JHD1_DROME
ID JHD1_DROME Reviewed; 1345 AA.
AC Q9VHH9; Q7YU79;
DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 07-MAR-2006, sequence version 2.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=JmjC domain-containing histone demethylation protein 1;
DE EC=1.14.11.27 {ECO:0000250|UniProtKB:P40034};
DE AltName: Full=Lysine (K)-specific demethylase 2;
DE AltName: Full=[Histone-H3]-lysine-36 demethylase 1;
GN Name=Kdm2; Synonyms=Jhd1; ORFNames=CG11033;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley; TISSUE=Embryo;
RA Stapleton M., Brokstein P., Hong L., Agbayani A., Carlson J.W., Champe M.,
RA Chavez C., Dorsett V., Dresnek D., Farfan D., Frise E., George R.A.,
RA Gonzalez M., Guarin H., Kronmiller B., Li P.W., Liao G., Miranda A.,
RA Mungall C.J., Nunoo J., Pacleb J.M., Paragas V., Park S., Patel S.,
RA Phouanenavong S., Wan K.H., Yu C., Lewis S.E., Rubin G.M., Celniker S.E.;
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-53; SER-58 AND SER-79, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Embryo;
RX PubMed=18327897; DOI=10.1021/pr700696a;
RA Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
RT "Phosphoproteome analysis of Drosophila melanogaster embryos.";
RL J. Proteome Res. 7:1675-1682(2008).
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-36'
CC of histone H3, thereby playing a central role in histone code.
CC {ECO:0000250|UniProtKB:P40034}.
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:P40034};
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 -!- DOMAIN: The JmjC domain mediates the demethylation activity.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; AE014297; AAF54335.2; -; Genomic_DNA.
DR EMBL; BT009941; AAQ22410.1; -; mRNA.
DR RefSeq; NP_001262400.1; NM_001275471.1.
DR RefSeq; NP_001262401.1; NM_001275472.1.
DR RefSeq; NP_001262402.1; NM_001275473.1.
DR RefSeq; NP_649864.2; NM_141607.3.
DR AlphaFoldDB; Q9VHH9; -.
DR SMR; Q9VHH9; -.
DR BioGRID; 66257; 11.
DR IntAct; Q9VHH9; 1.
DR STRING; 7227.FBpp0289915; -.
DR iPTMnet; Q9VHH9; -.
DR PaxDb; Q9VHH9; -.
DR PRIDE; Q9VHH9; -.
DR EnsemblMetazoa; FBtr0300691; FBpp0289915; FBgn0037659.
DR EnsemblMetazoa; FBtr0336758; FBpp0307734; FBgn0037659.
DR EnsemblMetazoa; FBtr0336759; FBpp0307735; FBgn0037659.
DR EnsemblMetazoa; FBtr0336760; FBpp0307736; FBgn0037659.
DR GeneID; 41090; -.
DR KEGG; dme:Dmel_CG11033; -.
DR UCSC; CG11033-RA; d. melanogaster.
DR CTD; 41090; -.
DR FlyBase; FBgn0037659; Kdm2.
DR VEuPathDB; VectorBase:FBgn0037659; -.
DR eggNOG; KOG1633; Eukaryota.
DR eggNOG; KOG1947; Eukaryota.
DR GeneTree; ENSGT00940000167551; -.
DR HOGENOM; CLU_003540_0_0_1; -.
DR InParanoid; Q9VHH9; -.
DR OMA; LWKRMNC; -.
DR OrthoDB; 324938at2759; -.
DR PhylomeDB; Q9VHH9; -.
DR BRENDA; 1.14.11.27; 1994.
DR SignaLink; Q9VHH9; -.
DR BioGRID-ORCS; 41090; 0 hits in 3 CRISPR screens.
DR GenomeRNAi; 41090; -.
DR PRO; PR:Q9VHH9; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR Bgee; FBgn0037659; Expressed in eye disc (Drosophila) and 24 other tissues.
DR ExpressionAtlas; Q9VHH9; baseline and differential.
DR Genevisible; Q9VHH9; DM.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0031519; C:PcG protein complex; IPI:FlyBase.
DR GO; GO:0019005; C:SCF ubiquitin ligase complex; ISM:FlyBase.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
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:0051864; F:histone H3-methyl-lysine-36 demethylase activity; ISS:FlyBase.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IMP:FlyBase.
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:0033522; P:histone H2A ubiquitination; IDA:FlyBase.
DR GO; GO:0070544; P:histone H3-K36 demethylation; IDA:FlyBase.
DR GO; GO:0034721; P:histone H3-K4 demethylation, trimethyl-H3-K4-specific; IMP:FlyBase.
DR GO; GO:0007526; P:larval somatic muscle development; IMP:FlyBase.
DR GO; GO:0031061; P:negative regulation of histone methylation; IMP:FlyBase.
DR GO; GO:0033183; P:negative regulation of histone ubiquitination; IMP:FlyBase.
