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Protein

Transcriptional activator DEMETER

Gene

DME

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Transcriptional activator involved in gene imprinting. Catalyzes the release of 5-methylcytosine (5-meC) from DNA by a glycosylase/lyase mechanism. Allows the expression of the maternal copy of the imprinted MEA gene before fertilization, possibly by antagonizing or suppressing DNA methylation on target promoter. Probably acts by nicking the MEA promoter. Required for stable reproducible patterns of floral and vegetative development.3 Publications

Miscellaneous

Although strongly related to DNA glycosylase proteins, it differs from these proteins because of its large size and its unique N-terminal basic domain. The DNA repair function has not been proved and may not exist.

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a role in catalysis, but is probably involved in the proper positioning of the enzyme along the DNA strand.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1629Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1636Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1639Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi1645Iron-sulfur (4Fe-4S)By similarity1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  • DNA-(apurinic or apyrimidinic site) endonuclease activity Source: TAIR
  • DNA binding Source: UniProtKB-KW
  • DNA N-glycosylase activity Source: TAIR
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • base-excision repair Source: InterPro
  • DNA methylation Source: TAIR
  • embryo development ending in seed dormancy Source: TAIR
  • regulation of gene expression by genetic imprinting Source: TAIR
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionActivator, DNA-binding, Hydrolase
Biological processTranscription, Transcription regulation
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Transcriptional activator DEMETER (EC:3.2.2.-)
Alternative name(s):
DNA glycosylase-related protein DME
Gene namesi
Name:DME
Ordered Locus Names:At5g04560/At5g04570/At5g04580
ORF Names:T32M21.160/T32M21.170/T32M21.180
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G04560
TAIRilocus:2184432 AT5G04560

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1562D → N: Loss of activity and abnormal MEA imprinting. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001022451 – 1987Transcriptional activator DEMETERAdd BLAST1987

Proteomic databases

PaxDbiQ8LK56
PRIDEiQ8LK56

Expressioni

Tissue specificityi

Mainly expressed in immature flower buds, then decreases as the flower matures. Expressed in the ovule carpels, but not expressed in pollen stamens. Expressed in developing and mature ovules (stages 12-14), then strongly decreases after fertilization.

Developmental stagei

Maternally expressed. Expressed primarily in the central cell of gametophyte before fertilization. Not expressed in endosperm and embryo after fertilization.

Gene expression databases

ExpressionAtlasiQ8LK56 baseline and differential
GenevisibleiQ8LK56 AT

Interactioni

Protein-protein interaction databases

BioGridi15614, 7 interactors
STRINGi3702.AT5G04560.2

Structurei

3D structure databases

ProteinModelPortaliQ8LK56
SMRiQ8LK56
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni955 – 1054DEMETERAdd BLAST100

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi291 – 366Lys-rich (basic)Add BLAST76
Compositional biasi473 – 625Gln-richAdd BLAST153

Domaini

The DEMETER domain, which is present in proteins of the subfamily, is related to the J-domain, but lacks some important conserved residues.

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG410IFAB Eukaryota
COG0177 LUCA
HOGENOMiHOG000112227
InParanoidiQ8LK56
OMAiLAMGNQQ
OrthoDBiEOG0936006D
PhylomeDBiQ8LK56

Family and domain databases

CDDicd00056 ENDO3c, 1 hit
Gene3Di1.10.1670.10, 1 hit
InterProiView protein in InterPro
IPR011257 DNA_glycosylase
IPR003651 Endonuclease3_FeS-loop_motif
IPR003265 HhH-GPD_domain
IPR023170 HTH_base_excis_C
IPR028924 Perm-CXXC
IPR028925 RRM_DME
PfamiView protein in Pfam
PF15629 Perm-CXXC, 1 hit
PF15628 RRM_DME, 1 hit
SMARTiView protein in SMART
SM00478 ENDO3c, 1 hit
SM00525 FES, 1 hit
SUPFAMiSSF48150 SSF48150, 2 hits

