JMJ18_ARATH
ID JMJ18_ARATH Reviewed; 819 AA.
AC F4I6G4; Q8W4M0; Q9SY24;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 76.
DE RecName: Full=Lysine-specific demethylase JMJ18 {ECO:0000303|PubMed:18713399};
DE EC=1.14.11.- {ECO:0000269|PubMed:22536163};
DE AltName: Full=Jumonji domain-containing protein 18 {ECO:0000303|PubMed:18713399};
DE Short=AtJMJ18 {ECO:0000303|PubMed:18713399};
DE Short=Protein JUMONJI 18 {ECO:0000303|PubMed:18713399};
DE AltName: Full=Lysine-specific histone demethylase JMJ18 {ECO:0000303|PubMed:18713399};
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) monodemethylase JMJ18 {ECO:0000305};
GN Name=JMJ18 {ECO:0000303|PubMed:18713399};
GN OrderedLocusNames=At1g30810 {ECO:0000312|Araport:AT1G30810};
GN ORFNames=T17H7.10 {ECO:0000312|EMBL:AAD32935.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP GENE FAMILY, NOMENCLATURE, AND TISSUE SPECIFICITY.
RX PubMed=18713399; DOI=10.1111/j.1744-7909.2008.00692.x;
RA Lu F., Li G., Cui X., Liu C., Wang X.-J., Cao X.;
RT "Comparative analysis of JmjC domain-containing proteins reveals the
RT potential histone demethylases in Arabidopsis and rice.";
RL J. Integr. Plant Biol. 50:886-896(2008).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=22536163; DOI=10.1371/journal.pgen.1002664;
RA Yang H., Han Z., Cao Y., Fan D., Li H., Mo H., Feng Y., Liu L., Wang Z.,
RA Yue Y., Cui S., Chen S., Chai J., Ma L.;
RT "A companion cell-dominant and developmentally regulated H3K4 demethylase
RT controls flowering time in Arabidopsis via the repression of FLC
RT expression.";
RL PLoS Genet. 8:E1002664-E1002664(2012).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' (H3K4me) of
CC histone H3 with a specific activity for H3K4me3 and H3K4me2. No
CC activity on H3K9me3/2, H3K27me3/2 and H3K36me3/2. Involved in the
CC control of flowering time by demethylating H3K4me3 at the FLC locus and
CC repressing its expression. The repression of FLC level and reduction in
CC H3K4me3 at the FLC locus results in induction of the flowering
CC activator FT, which is a downstream target of FLC.
CC {ECO:0000269|PubMed:22536163}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone
CC H3] + O2 = CO2 + formaldehyde + N(6),N(6)-dimethyl-L-lysyl(4)-
CC [histone H3] + succinate; Xref=Rhea:RHEA:60212, Rhea:RHEA-COMP:15537,
CC Rhea:RHEA-COMP:15540, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:61961, ChEBI:CHEBI:61976;
CC Evidence={ECO:0000269|PubMed:22536163};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60213;
CC Evidence={ECO:0000269|PubMed:22536163};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] +
CC O2 = CO2 + formaldehyde + N(6)-methyl-L-lysyl(4)-[histone H3] +
CC succinate; Xref=Rhea:RHEA:60216, Rhea:RHEA-COMP:15540, Rhea:RHEA-
CC COMP:15543, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:61929,
CC ChEBI:CHEBI:61976; Evidence={ECO:0000269|PubMed:22536163};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60217;
CC Evidence={ECO:0000269|PubMed:22536163};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q8GUI6};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q8GUI6};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00537,
CC ECO:0000255|PROSITE-ProRule:PRU00768, ECO:0000269|PubMed:22536163}.
CC -!- TISSUE SPECIFICITY: Expressed in vascular tissues of roots, cotyledons,
CC leaves and flowers (PubMed:22536163). Expressed predominantly in phloem
CC companion cells of roots (PubMed:22536163). Present in inflorescences,
CC roots, siliques, leaves and stems (PubMed:18713399).
CC {ECO:0000269|PubMed:18713399, ECO:0000269|PubMed:22536163}.
CC -!- DISRUPTION PHENOTYPE: Weak late-flowering phenotype.
CC {ECO:0000269|PubMed:22536163}.
CC -!- MISCELLANEOUS: Plants over-expressing JMJ18 show an early-flowering
CC phenotype. {ECO:0000305|PubMed:22536163}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD32935.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC004135; AAD32935.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE31274.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31275.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60555.1; -; Genomic_DNA.
DR EMBL; AY062485; AAL32563.1; -; mRNA.
DR RefSeq; NP_001185118.1; NM_001198189.1.
DR RefSeq; NP_001319118.1; NM_001332929.1.
DR RefSeq; NP_174367.6; NM_102818.7.
DR AlphaFoldDB; F4I6G4; -.
