JM706_ORYSJ
ID JM706_ORYSJ Reviewed; 858 AA.
AC Q336N8; A0A0P0XYM9; Q0IVD6; Q8W3G5;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=Lysine-specific demethylase JMJ706;
DE EC=1.14.11.66 {ECO:0000269|PubMed:18765808};
DE AltName: Full=Jumonji domain-containing protein 706;
DE AltName: Full=Lysine-specific histone demethylase JMJ706;
DE AltName: Full=Protein JUMONJI 706;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(9) demethylase JMJ706 {ECO:0000305};
GN Name=JMJ706; OrderedLocusNames=Os10g0577600, LOC_Os10g42690;
GN ORFNames=OSJNBa0035H01.2;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=cv. Zhonghua 11;
RX PubMed=18765808; DOI=10.1073/pnas.0805901105;
RA Sun Q., Zhou D.X.;
RT "Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required
RT for floral organ development.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:13679-13684(2008).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-9' (H3K9me) of
CC histone H3 with a specific activity for H3K9me3 and H3K9me2. No
CC activity on H3K4me3, H3K9me1, H3K27me2 and H3K36me3/2. Involved in the
CC control of floral organ development by demethylating H3K9me3 and
CC H3K9me2 in the promoter regions of DH1 and MADS47. The 'Lys-9'
CC demethylation of these two genes is required for induction of their
CC expression. {ECO:0000269|PubMed:18765808}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-
CC [histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L-
CC lysyl(9)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60200, Rhea:RHEA-
CC COMP:15538, Rhea:RHEA-COMP:15542, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, ChEBI:CHEBI:61961;
CC EC=1.14.11.66; Evidence={ECO:0000269|PubMed:18765808};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60201;
CC Evidence={ECO:0000269|PubMed:18765808};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q53WJ1};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q53WJ1};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00537,
CC ECO:0000269|PubMed:18765808}. Note=Localizes mainly in heterochromatin
CC foci.
CC -!- DISRUPTION PHENOTYPE: Defects in spikelet morphology, including floral
CC organ numbers, depletion of lemma and/or palea (Fig. 4D), increased
CC numbers of stamens and pistils. {ECO:0000269|PubMed:18765808}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL58187.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC027037; AAL58187.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; ABB48025.1; -; Genomic_DNA.
DR EMBL; AP008216; BAF27329.2; -; Genomic_DNA.
DR EMBL; AP014966; BAT12215.1; -; Genomic_DNA.
DR EMBL; AK073475; BAG93472.1; -; mRNA.
DR RefSeq; XP_015614674.1; XM_015759188.1.
DR RefSeq; XP_015614675.1; XM_015759189.1.
DR AlphaFoldDB; Q336N8; -.
DR SMR; Q336N8; -.
DR STRING; 4530.OS10T0577600-01; -.
DR PaxDb; Q336N8; -.
DR PRIDE; Q336N8; -.
DR EnsemblPlants; Os10t0577600-01; Os10t0577600-01; Os10g0577600.
DR GeneID; 4349499; -.
DR Gramene; Os10t0577600-01; Os10t0577600-01; Os10g0577600.
DR KEGG; osa:4349499; -.
DR eggNOG; KOG1246; Eukaryota.
DR HOGENOM; CLU_016978_0_0_1; -.
DR InParanoid; Q336N8; -.
DR OMA; QLMRFQR; -.
DR OrthoDB; 664180at2759; -.
DR BRENDA; 1.14.11.66; 4460.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR Genevisible; Q336N8; OS.
DR GO; GO:0000792; C:heterochromatin; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IDA:UniProtKB.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR GO; GO:0140684; F:histone H3-tri/dimethyl-lysine-9 demethylase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0045815; P:epigenetic maintenance of chromatin in transcription-competent conformation; IMP:UniProtKB.
DR GO; GO:0048439; P:flower morphogenesis; 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 Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..858
FT /note="Lysine-specific demethylase JMJ706"
FT /id="PRO_0000430002"
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 REGION 737..791
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 829..858
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 829..847
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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 BINDING 295
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 388
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
SQ SEQUENCE 858 AA; 96299 MW; 257F701D632A2398 CRC64;
MQQVEGRNCL PAEVRIGLET LKRRRLERMR LTAQNNAGDG PPVPARSGGD ALRTPANCGV
RLHANNGTAL PSRTTQNKDP FAKRRVDKFD MSSLEWIDKI EECPVYYPTK EEFEDPIGYI
QKIAPVASKY GICKIVSPVS ASVPAGVVLM KEQPGFKFMT RVQPLRLAKW AEDDTVTFFM
SERKYTFRDY EKMANKVFAK KYSSASCLPA KYVEEEFWRE IAFGKMDFVE YACDVDGSAF
SSSPHDQLGK SNWNLKNFSR LSNSVLRLLQ TPIPGVTDPM LYIGMLFSMF AWHVEDHYLY
SINYHHCGAF KTWYGIPGDA APGFEKVASQ FVYNKDILVG EGEDAAFDVL LGKTTMFPPN
VLLDHNVPVY KAVQKPGEFV ITFPRSYHAG FSHGFNCGEA VNFAISDWFP LGSVASRRYA
LLNRTPLLAH EELLCRSAVL LSHKLLNSDP KSLNKSEHPH SQRCLKSCFV QLMRFQRNTR
GLLAKMGSQI HYKPKTYPNL SCSMCRRDCY ITHVLCGCNF DPVCLHHEQE LRSCPCKSNQ
VVYVREDIQE LEALSRKFEK DICLDKEISG FDSYKQAEKN EPFFEITRNL RNTEVNLIED
AFSGATAADA AKSSPATSTL TSFAQHDVPV LAEAIVCANQ ADQLYSTTEQ TISSPLVKGT
DAVGANSSSM ADANNGTGSC NASAVEYSGN SDSESEIFRV KRRSGVSVKP ASDAKTSNLS
DQQVLRRLKK VRPEIQQHNK RPEDYGHCSV PSGRMSMKNL NSSSSCGEEH WRMKRRQLET
QQDESSYSAK QKSYSYPSTS YSFRGEFVEM SRDAAAEVRP KRLKIRLPSS STNRVVEQGS
SGQRFTRDDK SLGCWPAI
