DME_ARATH
ID DME_ARATH Reviewed; 1987 AA.
AC Q8LK56; Q1WEY5; Q84TL4; Q9LZ67; Q9LZ68; Q9LZ69;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2006, sequence version 2.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Transcriptional activator DEMETER;
DE EC=3.2.2.-;
DE AltName: Full=DNA glycosylase-related protein DME;
GN Name=DME; OrderedLocusNames=At5g04560/At5g04570/At5g04580;
GN ORFNames=T32M21.160/T32M21.170/T32M21.180;
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 [MRNA] (ISOFORM 1), FUNCTION, AND CHARACTERIZATION.
RC STRAIN=cv. Columbia; TISSUE=Flower;
RX PubMed=12150995; DOI=10.1016/s0092-8674(02)00807-3;
RA Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B.,
RA Jacobsen S.E., Fischer R.L.;
RT "DEMETER, a DNA glycosylase domain protein, is required for endosperm gene
RT imprinting and seed viability in Arabidopsis.";
RL Cell 110:33-42(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), AND FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=16624880; DOI=10.1073/pnas.0601109103;
RA Morales-Ruiz T., Ortega-Galisteo A.P., Ponferrada-Marin M.I.,
RA Martinez-Macias M.I., Ariza R.R., Roldan-Arjona T.;
RT "DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA
RT glycosylases.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:6853-6858(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [7]
RP FUNCTION, AND MUTAGENESIS OF ASP-1562.
RX PubMed=15128940; DOI=10.1073/pnas.0402328101;
RA Choi Y., Harada J.J., Goldberg R.B., Fischer R.L.;
RT "An invariant aspartic acid in the DNA glycosylase domain of DEMETER is
RT necessary for transcriptional activation of the imprinted MEDEA gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7481-7486(2004).
CC -!- FUNCTION: Transcriptional activator involved in gene imprinting.
CC Catalyzes the release of 5-methylcytosine (5-meC) from DNA by a
CC glycosylase/lyase mechanism. Allows the expression of the maternal copy
CC of the imprinted MEA gene before fertilization, possibly by
CC antagonizing or suppressing DNA methylation on target promoter.
CC Probably acts by nicking the MEA promoter. Required for stable
CC reproducible patterns of floral and vegetative development.
CC {ECO:0000269|PubMed:12150995, ECO:0000269|PubMed:15128940,
CC ECO:0000269|PubMed:16624880}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC role in catalysis, but is probably involved in the proper positioning
CC of the enzyme along the DNA strand. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=3;
CC IsoId=Q8LK56-3; Sequence=Displayed;
CC Name=1;
CC IsoId=Q8LK56-1; Sequence=VSP_019283;
CC Name=2;
CC IsoId=Q8LK56-2; Sequence=VSP_007455;
CC -!- TISSUE SPECIFICITY: Mainly expressed in immature flower buds, then
CC decreases as the flower matures. Expressed in the ovule carpels, but
CC not expressed in pollen stamens. Expressed in developing and mature
CC ovules (stages 12-14), then strongly decreases after fertilization.
CC -!- DEVELOPMENTAL STAGE: Maternally expressed. Expressed primarily in the
CC central cell of gametophyte before fertilization. Not expressed in
CC endosperm and embryo after fertilization.
CC -!- DOMAIN: The DEMETER domain, which is present in proteins of the
CC subfamily, is related to the J-domain, but lacks some important
CC conserved residues.
CC -!- MISCELLANEOUS: Although strongly related to DNA glycosylase proteins,
CC it differs from these proteins because of its large size and its unique
CC N-terminal basic domain. The DNA repair function has not been proved
CC and may not exist.
CC -!- SIMILARITY: Belongs to the DNA glycosylase family. DEMETER subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB85562.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.; Evidence={ECO:0000305};
CC Sequence=CAB85563.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.; Evidence={ECO:0000305};
CC Sequence=CAB85564.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.; Evidence={ECO:0000305};
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DR EMBL; AF521596; AAM77215.1; -; mRNA.
DR EMBL; DQ335243; ABC61677.1; -; mRNA.
DR EMBL; AL162875; CAB85562.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL162875; CAB85563.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL162875; CAB85564.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90760.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90761.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM69949.1; -; Genomic_DNA.
DR EMBL; AK117994; BAC42629.1; -; mRNA.
DR EMBL; BT005357; AAO63421.1; -; mRNA.
