JMJ13_ARATH
ID JMJ13_ARATH Reviewed; 787 AA.
AC F4KIX0; Q9FJS0;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=Lysine-specific demethylase JMJ13 {ECO:0000303|PubMed:30899015};
DE EC=1.14.11.- {ECO:0000269|PubMed:30899015};
DE AltName: Full=Jumonji domain-containing protein 13 {ECO:0000303|PubMed:18713399, ECO:0000303|PubMed:30899015};
DE Short=AtJMJ13 {ECO:0000303|PubMed:18713399};
DE Short=Protein JUMONJI 13 {ECO:0000303|PubMed:18713399, ECO:0000303|PubMed:30899015};
DE AltName: Full=Lysine-specific histone demethylase JMJ13 {ECO:0000303|PubMed:30899015};
DE AltName: Full=[histone H3]-trimethyl-L-lysine(27) monodemethylase JMJ13 {ECO:0000305};
GN Name=JMJ13 {ECO:0000303|PubMed:18713399, ECO:0000303|PubMed:30899015};
GN OrderedLocusNames=At5g46910 {ECO:0000312|Araport:AT5G46910};
GN ORFNames=MQD22.4 {ECO:0000312|EMBL:BAB10230.1};
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=9734815; DOI=10.1093/dnares/5.3.203;
RA Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence
RT features of the regions of 1,367,185 bp covered by 19 physically assigned
RT P1 and TAC clones.";
RL DNA Res. 5:203-216(1998).
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 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 [4]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 90-578 IN COMPLEX WITH HISTONE
RP H3; ZINC AND NICKEL, FUNCTION, MUTAGENESIS OF PHE-179; ASP-236; TYR-282;
RP GLU-295; ASP-296; HIS-388 AND ASN-402, DISRUPTION PHENOTYPE, AND CATALYTIC
RP ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=30899015; DOI=10.1038/s41467-019-09310-x;
RA Zheng S., Hu H., Ren H., Yang Z., Qiu Q., Qi W., Liu X., Chen X., Cui X.,
RA Li S., Zhou B., Sun D., Cao X., Du J.;
RT "The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and
RT photoperiod dependent flowering repressor.";
RL Nat. Commun. 10:1303-1303(2019).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-27' (H3K27me) of
CC histone H3 with a specific activity for H3K27me3 and involved in the
CC regulation of gene expression (PubMed:30899015). Acts as a temperature
CC and photoperiod dependent flowering repressor (PubMed:30899015).
CC {ECO:0000269|PubMed:30899015}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(27)-[histone
CC H3] + O2 = CO2 + formaldehyde + N(6),N(6)-dimethyl-L-lysyl(27)-
CC [histone H3] + succinate; Xref=Rhea:RHEA:60228, Rhea:RHEA-COMP:15535,
CC Rhea:RHEA-COMP:15539, 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:30899015};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60229;
CC Evidence={ECO:0000269|PubMed:30899015};
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}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in leaves, and, to a lower extent,
CC in inflorescences, roots, siliques and stems.
CC {ECO:0000269|PubMed:18713399}.
CC -!- INDUCTION: Accumulates in response to higher temperature and during
CC long days (at protein level). {ECO:0000269|PubMed:30899015}.
CC -!- DISRUPTION PHENOTYPE: Early flowering in both long and short days
CC conditions, but in a temperature sensitive manner only in short days.
CC {ECO:0000269|PubMed:30899015}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB10230.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB013394; BAB10230.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED95446.1; -; Genomic_DNA.
DR RefSeq; NP_199502.2; NM_124062.3.
DR PDB; 6IP0; X-ray; 2.40 A; A=90-578.
DR PDB; 6IP4; X-ray; 2.60 A; A=90-578.
DR PDBsum; 6IP0; -.
DR PDBsum; 6IP4; -.
DR SMR; F4KIX0; -.
DR STRING; 3702.AT5G46910.1; -.
DR PaxDb; F4KIX0; -.
DR PRIDE; F4KIX0; -.
DR ProteomicsDB; 207848; -.
DR EnsemblPlants; AT5G46910.1; AT5G46910.1; AT5G46910.
DR GeneID; 834736; -.
DR Gramene; AT5G46910.1; AT5G46910.1; AT5G46910.
DR Araport; AT5G46910; -.
DR TAIR; locus:2170982; AT5G46910.
DR eggNOG; KOG1246; Eukaryota.
DR HOGENOM; CLU_016978_0_0_1; -.
DR InParanoid; F4KIX0; -.
DR OrthoDB; 664180at2759; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4KIX0; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0042393; F:histone binding; IDA:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; IDA:TAIR.