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 3 (identifier: Q8LK56-3) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MNSRADPGDR YFRVPLENQT QQEFMGSWIP FTPKKPRSSL MVDERVINQD
60 70 80 90 100
LNGFPGGEFV DRGFCNTGVD HNGVFDHGAH QGVTNLSMMI NSLAGSHAQA
110 120 130 140 150
WSNSERDLLG RSEVTSPLAP VIRNTTGNVE PVNGNFTSDV GMVNGPFTQS
160 170 180 190 200
GTSQAGYNEF ELDDLLNPDQ MPFSFTSLLS GGDSLFKVRQ YGPPACNKPL
210 220 230 240 250
YNLNSPIRRE AVGSVCESSF QYVPSTPSLF RTGEKTGFLE QIVTTTGHEI
260 270 280 290 300
PEPKSDKSMQ SIMDSSAVNA TEATEQNDGS RQDVLEFDLN KTPQQKPSKR
310 320 330 340 350
KRKFMPKVVV EGKPKRKPRK PAELPKVVVE GKPKRKPRKA ATQEKVKSKE
360 370 380 390 400
TGSAKKKNLK ESATKKPANV GDMSNKSPEV TLKSCRKALN FDLENPGDAR
410 420 430 440 450
QGDSESEIVQ NSSGANSFSE IRDAIGGTNG SFLDSVSQID KTNGLGAMNQ
460 470 480 490 500
PLEVSMGNQP DKLSTGAKLA RDQQPDLLTR NQQCQFPVAT QNTQFPMENQ
510 520 530 540 550
QAWLQMKNQL IGFPFGNQQP RMTIRNQQPC LAMGNQQPMY LIGTPRPALV
560 570 580 590 600
SGNQQLGGPQ GNKRPIFLNH QTCLPAGNQL YGSPTDMHQL VMSTGGQQHG
610 620 630 640 650
LLIKNQQPGS LIRGQQPCVP LIDQQPATPK GFTHLNQMVA TSMSSPGLRP
660 670 680 690 700
HSQSQVPTTY LHVESVSRIL NGTTGTCQRS RAPAYDSLQQ DIHQGNKYIL
710 720 730 740 750
SHEISNGNGC KKALPQNSSL PTPIMAKLEE ARGSKRQYHR AMGQTEKHDL
760 770 780 790 800
NLAQQIAQSQ DVERHNSSTC VEYLDAAKKT KIQKVVQENL HGMPPEVIEI
810 820 830 840 850
EDDPTDGARK GKNTASISKG ASKGNSSPVK KTAEKEKCIV PKTPAKKGRA
860 870 880 890 900
GRKKSVPPPA HASEIQLWQP TPPKTPLSRS KPKGKGRKSI QDSGKARGPS
910 920 930 940 950
GELLCQDSIA EIIYRMQNLY LGDKEREQEQ NAMVLYKGDG ALVPYESKKR
960 970 980 990 1000
KPRPKVDIDD ETTRIWNLLM GKGDEKEGDE EKDKKKEKWW EEERRVFRGR
1010 1020 1030 1040 1050
ADSFIARMHL VQGDRRFSPW KGSVVDSVIG VFLTQNVSDH LSSSAFMSLA
1060 1070 1080 1090 1100
ARFPPKLSSS REDERNVRSV VVEDPEGCIL NLNEIPSWQE KVQHPSDMEV
1110 1120 1130 1140 1150
SGVDSGSKEQ LRDCSNSGIE RFNFLEKSIQ NLEEEVLSSQ DSFDPAIFQS
1160 1170 1180 1190 1200
CGRVGSCSCS KSDAEFPTTR CETKTVSGTS QSVQTGSPNL SDEICLQGNE
1210 1220 1230 1240 1250
RPHLYEGSGD VQKQETTNVA QKKPDLEKTM NWKDSVCFGQ PRNDTNWQTT
1260 1270 1280 1290 1300
PSSSYEQCAT RQPHVLDIED FGMQGEGLGY SWMSISPRVD RVKNKNVPRR
1310 1320 1330 1340 1350
FFRQGGSVPR EFTGQIIPST PHELPGMGLS GSSSAVQEHQ DDTQHNQQDE
1360 1370 1380 1390 1400
MNKASHLQKT FLDLLNSSEE CLTRQSSTKQ NITDGCLPRD RTAEDVVDPL
1410 1420 1430 1440 1450
SNNSSLQNIL VESNSSNKEQ TAVEYKETNA TILREMKGTL ADGKKPTSQW
1460 1470 1480 1490 1500
DSLRKDVEGN EGRQERNKNN MDSIDYEAIR RASISEISEA IKERGMNNML
1510 1520 1530 1540 1550
AVRIKDFLER IVKDHGGIDL EWLRESPPDK AKDYLLSIRG LGLKSVECVR
1560 1570 1580 1590 1600
LLTLHNLAFP VDTNVGRIAV RMGWVPLQPL PESLQLHLLE LYPVLESIQK
1610 1620 1630 1640 1650
FLWPRLCKLD QRTLYELHYQ LITFGKVFCT KSRPNCNACP MRGECRHFAS
1660 1670 1680 1690 1700
AYASARLALP APEERSLTSA TIPVPPESYP PVAIPMIELP LPLEKSLASG
1710 1720 1730 1740 1750
APSNRENCEP IIEEPASPGQ ECTEITESDI EDAYYNEDPD EIPTIKLNIE
1760 1770 1780 1790 1800
QFGMTLREHM ERNMELQEGD MSKALVALHP TTTSIPTPKL KNISRLRTEH
1810 1820 1830 1840 1850
QVYELPDSHR LLDGMDKREP DDPSPYLLAI WTPGETANSA QPPEQKCGGK
1860 1870 1880 1890 1900
ASGKMCFDET CSECNSLREA NSQTVRGTLL IPCRTAMRGS FPLNGTYFQV
1910 1920 1930 1940 1950
NELFADHESS LKPIDVPRDW IWDLPRRTVY FGTSVTSIFR GLSTEQIQFC
1960 1970 1980
FWKGFVCVRG FEQKTRAPRP LMARLHFPAS KLKNNKT
Length:1,987
Mass (Da):221,147
Last modified:June 13, 2006 - v2
Checksum:i4035C0D344DCF375
GO
Isoform 1 (identifier: Q8LK56-1) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-258: Missing.