DR PIR; T48452; T48452.
DR PIR; T48453; T48453.
DR PIR; T48454; T48454.
DR RefSeq; NP_001078527.1; NM_001085058.2. [Q8LK56-3]
DR RefSeq; NP_001331593.1; NM_001342781.1. [Q8LK56-1]
DR RefSeq; NP_196076.2; NM_120538.2. [Q8LK56-1]
DR AlphaFoldDB; Q8LK56; -.
DR SMR; Q8LK56; -.
DR BioGRID; 15614; 7.
DR STRING; 3702.AT5G04560.2; -.
DR PaxDb; Q8LK56; -.
DR PRIDE; Q8LK56; -.
DR ProteomicsDB; 222002; -. [Q8LK56-3]
DR EnsemblPlants; AT5G04560.1; AT5G04560.1; AT5G04560. [Q8LK56-1]
DR EnsemblPlants; AT5G04560.2; AT5G04560.2; AT5G04560. [Q8LK56-3]
DR EnsemblPlants; AT5G04560.3; AT5G04560.3; AT5G04560. [Q8LK56-1]
DR GeneID; 830335; -.
DR Gramene; AT5G04560.1; AT5G04560.1; AT5G04560. [Q8LK56-1]
DR Gramene; AT5G04560.2; AT5G04560.2; AT5G04560. [Q8LK56-3]
DR Gramene; AT5G04560.3; AT5G04560.3; AT5G04560. [Q8LK56-1]
DR KEGG; ath:AT5G04560; -.
DR Araport; AT5G04560; -.
DR TAIR; locus:2184432; AT5G04560.
DR eggNOG; ENOG502QQKH; Eukaryota.
DR InParanoid; Q8LK56; -.
DR OMA; MYLMGTQ; -.
DR OrthoDB; 164157at2759; -.
DR PhylomeDB; Q8LK56; -.
DR PRO; PR:Q8LK56; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LK56; baseline and differential.
DR Genevisible; Q8LK56; AT.
DR GO; GO:0005634; C:nucleus; ISS:TAIR.
DR GO; GO:0043078; C:polar nucleus; IDA:TAIR.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0035514; F:DNA demethylase activity; IEA:InterPro.
DR GO; GO:0019104; F:DNA N-glycosylase activity; IDA:TAIR.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032183; F:SUMO binding; IPI:TAIR.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IEA:InterPro.
DR GO; GO:0006306; P:DNA methylation; IDA:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IMP:TAIR.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR InterPro; IPR044811; DME/ROS1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR028924; Perm-CXXC.
DR InterPro; IPR028925; RRM_DME.
DR PANTHER; PTHR46213; PTHR46213; 1.
DR Pfam; PF15629; Perm-CXXC; 1.
DR Pfam; PF15628; RRM_DME; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Activator; Alternative splicing; DNA-binding; Hydrolase; Iron;
KW Iron-sulfur; Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..1987
FT /note="Transcriptional activator DEMETER"
FT /id="PRO_0000102245"
FT REGION 246..378
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 392..415
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 793..901
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 955..1054
FT /note="DEMETER"
FT REGION 1324..1351
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1439..1471
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 258..278
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 304..363
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 795..809
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 811..828
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 829..843
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1326..1341
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1448..1471
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1629
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1636
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1639
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1645
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..258
FT /note="Missing (in isoform 1)"
FT /evidence="ECO:0000303|PubMed:12150995"
FT /id="VSP_019283"
FT VAR_SEQ 259..1571
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11910074,
FT ECO:0000303|PubMed:14593172"
FT /id="VSP_007455"
FT MUTAGEN 1562
FT /note="D->N: Loss of activity and abnormal MEA imprinting."
