; NM_001005366.1. [Q8NHM5-4]
RefSeq; NP_115979.3; NM_032590.4. [Q8NHM5-1]
UniGene; Hs.524800; -.
PDB; 4O64; X-ray; 2.13 A; A/B/C=607-723.
PDB; 5JH5; X-ray; 2.55 A; A=1059-1336.
PDBsum; 4O64; -.
PDBsum; 5JH5; -.
ProteinModelPortal; Q8NHM5; -.
SMR; Q8NHM5; -.
BioGrid; 124197; 26.
CORUM; Q8NHM5; -.
IntAct; Q8NHM5; 12.
STRING; 9606.ENSP00000366271; -.
BindingDB; Q8NHM5; -.
ChEMBL; CHEMBL3779760; -.
iPTMnet; Q8NHM5; -.
PhosphoSitePlus; Q8NHM5; -.
BioMuta; KDM2B; -.
DMDM; 51316032; -.
EPD; Q8NHM5; -.
MaxQB; Q8NHM5; -.
PaxDb; Q8NHM5; -.
PeptideAtlas; Q8NHM5; -.
PRIDE; Q8NHM5; -.
ProteomicsDB; 73723; -.
ProteomicsDB; 73724; -. [Q8NHM5-2]
ProteomicsDB; 73725; -. [Q8NHM5-3]
ProteomicsDB; 73726; -. [Q8NHM5-4]
Ensembl; ENST00000377069; ENSP00000366269; ENSG00000089094. [Q8NHM5-4]
Ensembl; ENST00000377071; ENSP00000366271; ENSG00000089094. [Q8NHM5-1]
Ensembl; ENST00000611216; ENSP00000480847; ENSG00000089094. [Q8NHM5-5]
GeneID; 84678; -.
KEGG; hsa:84678; -.
UCSC; uc058uhm.1; human. [Q8NHM5-1]
UCSC; uc058uhn.1; human.
CTD; 84678; -.
DisGeNET; 84678; -.
EuPathDB; HostDB:ENSG00000089094.16; -.
GeneCards; KDM2B; -.
HGNC; HGNC:13610; KDM2B.
HPA; HPA071257; -.
MIM; 609078; gene.
neXtProt; NX_Q8NHM5; -.
OpenTargets; ENSG00000089094; -.
PharmGKB; PA164721242; -.
eggNOG; KOG1633; Eukaryota.
eggNOG; KOG1947; Eukaryota.
eggNOG; ENOG410XQXU; LUCA.
GeneTree; ENSGT00550000074396; -.
HOGENOM; HOG000007396; -.
InParanoid; Q8NHM5; -.
KO; K10276; -.
OMA; VVTWPKK; -.
OrthoDB; EOG091G00M1; -.
PhylomeDB; Q8NHM5; -.
TreeFam; TF106480; -.
Reactome; R-HSA-3214842; HDMs demethylate histones.
SignaLink; Q8NHM5; -.
SIGNOR; Q8NHM5; -.
ChiTaRS; KDM2B; human.
GenomeRNAi; 84678; -.
PRO; PR:Q8NHM5; -.
Proteomes; UP000005640; Chromosome 12.
Bgee; ENSG00000089094; -.
CleanEx; HS_FBXL10; -.
ExpressionAtlas; Q8NHM5; baseline and differential.
Genevisible; Q8NHM5; HS.
GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
GO; GO:0005634; C:nucleus; NAS:UniProtKB.
GO; GO:0003677; F:DNA binding; NAS:UniProtKB.
GO; GO:0032452; F:histone demethylase activity; TAS:BHF-UCL.
GO; GO:0051864; F:histone demethylase activity (H3-K36 specific); IEA:UniProtKB-EC.
GO; GO:0000978; F:RNA polymerase II proximal promoter sequence-specific DNA binding; IEA:Ensembl.
GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0048596; P:embryonic camera-type eye morphogenesis; ISS:BHF-UCL.
GO; GO:0030900; P:forebrain development; ISS:BHF-UCL.
GO; GO:0021592; P:fourth ventricle development; ISS:BHF-UCL.
GO; GO:0030902; P:hindbrain development; ISS:BHF-UCL.
