JMJ28_ARATH
ID JMJ28_ARATH Reviewed; 927 AA.
AC Q8H1S7; A7Y5W7; O65408;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=Lysine-specific demethylase JMJ28 {ECO:0000303|PubMed:18713399};
DE EC=1.14.11.- {ECO:0000250|UniProtKB:O64752};
DE AltName: Full=Jumonji domain-containing protein 28 {ECO:0000303|PubMed:18713399};
DE Short=AtJMJ28 {ECO:0000303|PubMed:18713399};
DE Short=Protein JUMONJI 28 {ECO:0000303|PubMed:18713399};
DE AltName: Full=Lysine-specific histone demethylase JMJ28 {ECO:0000303|PubMed:18713399};
DE AltName: Full=Protein B160 {ECO:0000312|EMBL:AEE84450.1};
DE AltName: Full=[histone H3]-trimethyl-L-lysine monodemethylase JMJ28 {ECO:0000305};
GN Name=JMJ28 {ECO:0000303|PubMed:18713399};
GN Synonyms=B160 {ECO:0000312|EMBL:AEE84450.1};
GN OrderedLocusNames=At4g21430 {ECO:0000312|Araport:AT4G21430};
GN ORFNames=F18E5.50 {ECO:0000312|EMBL:CAA18707.1},
GN T6K22.160 {ECO:0000312|EMBL:CAA20208.1};
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 [GENOMIC DNA].
RX PubMed=17656687; DOI=10.1126/science.1143153;
RA Tang C., Toomajian C., Sherman-Broyles S., Plagnol V., Guo Y.-L., Hu T.T.,
RA Clark R.M., Nasrallah J.B., Weigel D., Nordborg M.;
RT "The evolution of selfing in Arabidopsis thaliana.";
RL Science 317:1070-1072(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Fujita M.;
RT "ORF cloning and analysis of Arabidopsis transcription factor genes.";
RL Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
RP DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=28400174; DOI=10.1016/j.gep.2017.04.001;
RA Audonnet L., Shen Y., Zhou D.-X.;
RT "JMJ24 antagonizes histone H3K9 demethylase IBM1/JMJ25 function and
RT interacts with RNAi pathways for gene silencing.";
RL Gene Expr. Patterns 25:1-7(2017).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH FBH1; FBH2; FBH3 AND FBH4,
RP TISSUE SPECIFICITY, INDUCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=33604650; DOI=10.1093/plcell/koab014;
RA Hung F.-Y., Lai Y.-C., Wang J., Feng Y.-R., Shih Y.-H., Chen J.-H.,
RA Sun H.-C., Yang S., Li C., Wu K.;
RT "The Arabidopsis histone demethylase JMJ28 regulates CONSTANS by
RT interacting with FBH transcription factors.";
RL Plant Cell 33:1196-1211(2021).
CC -!- FUNCTION: May function as histone H3 lysine demethylase and be involved
CC in regulation of gene expression (By similarity). Regulates flowering
CC time by promoting CONSTANS (CO) and CONSTANS-LIKE genes (e.g. COL2 and
CC COL5) expression via interaction with FBH transcription factors (FBH1,
CC FBH2, FBH3 and FBH4) at their loci to remove H3K9me2 repressive histone
CC marks (PubMed:33604650). Modulates also the expression of several
CC develpmental genes such as MYB30, TFS1, AGL6 and RVE2
CC (PubMed:33604650). {ECO:0000250|UniProtKB:O64752,
CC ECO:0000269|PubMed:33604650}.
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 -!- SUBUNIT: Interacts with the FBH transcription factors FBH1, FBH2, FBH3
CC and FBH4. {ECO:0000269|PubMed:33604650}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:33604650}.
CC -!- TISSUE SPECIFICITY: Expressed in inflorescences, flowers, roots,
CC siliques, leaves and stems, especially in the vasculature (mainly
CC phloem), with highest levels in floral organs (PubMed:18713399).
CC Present at high levels in flowers, shoot apex and young seeds, but
CC observed at low levels in dry seeds, root apex and anthers
CC (PubMed:33604650). {ECO:0000269|PubMed:18713399,
CC ECO:0000269|PubMed:33604650}.
CC -!- INDUCTION: Follows a circadian cycle with lower levels in the early
CC morning and highest accumulation in the middle of the day.
CC {ECO:0000269|PubMed:33604650}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:28400174). Decreased
CC hypocotyl length (PubMed:33604650). Delayed flowering associated with
CC reduced FLOWERING LOCUS T (FT) and CONSTANS (CO) levels due to
CC increased H3K9me1/2 level at CO locus (PubMed:33604650).
CC {ECO:0000269|PubMed:28400174, ECO:0000269|PubMed:33604650}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA18707.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA20208.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81250.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EF637083; ABV21219.1; -; Genomic_DNA.