FT /evidence="ECO:0000269|PubMed:15128940"
FT CONFLICT 1679
FT /note="Y -> F (in Ref. 1; AAM77215)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1987 AA; 221147 MW; 4035C0D344DCF375 CRC64;
MNSRADPGDR YFRVPLENQT QQEFMGSWIP FTPKKPRSSL MVDERVINQD LNGFPGGEFV
DRGFCNTGVD HNGVFDHGAH QGVTNLSMMI NSLAGSHAQA WSNSERDLLG RSEVTSPLAP
VIRNTTGNVE PVNGNFTSDV GMVNGPFTQS GTSQAGYNEF ELDDLLNPDQ MPFSFTSLLS
GGDSLFKVRQ YGPPACNKPL YNLNSPIRRE AVGSVCESSF QYVPSTPSLF RTGEKTGFLE
QIVTTTGHEI PEPKSDKSMQ SIMDSSAVNA TEATEQNDGS RQDVLEFDLN KTPQQKPSKR
KRKFMPKVVV EGKPKRKPRK PAELPKVVVE GKPKRKPRKA ATQEKVKSKE TGSAKKKNLK
ESATKKPANV GDMSNKSPEV TLKSCRKALN FDLENPGDAR QGDSESEIVQ NSSGANSFSE
IRDAIGGTNG SFLDSVSQID KTNGLGAMNQ PLEVSMGNQP DKLSTGAKLA RDQQPDLLTR
NQQCQFPVAT QNTQFPMENQ QAWLQMKNQL IGFPFGNQQP RMTIRNQQPC LAMGNQQPMY
LIGTPRPALV SGNQQLGGPQ GNKRPIFLNH QTCLPAGNQL YGSPTDMHQL VMSTGGQQHG
LLIKNQQPGS LIRGQQPCVP LIDQQPATPK GFTHLNQMVA TSMSSPGLRP HSQSQVPTTY
LHVESVSRIL NGTTGTCQRS RAPAYDSLQQ DIHQGNKYIL SHEISNGNGC KKALPQNSSL
PTPIMAKLEE ARGSKRQYHR AMGQTEKHDL NLAQQIAQSQ DVERHNSSTC VEYLDAAKKT
KIQKVVQENL HGMPPEVIEI EDDPTDGARK GKNTASISKG ASKGNSSPVK KTAEKEKCIV
PKTPAKKGRA GRKKSVPPPA HASEIQLWQP TPPKTPLSRS KPKGKGRKSI QDSGKARGPS
GELLCQDSIA EIIYRMQNLY LGDKEREQEQ NAMVLYKGDG ALVPYESKKR KPRPKVDIDD
ETTRIWNLLM GKGDEKEGDE EKDKKKEKWW EEERRVFRGR ADSFIARMHL VQGDRRFSPW
KGSVVDSVIG VFLTQNVSDH LSSSAFMSLA ARFPPKLSSS REDERNVRSV VVEDPEGCIL
NLNEIPSWQE KVQHPSDMEV SGVDSGSKEQ LRDCSNSGIE RFNFLEKSIQ NLEEEVLSSQ
DSFDPAIFQS CGRVGSCSCS KSDAEFPTTR CETKTVSGTS QSVQTGSPNL SDEICLQGNE
RPHLYEGSGD VQKQETTNVA QKKPDLEKTM NWKDSVCFGQ PRNDTNWQTT PSSSYEQCAT
RQPHVLDIED FGMQGEGLGY SWMSISPRVD RVKNKNVPRR FFRQGGSVPR EFTGQIIPST
PHELPGMGLS GSSSAVQEHQ DDTQHNQQDE MNKASHLQKT FLDLLNSSEE CLTRQSSTKQ
NITDGCLPRD RTAEDVVDPL SNNSSLQNIL VESNSSNKEQ TAVEYKETNA TILREMKGTL
ADGKKPTSQW DSLRKDVEGN EGRQERNKNN MDSIDYEAIR RASISEISEA IKERGMNNML
AVRIKDFLER IVKDHGGIDL EWLRESPPDK AKDYLLSIRG LGLKSVECVR LLTLHNLAFP
VDTNVGRIAV RMGWVPLQPL PESLQLHLLE LYPVLESIQK FLWPRLCKLD QRTLYELHYQ
LITFGKVFCT KSRPNCNACP MRGECRHFAS AYASARLALP APEERSLTSA TIPVPPESYP
PVAIPMIELP LPLEKSLASG APSNRENCEP IIEEPASPGQ ECTEITESDI EDAYYNEDPD
EIPTIKLNIE QFGMTLREHM ERNMELQEGD MSKALVALHP TTTSIPTPKL KNISRLRTEH
QVYELPDSHR LLDGMDKREP DDPSPYLLAI WTPGETANSA QPPEQKCGGK ASGKMCFDET
CSECNSLREA NSQTVRGTLL IPCRTAMRGS FPLNGTYFQV NELFADHESS LKPIDVPRDW
IWDLPRRTVY FGTSVTSIFR GLSTEQIQFC FWKGFVCVRG FEQKTRAPRP LMARLHFPAS
KLKNNKT