GO; GO:0035518; P:histone H2A monoubiquitination; IDA:UniProtKB.
GO; GO:0021993; P:initiation of neural tube closure; ISS:BHF-UCL.
GO; GO:0021670; P:lateral ventricle development; ISS:BHF-UCL.
GO; GO:0030901; P:midbrain development; ISS:BHF-UCL.
GO; GO:0021555; P:midbrain-hindbrain boundary morphogenesis; ISS:BHF-UCL.
GO; GO:2000178; P:negative regulation of neural precursor cell proliferation; ISS:BHF-UCL.
GO; GO:0043524; P:negative regulation of neuron apoptotic process; ISS:BHF-UCL.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISS:BHF-UCL.
GO; GO:0030307; P:positive regulation of cell growth; IEA:Ensembl.
GO; GO:1902459; P:positive regulation of stem cell population maintenance; IEA:Ensembl.
GO; GO:0007283; P:spermatogenesis; ISS:BHF-UCL.
GO; GO:0021678; P:third ventricle development; ISS:BHF-UCL.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 3.30.40.10; -; 1.
Gene3D; 3.80.10.10; -; 1.
InterPro; IPR001810; F-box_dom.
InterPro; IPR003347; JmjC_dom.
InterPro; IPR006553; Leu-rich_rpt_Cys-con_subtyp.
InterPro; IPR032675; LRR_dom_sf.
InterPro; IPR002857; Znf_CXXC.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF00646; F-box; 1.
Pfam; PF16866; PHD_4; 1.
Pfam; PF02008; zf-CXXC; 1.
SMART; SM00558; JmjC; 1.
SMART; SM00367; LRR_CC; 6.
SMART; SM00249; PHD; 1.
SUPFAM; SSF57903; SSF57903; 1.
PROSITE; PS51184; JMJC; 1.
PROSITE; PS51058; ZF_CXXC; 1.
PROSITE; PS50016; ZF_PHD_2; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chromatin regulator; Coiled coil;
Complete proteome; Dioxygenase; Iron; Isopeptide bond;
Leucine-rich repeat; Metal-binding; Nucleus; Oxidoreductase;
Phosphoprotein; Reference proteome; Repeat; Repressor; RNA-binding;
rRNA-binding; Transcription; Transcription regulation;
Ubl conjugation; Ubl conjugation pathway; Zinc; Zinc-finger.
CHAIN 1 1336 Lysine-specific demethylase 2B.
/FTId=PRO_0000119853.
DOMAIN 178 346 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
DOMAIN 1059 1105 F-box.
REPEAT 1093 1120 LRR 1.
REPEAT 1133 1154 LRR 2.
REPEAT 1156 1182 LRR 3.
REPEAT 1222 1247 LRR 4.
REPEAT 1248 1277 LRR 5.
REPEAT 1278 1302 LRR 6.
REPEAT 1303 1336 LRR 7.
ZN_FING 606 652 CXXC-type. {ECO:0000255|PROSITE-
ProRule:PRU00509}.
ZN_FING 659 725 PHD-type. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
COILED 943 971 {ECO:0000255}.
COMPBIAS 409 430 Glu-rich.
COMPBIAS 1014 1056 Pro-rich.
METAL 242 242 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 244 244 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 314 314 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
BINDING 239 239 Substrate. {ECO:0000250}.
BINDING 259 259 Substrate. {ECO:0000250}.
MOD_RES 57 57 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 474 474 Phosphoserine.
{ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163}.
MOD_RES 477 477 Phosphoserine.
{ECO:0000244|PubMed:21406692}.
MOD_RES 493 493 Phosphothreonine.
{ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:21406692}.
MOD_RES 497 497 Phosphoserine.
{ECO:0000244|PubMed:21406692}.
MOD_RES 951 951 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 975 975 Phosphoserine.
{ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:23186163}.
MOD_RES 979 979 Phosphoserine.
{ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:23186163}.
MOD_RES 1018 1018 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 1031 1031 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
CROSSLNK 857 857 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 890 890 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:25218447,
ECO:0000244|PubMed:25755297,
ECO:0000244|PubMed:25772364,
ECO:0000244|PubMed:28112733}.