DR SMR; F4I6G4; -.
DR BioGRID; 25198; 4.
DR IntAct; F4I6G4; 1.
DR STRING; 3702.AT1G30810.1; -.
DR iPTMnet; F4I6G4; -.
DR PaxDb; F4I6G4; -.
DR PRIDE; F4I6G4; -.
DR ProteomicsDB; 238989; -.
DR EnsemblPlants; AT1G30810.1; AT1G30810.1; AT1G30810.
DR EnsemblPlants; AT1G30810.2; AT1G30810.2; AT1G30810.
DR EnsemblPlants; AT1G30810.3; AT1G30810.3; AT1G30810.
DR GeneID; 839963; -.
DR Gramene; AT1G30810.1; AT1G30810.1; AT1G30810.
DR Gramene; AT1G30810.2; AT1G30810.2; AT1G30810.
DR Gramene; AT1G30810.3; AT1G30810.3; AT1G30810.
DR KEGG; ath:AT1G30810; -.
DR Araport; AT1G30810; -.
DR TAIR; locus:2196979; AT1G30810.
DR eggNOG; KOG1246; Eukaryota.
DR HOGENOM; CLU_000991_8_1_1; -.
DR InParanoid; F4I6G4; -.
DR OMA; QYALSGW; -.
DR OrthoDB; 664180at2759; -.
DR PRO; PR:F4I6G4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; F4I6G4; baseline and differential.
DR Genevisible; F4I6G4; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0032453; F:histone H3-methyl-lysine-4 demethylase activity; IDA:TAIR.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0048573; P:photoperiodism, flowering; IMP:TAIR.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR InterPro; IPR003889; FYrich_C.
DR InterPro; IPR003888; FYrich_N.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR004198; Znf_C5HC2.
DR Pfam; PF05965; FYRC; 1.
DR Pfam; PF05964; FYRN; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM00542; FYRC; 1.
DR SMART; SM00541; FYRN; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR PROSITE; PS51543; FYRC; 1.
DR PROSITE; PS51542; FYRN; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..819
FT /note="Lysine-specific demethylase JMJ18"
FT /id="PRO_0000429996"
FT DOMAIN 59..100
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 261..427
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 644..702
FT /note="FYR N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT DOMAIN 704..788
FT /note="FYR C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT ZN_FING 519..571
FT /note="C5HC2"
FT /evidence="ECO:0000255"
FT REGION 1..39
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 120..171
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 130..137
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 131..149
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 150..170
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 307
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 309
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 395
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 519
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 522
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 533
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 535
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 542
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 545
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 550
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT BINDING 552
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8GUI6"
FT CONFLICT 683
FT /note="F -> S (in Ref. 3; AAL32563)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 819 AA; 92809 MW; 772A15C0D5361DCC CRC64;
MENPPLESEI KEDMSLKNHP PDKDKDKDTI MEQPSSPRHR KVVARWLPDE AQRPIINDAP
VFTPSLEEFV DPLAYIEKIR PLAEPYGICR IIPPSTWKPP CRLKEKSIWE QTKFPTRIQT
VDLLQNREPM KKKPKSRKRK RRRNSRMGSS KRRSGSSPAE STSSPEAEEK FGFNSGSDFT
LDEFEKYALH FKDSYFEKKD SGGDIVKWTP SVDDIEGEYW RIVEQPTDEV EVYYGADLEN
GVLGSGFYKR AEKFTGSDME QYTLSGWNLN NLPRLPGSVL SFEDCDISGV LVPWLYVGMC
FSSFCWHVED HHLYSLNYHH FGEPKVWYGV PGSNATALEK AMRKHLPDLF EEQPDLLHGL
VTQFSPSILK DEGVQAYRVV QNSGEYVLTF PRAYHAGFNC GFNCAEAVNV APVDWLAHGQ
NAVELYSKET RKTSLSHDKL LLGAAYEAVK ALWELSASEG KENTTNLRWK SFCGKNGTLT
NAIQARLQME EGRITALGRD SSSLKKMEKD FDSNCERECF SCFYDLHLSA SGCKCSPEEY
ACLKHADDLC SCDVKDGFIL LRYTMDELSS LVRALEGESD DLKIWASKVL GIEHSDEDQT
KTSSVISEEK KLKEGSFDLN IDLEMDYQED VKEEASTSGG ELTASENLGV SVEPINLGFL
IFGKLWCNKY AIFPKGFRSR VKFYNVLDPT RMSNYISEVL DAGLMGPLFR VTLEESPDES
FFNVSAQQCW EMVMRRVKDT STSLGLPILP QFESINGLQM FGFLSPSIVQ AIEALDPNHR
LVEYWNHKNQ TSSDSKDHFI SSNCSASLTK GKLFGVDLM