Show »
Length:1,729
Mass (Da):192,905
Checksum:iD4A3EA9C65AD1FE2
GO
Isoform 2 (identifier: Q8LK56-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     259-1571: Missing.

Show »
Length:674
Mass (Da):75,340
Checksum:i74F337BA8947ACB6
GO

Sequence cautioni

The sequence CAB85562 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.Curated
The sequence CAB85563 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.Curated
The sequence CAB85564 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1679Y → F in AAM77215 (PubMed:12150995).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0192831 – 258Missing in isoform 1. 1 PublicationAdd BLAST258
Alternative sequenceiVSP_007455259 – 1571Missing in isoform 2. 2 PublicationsAdd BLAST1313

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF521596 mRNA Translation: AAM77215.1
DQ335243 mRNA Translation: ABC61677.1
AL162875 Genomic DNA Translation: CAB85562.1 Sequence problems.
AL162875 Genomic DNA Translation: CAB85563.1 Sequence problems.
AL162875 Genomic DNA Translation: CAB85564.1 Sequence problems.
CP002688 Genomic DNA Translation: AED90760.1
CP002688 Genomic DNA Translation: AED90761.1
CP002688 Genomic DNA Translation: ANM69949.1
AK117994 mRNA Translation: BAC42629.1
BT005357 mRNA Translation: AAO63421.1
PIRiT48452
T48453
T48454
RefSeqiNP_001078527.1, NM_001085058.2 [Q8LK56-3]
NP_001331593.1, NM_001342781.1 [Q8LK56-1]
NP_196076.2, NM_120538.2 [Q8LK56-1]
UniGeneiAt.33104

Genome annotation databases

EnsemblPlantsiAT5G04560.1; AT5G04560.1; AT5G04560 [Q8LK56-1]
AT5G04560.2; AT5G04560.2; AT5G04560 [Q8LK56-3]
AT5G04560.3; AT5G04560.3; AT5G04560 [Q8LK56-1]
GeneIDi830335
GrameneiAT5G04560.1; AT5G04560.1; AT5G04560 [Q8LK56-1]
AT5G04560.2; AT5G04560.2; AT5G04560 [Q8LK56-3]
AT5G04560.3; AT5G04560.3; AT5G04560 [Q8LK56-1]
KEGGiath:AT5G04560

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiDME_ARATH
AccessioniPrimary (citable) accession number: Q8LK56
Secondary accession number(s): Q1WEY5
, Q84TL4, Q9LZ67, Q9LZ68, Q9LZ69
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: June 13, 2006
Last modified: May 23, 2018
This is version 131 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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