VAR_SEQ 1 117 Missing (in isoform 5).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_057394.
VAR_SEQ 1 42 MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESAT
Q -> MEAEKDSGRRL (in isoform 4).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_043146.
VAR_SEQ 654 676 PVLPHTAVCLVCGEAGKEDTVEE -> TAIRSLISACPSSN
AVETSVILT (in isoform 5).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_057395.
VAR_SEQ 677 1336 Missing (in isoform 5).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_057396.
VAR_SEQ 730 730 K -> KAYK (in isoform 2).
{ECO:0000303|Ref.6}.
/FTId=VSP_011340.
VAR_SEQ 818 855 Missing (in isoform 4).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_043147.
VAR_SEQ 856 868 LKPGKEDKLFRKK -> Q (in isoform 3).
{ECO:0000303|PubMed:17974005}.
/FTId=VSP_017475.
VAR_SEQ 1204 1204 G -> GPG (in isoform 3).
{ECO:0000303|PubMed:17974005}.
/FTId=VSP_017476.
VAR_SEQ 1277 1336 DCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAE
MSVSVQFGQVEEKLLQKLS -> ASLLGRVFGLQFWGICEP
QARKNAGWA (in isoform 2).
{ECO:0000303|Ref.6}.
/FTId=VSP_011341.
VAR_SEQ 1320 1336 VSVQFGQVEEKLLQKLS -> SFQGRSCSTTRLGDE (in
isoform 4).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_043148.
CONFLICT 864 864 L -> F (in Ref. 6; BAC11159).
{ECO:0000305}.
CONFLICT 1226 1226 T -> R (in Ref. 6; BAC11159).
{ECO:0000305}.
CONFLICT 1295 1295 I -> T (in Ref. 6; BAC11159).
{ECO:0000305}.
CONFLICT 1334 1334 K -> R (in Ref. 6; BAC11159).
{ECO:0000305}.
HELIX 617 620 {ECO:0000244|PDB:4O64}.
HELIX 628 632 {ECO:0000244|PDB:4O64}.
HELIX 634 636 {ECO:0000244|PDB:4O64}.
HELIX 647 649 {ECO:0000244|PDB:4O64}.
TURN 663 665 {ECO:0000244|PDB:4O64}.
HELIX 671 673 {ECO:0000244|PDB:4O64}.
HELIX 677 682 {ECO:0000244|PDB:4O64}.
STRAND 686 688 {ECO:0000244|PDB:4O64}.
TURN 689 691 {ECO:0000244|PDB:4O64}.
HELIX 697 699 {ECO:0000244|PDB:4O64}.
STRAND 711 713 {ECO:0000244|PDB:4O64}.
STRAND 716 718 {ECO:0000244|PDB:4O64}.
TURN 720 722 {ECO:0000244|PDB:4O64}.
HELIX 1067 1074 {ECO:0000244|PDB:5JH5}.
HELIX 1079 1086 {ECO:0000244|PDB:5JH5}.
HELIX 1092 1095 {ECO:0000244|PDB:5JH5}.
HELIX 1099 1102 {ECO:0000244|PDB:5JH5}.
STRAND 1103 1106 {ECO:0000244|PDB:5JH5}.
HELIX 1115 1124 {ECO:0000244|PDB:5JH5}.
STRAND 1127 1130 {ECO:0000244|PDB:5JH5}.
HELIX 1138 1147 {ECO:0000244|PDB:5JH5}.
STRAND 1153 1155 {ECO:0000244|PDB:5JH5}.
HELIX 1161 1164 {ECO:0000244|PDB:5JH5}.
HELIX 1165 1168 {ECO:0000244|PDB:5JH5}.
STRAND 1169 1171 {ECO:0000244|PDB:5JH5}.
STRAND 1176 1179 {ECO:0000244|PDB:5JH5}.
HELIX 1188 1195 {ECO:0000244|PDB:5JH5}.
TURN 1211 1214 {ECO:0000244|PDB:5JH5}.
STRAND 1217 1219 {ECO:0000244|PDB:5JH5}.
HELIX 1227 1236 {ECO:0000244|PDB:5JH5}.
