KDM2B_XENLA
ID KDM2B_XENLA Reviewed; 1259 AA.
AC Q640I9; Q6GNT8;
DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Lysine-specific demethylase 2B;
DE EC=1.14.11.27 {ECO:0000250|UniProtKB:Q8NHM5};
DE AltName: Full=F-box and leucine-rich repeat protein 10;
DE AltName: Full=F-box/LRR-repeat protein 10;
DE AltName: Full=JmjC domain-containing histone demethylation protein 1B;
DE AltName: Full=[Histone-H3]-lysine-36 demethylase 1B;
GN Name=kdm2b; Synonyms=fbxl10, jhdm1b;
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of
CC histone H3, thereby playing a central role in histone code.
CC Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated
CC H3 'Lys-36' residue while it has weak or no activity for mono- and tri-
CC methylated H3 'Lys-36'. Preferentially binds the transcribed region of
CC ribosomal RNA and represses the transcription of ribosomal RNA genes
CC which inhibits cell growth and proliferation (By similarity).
CC {ECO:0000250|UniProtKB:Q8NHM5}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(36)-[histone H3]
CC + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl(36)-[histone H3] + 2
CC succinate; Xref=Rhea:RHEA:42032, Rhea:RHEA-COMP:9785, Rhea:RHEA-
CC COMP:9787, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:61976; EC=1.14.11.27;
CC Evidence={ECO:0000250|UniProtKB:Q8NHM5};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q8NHM5};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9Y2K7};
CC -!- ACTIVITY REGULATION: Histone demethylase activity is inhibited by
CC fumarate. {ECO:0000250|UniProtKB:Q8NHM5}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q8NHM5}. Nucleus {ECO:0000250|UniProtKB:Q8NHM5}.
CC Chromosome {ECO:0000250|UniProtKB:Q8NHM5}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q640I9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q640I9-2; Sequence=VSP_017479, VSP_017480;
CC -!- DOMAIN: The CXXC zinc finger mediates binding to DNA containing
CC unmethylated cytidine-phosphate-guanosine (CpG) dinucleotides.
CC {ECO:0000250|UniProtKB:Q8NHM5}.
CC -!- DOMAIN: The JmjC domain mediates demethylation activity. It is also
CC required for repression of ribosomal RNA genes (By similarity).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; BC073414; AAH73414.1; -; mRNA.
DR EMBL; BC082636; AAH82636.1; -; mRNA.
DR AlphaFoldDB; Q640I9; -.
DR SMR; Q640I9; -.
DR MaxQB; Q640I9; -.
DR PRIDE; Q640I9; -.
DR Proteomes; UP000186698; Genome assembly.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0140680; F:histone H3-di/monomethyl-lysine-36 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; ISS:UniProtKB.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0045322; F:unmethylated CpG binding; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0070544; P:histone H3-K36 demethylation; ISS:UniProtKB.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.80.10.10; -; 2.
DR InterPro; IPR001810; F-box_dom.
DR InterPro; IPR041070; JHD.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR006553; Leu-rich_rpt_Cys-con_subtyp.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR002857; Znf_CXXC.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00646; F-box; 1.
DR Pfam; PF17811; JHD; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF16866; PHD_4; 1.