DR EMBL; AL022603; CAA18707.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL031187; CAA20208.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161555; CAB81250.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84450.1; -; Genomic_DNA.
DR EMBL; AY142484; AAN13035.1; -; mRNA.
DR EMBL; AB493691; BAH30529.1; -; mRNA.
DR PIR; T05151; T05151.
DR RefSeq; NP_193874.2; NM_118263.3.
DR SMR; Q8H1S7; -.
DR STRING; 3702.AT4G21430.1; -.
DR PRIDE; Q8H1S7; -.
DR ProteomicsDB; 183312; -.
DR EnsemblPlants; AT4G21430.1; AT4G21430.1; AT4G21430.
DR GeneID; 827895; -.
DR Gramene; AT4G21430.1; AT4G21430.1; AT4G21430.
DR KEGG; ath:AT4G21430; -.
DR Araport; AT4G21430; -.
DR TAIR; locus:2141221; AT4G21430.
DR eggNOG; KOG1356; Eukaryota.
DR HOGENOM; CLU_001811_2_0_1; -.
DR OMA; MVLKREV; -.
DR OrthoDB; 1185631at2759; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8H1S7; baseline and differential.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0048188; C:Set1C/COMPASS complex; IDA:TAIR.
DR GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IBA:GO_Central.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0033169; P:histone H3-K9 demethylation; IMP:UniProtKB.
DR GO; GO:0036123; P:histone H3-K9 dimethylation; IMP:UniProtKB.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR InterPro; IPR045109; JHDM2-like.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR014977; WRC_dom.
DR InterPro; IPR001841; Znf_RING.
DR PANTHER; PTHR12549; PTHR12549; 2.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF08879; WRC; 1.
DR SMART; SM00558; JmjC; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51667; WRC; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW Developmental protein; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..927
FT /note="Lysine-specific demethylase JMJ28"
FT /id="PRO_0000456194"
FT DOMAIN 7..52
FT /note="WRC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01002"
FT DOMAIN 601..881
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 227..273
FT /note="RING-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT MOTIF 30..37
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 127..134
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT BINDING 227
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 230
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 241
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 244
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 250
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 253
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 269
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 272
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT CONFLICT 67
FT /note="V -> A (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 135..137
FT /note="SNN -> KMK (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 370..372
FT /note="QRM -> KRI (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 391
FT /note="E -> G (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 404
FT /note="N -> K (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 604
FT /note="H -> Y (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
FT CONFLICT 923
FT /note="L -> S (in Ref. 1; ABV21219)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 927 AA; 105143 MW; 109848CBD4E3199C CRC64;
MSENEIVPDE FRCNRSDGKQ WRCKRRALEG KKMCESHHSQ QSLKRSKQKV AESSKLVRSR
RGGGDEVASS EIEPNESRIR SKRLGKSKRK RVMGEAEAMD EAVKKMKLKR GDLQLDLIRM
VLKREVEKRK RLPNSNNKKK SNGGFSEFVG EELTRVLPNG IMAISPPSPT TSNVSSPCDV
KVGEEPISMI KRRFRSKNIE PLPIGKMQVV PFKGDLVNGR KEKKMRCHWC GTRGFGDLIS
CLSCEREFFC IDCIEKRNKG SKEEVEKKCP VCRGSCRCKV CSVTNSGVTE CKDSQSVRSD
IDRVLHLHYA VCMLLPVLKE INAEHKVEVE NDAEKKEGNP AEPQIHSSEL TSDDRQPCSN
GRDFAVVDLQ RMCTRSSSVL RLNSDQDQSQ ESLSRKVGSV KCSNGIKSPK VCKRKEVKGC
SNNLFLSLFP LELTSKLEIS AEEVVSCYEL PEILDKYSGC PFCIGMETQS SSSDSHLKEA
SKTREDGTGN FLYYPTVLDF HQNNLEHFQT HWSKGHPVIV RSVIKSGSSL NWDPVALFCH
YLMNRNNKTG NTTDCMDWFE VEIGVKQFFL GSLRGKAETN TCQERLKLEG WLSSSLFKEQ
FPNHYAEILN ILPISHYMDP KRGLLNIAAN LPDTVQPPDF GPCLNISYRS GEEYAQPDSV
KKLGFETCDM VDILLYVTET PVSTNQICRI RKLMKNIGRV RSKNPAKGRE SRFDKGKKRD
RLDDYSSSDS ESSQHCLGAK CRGSEFEGEE RESCNYSCEE ESLSNTYGAQ WDVFQKQDVS
KLLEYIKNHS LELESMDSSK KKVSHPLLEQ SYYLDEYHKA RLKEEFDVEP WSFDQCVGEA
VILPAGCPYQ IRKNKSCVNA VLKFLSPEHV SESIKRVKEL NQLPQSVKSK ANKIEVKKMA
IHKISEAVKE IRELTSSDST GALRLYN
