JM703_ORYSJ
ID JM703_ORYSJ Reviewed; 1238 AA.
AC Q53WJ1; A0A0P0WIZ4; B9FMY1;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Lysine-specific demethylase JMJ703;
DE EC=1.14.11.67 {ECO:0000269|PubMed:23319643, ECO:0000269|PubMed:23357881};
DE AltName: Full=Jumonji domain-containing protein 703;
DE AltName: Full=Lysine-specific histone demethylase JMJ703;
DE AltName: Full=Protein JUMONJI 703;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase JMJ703 {ECO:0000305};
GN Name=JMJ703; OrderedLocusNames=Os05g0196500, LOC_Os05g10770;
GN ORFNames=P0617H07.8;
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=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
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 GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
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 [7]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 139-498 IN COMPLEX WITH IRON AND
RP ALPHA-KETOGLUTARATE, FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION,
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF TYR-321; GLY-376; TRP-381;
RP HIS-394; GLU-396; ASN-404; LYS-412; LEU-447; HIS-482; ALA-494 AND ASN-496.
RC STRAIN=cv. Zhonghua 11;
RX PubMed=23357881; DOI=10.1371/journal.pgen.1003239;
RA Chen Q., Chen X., Wang Q., Zhang F., Lou Z., Zhang Q., Zhou D.X.;
RT "Structural basis of a histone H3 lysine 4 demethylase required for stem
RT elongation in rice.";
RL PLoS Genet. 9:E1003239-E1003239(2013).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF HIS-394.
RX PubMed=23319643; DOI=10.1073/pnas.1217020110;
RA Cui X., Jin P., Cui X., Gu L., Lu Z., Xue Y., Wei L., Qi J., Song X.,
RA Luo M., An G., Cao X.;
RT "Control of transposon activity by a histone H3K4 demethylase in rice.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:1953-1958(2013).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' (H3K4me) of
CC histone H3 with a specific activity for H3K4me3, H3K4me2 and H3K4me1.
CC No activity on H3K9me3/2/1, H3K27me3/2/1 and H3K36me3/2/1. Involved in
CC the control of stem elongation by regulating methylation states of
CC H3K4me3 on cytokinin oxidase (CKX) gene family, which may cause
CC increased expression of CKX genes and reduced cytokinin levels.
CC Prevents ectopic retrotransposition by regulating the levels of H3K4me3
CC in two non-LTR retrotransposons KARMA and LINE-1 (L1) and reinforcing
CC their repressed states. {ECO:0000269|PubMed:23319643,
CC ECO:0000269|PubMed:23357881}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-
CC [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone
CC H3] + 3 succinate; Xref=Rhea:RHEA:60208, Rhea:RHEA-COMP:15537,
CC Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61961; EC=1.14.11.67;
CC Evidence={ECO:0000269|PubMed:23319643, ECO:0000269|PubMed:23357881};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60209;
CC Evidence={ECO:0000269|PubMed:23319643, ECO:0000269|PubMed:23357881};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:23357881};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:23357881};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00537,
CC ECO:0000269|PubMed:23319643, ECO:0000269|PubMed:23357881}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaf sheaths, stems and
CC panicles. {ECO:0000269|PubMed:23319643}.
CC -!- DISRUPTION PHENOTYPE: Semi-dwarf plants and reduced seed size. Small
CC panicle enclosure phenotype. {ECO:0000269|PubMed:23319643,
CC ECO:0000269|PubMed:23357881}.
CC -!- SEQUENCE CAUTION:
CC Sequence=EEE62643.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC135427; AAV59453.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF16781.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS92678.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE62643.1; ALT_INIT; Genomic_DNA.
DR EMBL; AK121381; BAH00458.1; -; mRNA.
DR RefSeq; XP_015639402.1; XM_015783916.1.
DR PDB; 4IGO; X-ray; 2.40 A; A=139-498.
DR PDB; 4IGP; X-ray; 3.00 A; A=139-498.
DR PDB; 4IGQ; X-ray; 2.35 A; A=139-498.
DR PDBsum; 4IGO; -.
DR PDBsum; 4IGP; -.
DR PDBsum; 4IGQ; -.
DR AlphaFoldDB; Q53WJ1; -.
DR SMR; Q53WJ1; -.
DR STRING; 4530.OS05T0196500-01; -.
DR PaxDb; Q53WJ1; -.
DR PRIDE; Q53WJ1; -.
DR EnsemblPlants; Os05t0196500-01; Os05t0196500-01; Os05g0196500.
DR GeneID; 4338043; -.
DR Gramene; Os05t0196500-01; Os05t0196500-01; Os05g0196500.
DR KEGG; osa:4338043; -.
DR eggNOG; KOG1246; Eukaryota.
DR HOGENOM; CLU_000991_8_0_1; -.
DR InParanoid; Q53WJ1; -.
DR OMA; LWGIHND; -.
DR OrthoDB; 664180at2759; -.
DR BRENDA; 1.14.11.67; 4460.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; Q53WJ1; OS.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0008198; F:ferrous iron binding; IDA:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0032453; F:histone H3-methyl-lysine-4 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:0045814; P:negative regulation of gene expression, epigenetic; IDA:UniProtKB.
DR GO; GO:0040010; P:positive regulation of growth rate; IMP:UniProtKB.