DR Pfam; PF02008; zf-CXXC; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00367; LRR_CC; 5.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51058; ZF_CXXC; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chromatin regulator; Chromosome; Coiled coil;
KW Dioxygenase; DNA-binding; Iron; Leucine-rich repeat; Metal-binding;
KW Nucleus; Oxidoreductase; Phosphoprotein; Reference proteome; Repeat;
KW Repressor; RNA-binding; rRNA-binding; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1259
FT /note="Lysine-specific demethylase 2B"
FT /id="PRO_0000226786"
FT DOMAIN 147..315
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 985..1030
FT /note="F-box"
FT REPEAT 1056..1081
FT /note="LRR 1"
FT REPEAT 1082..1105
FT /note="LRR 2"
FT REPEAT 1145..1170
FT /note="LRR 3"
FT REPEAT 1171..1200
FT /note="LRR 4"
FT REPEAT 1201..1225
FT /note="LRR 5"
FT ZN_FING 567..613
FT /note="CXXC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT ZN_FING 620..686
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 388..463
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 536..562
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 729..958
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 864..891
FT /evidence="ECO:0000255"
FT COMPBIAS 398..414
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 729..785
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 794..831
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 832..846
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 864..878
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 889..912
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 208
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 213
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 228
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 283
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 574
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 577
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 580
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 585
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 588
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 591
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 607
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 612
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 623
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 626
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 649
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 652
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 657
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 660
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 680
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT BINDING 683
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8NHM5"
FT VAR_SEQ 1..521
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_017479"
FT VAR_SEQ 522..539
FT /note="NLAISGVPVVMWPKKPSK -> MALSLSNDDEEYDSEQEQ (in isoform
FT 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_017480"
FT CONFLICT 919
FT /note="N -> H (in Ref. 1; AAH73414)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1259 AA; 144054 MW; 8FAAAE440E4765C3 CRC64;
MEAKKDSARR LRSIDRTRYA EHEDLSDVED MVSIRGFSLE QKVSCNAYRG NFVRYMEGKD
FTYEYVQREA LQTPLLFSTK EGLGIKMPEQ DFTVRDVKLL VGSRRVVDVM DVNTQKSIDM
SMSQFVRYYE TPEMEREKLY NVISLEFSHT KLERVVKRPT VVDAVDWVDN MWPRHLKEQQ
KESTNVIAEM KYPKVKKYCL MSVKGCYTDF HIDFGGTSVW YHVFRGGKVF WLIPPTGHNL
QLYEEWLLSG KQTDIFLGDR SEGCQRIELK QGQTFFIPSG WIHAVYTPAD SLVFGGNILH
SFNIPMQLRV FEIEDRTRVN AKFRYPFYYE MCWYVLERYV CTLTKRSHLI KEYQRESMIT
DRKPSLDSHS SDSWLEMEEE SCDIHIKEEK GNLVEKPSKQ SGDESSTTNS THSNGKDAAE
KKQKATLMQQ LKRTLSNDSD ESSKSIVHSD FPKTPTGSPA TDMPCKLTHL TEFELKGLKA
LVEKLESLPE NKKCVPEGIE DPQALLEDMK TVLKEHADDD NNLAISGVPV VMWPKKPSKN
RAVGRPKGKI ASSPAVKLSA NRTSAGARRR RTRCRKCEAC LRTECGECHF CKDMKKFGGP
GRMKQSCIMR QCIAPVLPHT AVCLVCGEAG KEDCVEGQEA KFNVMLMECS ICNEIIHPGC
LKTKESDGVV NDELPNCWEC PKCNHAGKTG KVYKQKRGPG FKYASNLPGS LLKEQKVNRD
NKELTEIVKK KVEREETPKQ IPEEQPKKKP TEGIIKKKPE DGHVRKKRKF EKPPDPSVRK
RLKLVKEEKL LRKKRRSWKT PDERAMMAKT LRRIKQEPDD DLTEAAPKAK ESDQSRSSSP
TAGPSTEGSE PKEKKKIRRK RRVSNKELSK ELSKELNQEI QKTESSLASE NHHPIKSEPE
SDNEESKKCI STNGERMHNF SKGLNGTPKE LRHELFPSLK TTPRANNRPP PSLSPPKCMQ
MERHVIRPPP ISPPPDSLPL ANGAAHVMQR EVWMAIFSYL SHRDLCICMR ICRTWNRWCC
DKRLWTQIDL NRCKSITPLM LSGIIRRQPA SLDLSWTNIS KKQLSWLINR LPALRDLNLS
GCSWIAVSAL CSSCCPLLRT LNVQWVEGLK DAQMRDLLSP PTDNRPGQID NRSKLRNITE
LRLAGLDITD ASLRLMIRHM PLLAKLDLSY CNHVTDQSIN LLTAVGTSTR DTLLEMNLSD
CNNVTDQCLT FFKRCGNICL IDLRFCKQVS KESCEQFIAE MSVIVQFGQT EEKLLQKVS