DR GO; GO:0071558; F:histone H3-tri/di-methyl-lysine-27 demethylase activity; IDA:UniProtKB.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0048571; P:long-day photoperiodism; IEP:UniProtKB.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:0048579; P:negative regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0048577; P:negative regulation of short-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR GO; GO:0009266; P:response to temperature stimulus; IMP:UniProtKB.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR004198; Znf_C5HC2.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flowering; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome; Repressor; Transcription; Transcription regulation;
KW Zinc; Zinc-finger.
FT CHAIN 1..787
FT /note="Lysine-specific demethylase JMJ13"
FT /id="PRO_0000456188"
FT DOMAIN 103..144
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 250..420
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 617..675
FT /note="FYR N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT DOMAIN 677..756
FT /note="FYR C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT ZN_FING 500..551
FT /note="C4HCHC"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT ZN_FING 500..551
FT /note="C5HC2"
FT /evidence="ECO:0000255"
FT MOTIF 752..759
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT BINDING 293
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538,
FT ECO:0000305|PubMed:30899015, ECO:0007744|PDB:6IP0,
FT ECO:0007744|PDB:6IP4"
FT BINDING 295
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538,
FT ECO:0000305|PubMed:30899015, ECO:0007744|PDB:6IP0,
FT ECO:0007744|PDB:6IP4"
FT BINDING 388
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538,
FT ECO:0000305|PubMed:30899015, ECO:0007744|PDB:6IP0,
FT ECO:0007744|PDB:6IP4"
FT BINDING 500
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 503
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 514
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 516
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 519
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 522
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 525
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT BINDING 534
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP0, ECO:0007744|PDB:6IP4"
FT SITE 179
FT /note="Histone H3 binding"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP4"
FT SITE 236
FT /note="Histone H3 binding"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP4"
FT SITE 282
FT /note="Histone H3 binding"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP4"
FT SITE 296
FT /note="Histone H3 binding"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP4"
FT SITE 402
FT /note="Histone H3 binding"
FT /evidence="ECO:0000269|PubMed:30899015,
FT ECO:0007744|PDB:6IP4"
FT MUTAGEN 179
FT /note="F->N: Strongly reduced demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 179
FT /note="F->S: Slightly reduced demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 236
FT /note="D->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 282
FT /note="Y->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 295
FT /note="E->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 296
FT /note="D->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 388
FT /note="H->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT MUTAGEN 402
FT /note="N->A: Impaired demethylase activity."
FT /evidence="ECO:0000269|PubMed:30899015"
FT CONFLICT 639
FT /note="Y -> YQ (in Ref. 1; BAB10230)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 787 AA; 88821 MW; 0313F217FEF3FF94 CRC64;
MAERRICLSK EAKDGLEFLK RKKLQKMRSD SVNETVGFST MARSGGDALR PTSASCGMRL
RVTSSDTVSK VHGASTVRGG LMKEKVEKLE TDDLKWTERL PECPVYRPTK EEFEDPLTYL
QKIFPEASKY GICKIVSPLT ATVPAGAVLM KEKSNFKFTT RVQPLRLAEW DSDDKVTFFM
SGRTYTFRDY EKMANKVFAR RYCSGGSLPD SFLEKEFWKE IACGKTETVE YACDVDGSAF
SSAPGDPLGS SKWNLNKVSR LPKSTLRLLE TSIPGVTEPM LYIGMLFSMF AWHVEDHYLY
SINYQHCGAS KTWYGIPGSA ALKFEKVVKE CVYNDDILST NGEDGAFDVL LGKTTIFPPK
TLLDHNVPVY KAVQKPGEFV VTFPRAYHAG FSHGFNCGEA VNFAMGDWFP FGAIASCRYA
HLNRVPLLPH EELICKEAML LNSSSKSENL DLTPTELSGQ RSIKTAFVHL IRFLHLARWS
LMKSGLCTGL VSNTYGTIVC SLCKRDCYLA FINCECYSHP VCLRHDVKKL DLPCGTTHTL
YLRDNIEDME AAAMKFEKED GVSDLITTDE DLYKYPSSIT LPAAKEDGYT PYSTIYFDFY
TEVEMTSHDQ LQSGNPVMSY EANASCISSV ADDYECSDYV NRRANCSSSS DSKLSEEVAC
SSSKKTRFFP VVQDEQLVAD QESDGSDSEC FRVKRRSSLK FENRTVVLDT RESDHHQELK
RLKKSHHHEG RYSSSSSVSR QEEEEDELVI SNRKETQQQS DVKMQKKRIE NHFGGFKRLK
VKGLIKP
