KDM2A_XENTR
ID KDM2A_XENTR Reviewed; 1146 AA.
AC Q5U263;
DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Lysine-specific demethylase 2A;
DE EC=1.14.11.27 {ECO:0000250|UniProtKB:Q9Y2K7};
DE AltName: Full=F-box and leucine-rich repeat protein 11;
DE AltName: Full=F-box/LRR-repeat protein 11;
DE AltName: Full=JmjC domain-containing histone demethylation protein 1A;
DE AltName: Full=[Histone-H3]-lysine-36 demethylase 1A;
GN Name=kdm2a; Synonyms=fbxl11, jhdm1a;
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-36'
CC of histone H3, thereby playing a central role in histone code.
CC Preferentially demethylates dimethylated H3 'Lys-36' residue while it
CC has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May
CC also recognize and bind to some phosphorylated proteins and promote
CC their ubiquitination and degradation. Required to maintain the
CC heterochromatic state. Associates with centromeres and represses
CC transcription of small non-coding RNAs that are encoded by the clusters
CC of satellite repeats at the centromere. Required to sustain centromeric
CC integrity and genomic stability, particularly during mitosis (By
CC similarity). May play a role in the regulation of circadian gene
CC expression (By similarity). {ECO:0000250|UniProtKB:Q9Y2K7}.
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:Q9Y2K7};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q9Y2K7};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9Y2K7};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000250|UniProtKB:Q9Y2K7}.
CC -!- DOMAIN: The JmjC domain mediates demethylation activity and is required
CC for satellite silencing. {ECO:0000250|UniProtKB:Q9Y2K7}.
CC -!- DOMAIN: The CXXC zinc finger preferentially recognizes nonmethylated
CC CpG DNA, and binding is blocked when the CpG DNA is methylated.
CC {ECO:0000250|UniProtKB:Q9Y2K7}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; BC086264; AAH86264.1; -; mRNA.
DR RefSeq; NP_001011176.1; NM_001011176.1.
DR AlphaFoldDB; Q5U263; -.
DR SMR; Q5U263; -.
DR STRING; 8364.ENSXETP00000034422; -.
DR PaxDb; Q5U263; -.
DR DNASU; 496596; -.
DR GeneID; 496596; -.
DR KEGG; xtr:496596; -.
DR CTD; 22992; -.
DR Xenbase; XB-GENE-5900838; kdm2a.
DR eggNOG; KOG1633; Eukaryota.
DR InParanoid; Q5U263; -.
DR OrthoDB; 324938at2759; -.
DR Reactome; R-XTR-3214842; HDMs demethylate histones.
DR Proteomes; UP000008143; Chromosome 7.
DR Proteomes; UP000790000; Unplaced.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0140680; F:histone H3-di/monomethyl-lysine-36 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0006482; P:protein demethylation; IBA:GO_Central.
DR GO; GO:0042752; P:regulation of circadian rhythm; ISS:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0048511; P:rhythmic process; IEA:UniProtKB-KW.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.80.10.10; -; 1.
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; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR002857; Znf_CXXC.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF12937; F-box-like; 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 SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51058; ZF_CXXC; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 2: Evidence at transcript level;
KW Biological rhythms; Chromatin regulator; Dioxygenase; DNA-binding; Iron;
KW Leucine-rich repeat; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome; Repeat; Repressor; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1146
FT /note="Lysine-specific demethylase 2A"
FT /id="PRO_0000226787"
FT DOMAIN 146..314
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 874..919
FT /note="F-box"
FT REPEAT 945..966
FT /note="LRR 1"
FT REPEAT 968..994
FT /note="LRR 2"
FT REPEAT 1032..1057
FT /note="LRR 3"
FT REPEAT 1058..1087
FT /note="LRR 4"
FT REPEAT 1088..1112
FT /note="LRR 5"
FT REPEAT 1113..1138
FT /note="LRR 6"
FT ZN_FING 585..631
FT /note="CXXC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT ZN_FING 638..699
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 363..467
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 554..585
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 733..800
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 832..867
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 367..390
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 398..441
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 450..467
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 559..584
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 736..765
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 772..800
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 848..864
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 207
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 210
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 212
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 227
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 282
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 592
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 595
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 598
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 603
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 606
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 609
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 625
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 630
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
SQ SEQUENCE 1146 AA; 131750 MW; C2812F2A5FD45816 CRC64;
MEEEQLRYSR RLRHTLRRRY EDDGISDDEI EGKRTFDLEE KLRSSKYNSN FITYMEGKDF
NMKFIQEGGL RDPIIFTKSE GLGIKMPDPN FSVNDVKMFV GSRRVVDVMD VGTQKGIEMT
MAQWAKYYET PEEEREKLYN VISLEFSHTK LENLVQRPTT VDQIDWVDNI WPRHLKDRQT
ESTNVIQEMQ YPKVQKYCLM SVRGCYTDFH VDFGGTSVWY HILRGGKVFW LIPPTDQNLE
LYENWLLSGK QGDVFLGDRV TECQRIELKQ GYTFVIPSGW IHAVYTPQDT LVFGGNFLHS
FNIPMQLRIY SIEDRTRVPT KFRYPFYYEM CWYVLERYVY CMMRRSHLTK EFQRESLSID
LELNGRQRPD TPSSSSSSSS SGLSSSSDND DSSDQDWEEE EGLRKRERDR CRVERELQRK
RNRDRQQRDQ ERDRHGRTER IIIHTLPASL RPLTPPPSLP LPTPDSPPST SPFLTWFEVE
GLRCLVLKLE SLPPLKKCLP DGIHDPEALI FDIKRLLEDH AHDPPELALT GVPIIQWPKR
SQYKVHLRPK IQFTKPHTMR PASRHSTAPP RTSGTPSGTT ASSGARRRRV RCRKCQACVQ
RECGTCHYCK DMKKFGGPGR MKQSCVLRQC LAPRLPHSVT CALCGEVDQT NDTQDFERKL
MECSVCNEIV HPGCLEMDGE GLLSDELPNY WECPKCYEGQ KHTVEANHDR ILLHSKRKAA
DNYESSHYYP AKVLRPPLGQ SPPSPPLLLL PPSPSSAPPT PPSAQTQVPL ASREERAKRR
QLAREKENHP TGCDQSEGDR LRLRGPYLTV TLQRPPKELS STSIVPKLQA ITPNPRQPIR
AAPLHQDEER EEEEEEEEEE EETENVMLGQ RKDSTSMQKD VWLSVFHYLT HEELCICMRV
CKAWYKWGCD KRLWSRIDVS RCKSLVPQAL SGIIKRQPIY LDLSWTNVSK KQLIWLINRL
PGLKDLILAG CTWSAVSALA SCSCPLLRTL DLRWTVGIKD TQIRDLLTPA SDKSGHDSRS
KLRLLTDLRL SGLDISDVTL RLIIRHCPLL SKLDLSHCPL LSDQSVNLLT AVGSSTRGTL
THIHLAGCKG VTDESLLYLR RATNLSLIDL HGCKQVTRGA CEEFISDLSV STLYCLSDDK
LIQRIS