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 3D-structure; Chromatin regulator; Dioxygenase; Iron; Metal-binding;
KW Nucleus; Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..1238
FT /note="Lysine-specific demethylase JMJ703"
FT /id="PRO_0000430000"
FT DOMAIN 154..195
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 348..514
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT DOMAIN 1019..1077
FT /note="FYR N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT DOMAIN 1079..1169
FT /note="FYR C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT REGION 56..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 215..266
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 699..725
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 777..798
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 834..863
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 910..978
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 245..259
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 702..723
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 910..938
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 959..978
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 394
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:23357881"
FT BINDING 396
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:23357881"
FT BINDING 482
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 321
FT /note="Y->A: Loss of activity on H3K4me3."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 376
FT /note="G->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 381
FT /note="W->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 383
FT /note="Y->A: Loss of activity on H3K4me3/1."
FT MUTAGEN 394
FT /note="H->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23319643,
FT ECO:0000269|PubMed:23357881"
FT MUTAGEN 396
FT /note="E->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 404
FT /note="N->A: No effect on demethylase activity."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 412
FT /note="K->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 447
FT /note="L->A: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 482
FT /note="H->Y: Loss of activity on H3K4me3/2/1."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 494
FT /note="A->S: Loss of activity on H3K4me3/2."
FT /evidence="ECO:0000269|PubMed:23357881"
FT MUTAGEN 496
FT /note="N->A: Loss of activity on H3K4me3."
FT /evidence="ECO:0000269|PubMed:23357881"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 161..164
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 167..178
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 182..186
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 201..206
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 266..270
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 272..286
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 299..311
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 318..326
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 356..358
FT /evidence="ECO:0007829|PDB:4IGQ"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 381..385
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 390..394
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 397..399
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 401..410
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 412..417
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 419..421
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 422..432
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 434..439
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 443..446
FT /evidence="ECO:0007829|PDB:4IGQ"
FT HELIX 453..458
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 464..468
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 473..476
FT /evidence="ECO:0007829|PDB:4IGQ"
FT STRAND 481..497
FT /evidence="ECO:0007829|PDB:4IGQ"
SQ SEQUENCE 1238 AA; 137382 MW; 03DCE4EE8B44A1BC CRC64;
MMGVTTTLNE DTEPSIPPGF GPFATLPLWG IHNDAKPAVT HSTPVQALQS IRKDSEECQP
SAAVSRSDTP CSTSGTQTCR KSLRNRPPID YSRFEHISDE DSDVEIVEKD VSSTRRRQQL
PKGVLRGCAE CSDCQKVIAK WNPAGARRPV LDEAPVFYPT EEEFEDTLKY IESIRPMAEP
YGICRIVPPS SWKPPCLLKD KSIWEGSKFS TRVQKVDKLQ NRKSSKKGRR GGMMKRRKLA
ESEENSATAH TQTGMQQSPE RFGFEPGPEF TLQTFQKYAD DFSKQYFRKD TSMDSVPSVE
DIEGEYWRIV EVPTEEIEVI YGADLETGTF GSGFPKLSPE TKSDAEDKYA QSGWNLNNLP
RLQGSVLSFE GGDISGVLVP WVYVGMCFSS FCWHVEDHHL YSLNYMHWGA PKLWYGVPGK
DAVNLESAMR KHLPELFEEQ PDLLHNLVTQ FSPSLLKSEG VHVYRCVQHE GEFVLTFPRA
YHAGFNCGFN CAEAVNVAPI DWLPIGHNAV ELYREQARKI TISHDKLLLG AAREAIRAQW
DILFLKRNTA DNMRWKSICG ADSTIFKALK ARIETELVQR KTLGVPAQSR KMDAEFDSID
RECALCYYDL HLSASGCPCC PEKYACLVHA KQLCSCDWDK RFFLFRYDVN ELNILADALG
GKLSAIHRWG VSDLGLSLSS CVKREKVQDS KTVRRLTDGP RRSYMSQASA VSLVSSSTSN
EQKDEGNKIM KIASPQTNNV CPSVEQRKSE NISPLKEPCV RNELSCTTNS DSNGLQYNGG
LGGHKGSAPG LPVSSSPSFS SNVATRPIST SSVSMKIVQG LVASKSCIQA SSRTGDSRSL
LGEHHNRSPA MIHDGTNMKS SLESSNNSCR LIASDYNATP CHSSKDQVLV TPGTNASVVT
LKDSSQVHSA SSQQFVRTGP WTQSASHEAS SPSTSALKPS LDPPAMKNLY GGFTQGSAHP
GPPSFSNQQP NDGRLQRTSE SLPGVEARAR GHPTVTAQPA LEIHSRNGGA QKGPRIANVV
HRFKCSVEPL EIGVVLSGRL WSSSQAIFPK GFRSRVKYFS IVDPIQMAYY ISEILDAGMQ
GPLFMVKLEN CPGEVFINLS PTKCWNMVRE RLNMEIRRQL NMGKSNLPTL QPPGSVDGLE
MFGLLSPPIV QAIWARDRDH ICTEYWRSRP HVLIEDPNNR HMLSQGPPLL ALRGLIQRAN
RDELQVLRSL MTNSNNLDDS SRQQAAHIIE EEIAKQLC