DR GO; GO:0006482; P:protein demethylation; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0031146; P:SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; ISM:FlyBase.
DR GO; GO:0007379; P:segment specification; IGI:FlyBase.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.80.10.10; -; 2.
DR InterPro; IPR001810; F-box_dom.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR001611; Leu-rich_rpt.
DR InterPro; IPR006553; Leu-rich_rpt_Cys-con_subtyp.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR002857; Znf_CXXC.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF12937; F-box-like; 1.
DR Pfam; PF13516; LRR_6; 1.
DR Pfam; PF16866; PHD_4; 1.
DR Pfam; PF02008; zf-CXXC; 1.
DR SMART; SM00256; FBOX; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00367; LRR_CC; 5.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51058; ZF_CXXC; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Phosphoprotein; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1345
FT /note="JmjC domain-containing histone demethylation protein
FT 1"
FT /id="PRO_0000226790"
FT DOMAIN 180..348
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 1059..1105
FT /note="F-box"
FT ZN_FING 671..717
FT /note="CXXC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT REGION 1..44
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 503..522
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 816..848
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 876..1053
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..38
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 947..990
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 998..1053
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 241
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 244
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 246
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 316
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 678
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 681
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 684
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 689
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 692
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 695
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 711
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT BINDING 716
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT MOD_RES 53
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT MOD_RES 79
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18327897"
FT CONFLICT 469
FT /note="Q -> L (in Ref. 3; AAQ22410)"
FT /evidence="ECO:0000305"
FT CONFLICT 950
FT /note="N -> T (in Ref. 3; AAQ22410)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1345 AA; 146178 MW; 3157AD3B9E1AE619 CRC64;
MSTAVETGSS PAKSNSNNSS SGGNNNNGNG NLSPNAKGVQ RRQLRERKQR KLYLEEWSLG
DEDGEGTRGF SVAEKLESSK FAQAGMVREM RGCDLTVAFL QQHGFNIPLL FRDKAGLGLR
MPDPQEFTVN DVRLCVGSRR LLDVMDVNTQ KNLQMTMKEW QQYYDSPQKD RLLNVISLEF
SHTRLDRFVQ SPEIVRQIDW VDVVWPKQLK DAQREGTNLL GGMMYPKVQK YCLMSVKNCY
TDFHIDFGGT SVWYHILRGS KVFWLIPPTD RNLQLYEKWV LSGKQADIFF GDTVEKCARV
YLTAGNTFFI PTGWIHAVYT PTQSLVFGGN FLHSFGIVKQ LKTASVEDST KVPQKFRYPF
FTEMLWYVLA RYVHTLLGHS HLEGEASLSE DEMAARPHTH LTHHELFGLK EIVMYLYDLP
PQKKNVPSLV LDPVALIKDV RSLVERHCKD QQDLAITGVS VLKSPPGSQP PFLLYDRTRV
KQEIKQEIAR KNAEVIREQQ QLEAGRAREA ESDTSQSTGV GSVIGMGAGV EYSNGVMKKE
QLENGSGVTV GGHGSQPEAT FALPTDTLKY RPPKKMHLAT ALVAAAASSS SGGGGPVAGV
GGSAVVGSSH SPTGGGVGPV TGAGGAISVI ATSSSYIEGG QVGGILNMDN CHSPEGGGAK
LSPNLTGTGQ PRRRRTRCKN CAACQRSDCG TCPFCMDMVK FGGPGRAKQT CMMRQCLSPM
LPVTAQCVYC HLDGWRQTPV SPQTKQLASA DGPSALMECS VCYEIAHPDC ALSQLDGTED
AADAKGIVNE DLPNSWECPS CCRSGKNYDY KPRHFRARQK SSEVRRVSVS HGQGGAEGHA
DGNTLLPPPV GQYNDFVFTS ESEMESGTVS GHMTHWKHGM KRHHQLEVKT ERNNSCDTPS
PGISPNAIGG DSKVGKRRKS DDGTSVSSSM HESNDAPCGS SAEGAGGAGN ANVSTNQWSG
SGGGGGSRKK NSIRSQLAQQ MLNSSTRVLK KPQYVVRPAS GTGSSSSSGN GGSASATNGI
SNGSNQSGAN SCGAGNGERG TNNGGLSGSN GLGNQHYSSS QNLALDPTVL KIIFRYLPQD
TLVTCCSVCK VWSNAAVDPD LWKKMNCSEH KMSASLLTAI VRRQPEHLIL DWTQIAKRQL
AWLVARLPAL KNLSLQNCPI QAVLALHTCL CPPLQTLDLS FVRGLNDAAI RDILSPPKDS
RPGLSDSKTR LRDLKVMKLA GTDISDVAVR YITQSLPYLR HLDLSSCQRI TDAGVAQIGT
STTATARLTE LNLSACRLVS ENALEHLAKC EGLIWLDLRH VPQVSTQSVI RFASNSKHDL
CVRDIKLVER RRRNSTTANR SWHHD