STRAND 1242 1244 {ECO:0000244|PDB:5JH5}.
HELIX 1253 1259 {ECO:0000244|PDB:5JH5}.
HELIX 1265 1269 {ECO:0000244|PDB:5JH5}.
STRAND 1272 1274 {ECO:0000244|PDB:5JH5}.
HELIX 1284 1289 {ECO:0000244|PDB:5JH5}.
STRAND 1297 1299 {ECO:0000244|PDB:5JH5}.
HELIX 1308 1318 {ECO:0000244|PDB:5JH5}.
TURN 1319 1321 {ECO:0000244|PDB:5JH5}.
STRAND 1331 1334 {ECO:0000244|PDB:5JH5}.
SEQUENCE 1336 AA; 152615 MW; 3A1A17B8EA9EA953 CRC64;
MAGPQMGGSA EDHPPRKRHA AEKQKKKTVI YTKCFEFESA TQRPIDRQRY DENEDLSDVE
EIVSVRGFSL EEKLRSQLYQ GDFVHAMEGK DFNYEYVQRE ALRVPLIFRE KDGLGIKMPD
PDFTVRDVKL LVGSRRLVDV MDVNTQKGTE MSMSQFVRYY ETPEAQRDKL YNVISLEFSH
TKLEHLVKRP TVVDLVDWVD NMWPQHLKEK QTEATNAIAE MKYPKVKKYC LMSVKGCFTD
FHIDFGGTSV WYHVFRGGKI FWLIPPTLHN LALYEEWVLS GKQSDIFLGD RVERCQRIEL
KQGYTFFIPS GWIHAVYTPV DSLVFGGNIL HSFNVPMQLR IYEIEDRTRV QPKFRYPFYY
EMCWYVLERY VYCVTQRSHL TQEYQRESML IDAPRKPSID GFSSDSWLEM EEEACDQQPQ
EEEEKDEEGE GRDRAPKPPT DGSTSPTSTP SEDQEALGKK PKAPALRFLK RTLSNESEES
VKSTTLAVDY PKTPTGSPAT EVSAKWTHLT EFELKGLKAL VEKLESLPEN KKCVPEGIED
PQALLEGVKN VLKEHADDDP SLAITGVPVV TWPKKTPKNR AVGRPKGKLG PASAVKLAAN
RTTAGARRRR TRCRKCEACL RTECGECHFC KDMKKFGGPG RMKQSCIMRQ CIAPVLPHTA
VCLVCGEAGK EDTVEEEEGK FNLMLMECSI CNEIIHPGCL KIKESEGVVN DELPNCWECP
KCNHAGKTGK QKRGPGFKYA SNLPGSLLKE QKMNRDNKEG QEPAKRRSEC EEAPRRRSDE
HSKKVPPDGL LRRKSDDVHL RKKRKYEKPQ ELSGRKRASS LQTSPGSSSH LSPRPPLGSS
LSPWWRSSLT YFQQQLKPGK EDKLFRKKRR SWKNAEDRMA LANKPLRRFK QEPEDELPEA
PPKTRESDHS RSSSPTAGPS TEGAEGPEEK KKVKMRRKRR LPNKELSREL SKELNHEIQR
TENSLANENQ QPIKSEPESE GEEPKRPPGI CERPHRFSKG LNGTPRELRH QLGPSLRSPP
RVISRPPPSV SPPKCIQMER HVIRPPPISP PPDSLPLDDG AAHVMHREVW MAVFSYLSHQ
DLCVCMRVCR TWNRWCCDKR LWTRIDLNHC KSITPLMLSG IIRRQPVSLD LSWTNISKKQ
LSWLINRLPG LRDLVLSGCS WIAVSALCSS SCPLLRTLDV QWVEGLKDAQ MRDLLSPPTD
NRPGQMDNRS KLRNIVELRL AGLDITDASL RLIIRHMPLL SKLHLSYCNH VTDQSINLLT
AVGTTTRDSL TEINLSDCNK VTDQCLSFFK RCGNICHIDL RYCKQVTKEG CEQFIAEMSV
SVQFGQVEEK LLQKLS


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