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Q8LK56 (DME_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transcriptional activator DEMETER

EC=3.2.2.-
Alternative name(s):
DNA glycosylase-related protein DME
Gene names
Name:DME
Ordered Locus Names:At5g04560/At5g04570/At5g04580
ORF Names:T32M21.160/T32M21.170/T32M21.180
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length1987 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.2 Ref.7

Cofactor

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.

Subcellular location

Nucleus.

Tissue specificity

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 stage

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

Domain

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

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.

Sequence similarities

Belongs to the DNA glycosylase family. DEMETER subfamily.

Sequence caution

The sequence CAB85562.1 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.

The sequence CAB85563.1 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.

The sequence CAB85564.1 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At5g04560, At5g04570 and At5g04580.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   Ligand4Fe-4S
DNA-binding
Iron
Iron-sulfur
Metal-binding
   Molecular functionActivator
Hydrolase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA catabolic process, endonucleolytic

Inferred from direct assay Ref.2. Source: GOC

DNA methylation

Inferred from direct assay Ref.2. Source: TAIR

base-excision repair

Inferred from electronic annotation. Source: InterPro

embryo development ending in seed dormancy

Inferred from mutant phenotype Ref.1. Source: TAIR

regulation of gene expression by genetic imprinting

Inferred from mutant phenotype PubMed 16469697. Source: TAIR

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from sequence or structural similarity Ref.1. Source: TAIR

polar nucleus

Inferred from direct assay Ref.1. Source: TAIR

   Molecular_function4 iron, 4 sulfur cluster binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA N-glycosylase activity

Inferred from direct assay Ref.2. Source: TAIR

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-(apurinic or apyrimidinic site) lyase activity

Inferred from direct assay Ref.2. Source: TAIR

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 3 (identifier: Q8LK56-3)

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.
Isoform 1 (identifier: Q8LK56-1)

The sequence of this isoform differs from the canonical sequence as follows:
     1-258: Missing.
Isoform 2 (identifier: Q8LK56-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 19871987Transcriptional activator DEMETER
PRO_0000102245

Regions

Region955 – 1054100DEMETER
Compositional bias291 – 36676Lys-rich (basic)
Compositional bias473 – 625153Gln-rich

Sites

Metal binding16291Iron-sulfur (4Fe-4S) By similarity
Metal binding16361Iron-sulfur (4Fe-4S) By similarity
Metal binding16391Iron-sulfur (4Fe-4S) By similarity
Metal binding16451Iron-sulfur (4Fe-4S) By similarity

Natural variations

Alternative sequence1 – 258258Missing in isoform 1.
VSP_019283
Alternative sequence259 – 15711313Missing in isoform 2.
VSP_007455

Experimental info

Mutagenesis15621D → N: Loss of activity and abnormal MEA imprinting. Ref.7
Sequence conflict16791Y → F in AAM77215. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 3 [UniParc].

Last modified June 13, 2006. Version 2.
Checksum: 4035C0D344DCF375

FASTA1,987221,147
        10         20         30         40         50         60 
MNSRADPGDR YFRVPLENQT QQEFMGSWIP FTPKKPRSSL MVDERVINQD LNGFPGGEFV 

        70         80         90        100        110        120 
DRGFCNTGVD HNGVFDHGAH QGVTNLSMMI NSLAGSHAQA WSNSERDLLG RSEVTSPLAP 

       130        140        150        160        170        180 
VIRNTTGNVE PVNGNFTSDV GMVNGPFTQS GTSQAGYNEF ELDDLLNPDQ MPFSFTSLLS 

       190        200        210        220        230        240 
GGDSLFKVRQ YGPPACNKPL YNLNSPIRRE AVGSVCESSF QYVPSTPSLF RTGEKTGFLE 

       250        260        270        280        290        300 
QIVTTTGHEI PEPKSDKSMQ SIMDSSAVNA TEATEQNDGS RQDVLEFDLN KTPQQKPSKR 

       310        320        330        340        350        360 
KRKFMPKVVV EGKPKRKPRK PAELPKVVVE GKPKRKPRKA ATQEKVKSKE TGSAKKKNLK 

       370        380        390        400        410        420 
ESATKKPANV GDMSNKSPEV TLKSCRKALN FDLENPGDAR QGDSESEIVQ NSSGANSFSE 

       430        440        450        460        470        480 
IRDAIGGTNG SFLDSVSQID KTNGLGAMNQ PLEVSMGNQP DKLSTGAKLA RDQQPDLLTR 

       490        500        510        520        530        540 
NQQCQFPVAT QNTQFPMENQ QAWLQMKNQL IGFPFGNQQP RMTIRNQQPC LAMGNQQPMY 

       550        560        570        580        590        600 
LIGTPRPALV SGNQQLGGPQ GNKRPIFLNH QTCLPAGNQL YGSPTDMHQL VMSTGGQQHG 

       610        620        630        640        650        660 
LLIKNQQPGS LIRGQQPCVP LIDQQPATPK GFTHLNQMVA TSMSSPGLRP HSQSQVPTTY 

       670        680        690        700        710        720 
LHVESVSRIL NGTTGTCQRS RAPAYDSLQQ DIHQGNKYIL SHEISNGNGC KKALPQNSSL 

       730        740        750        760        770        780 
PTPIMAKLEE ARGSKRQYHR AMGQTEKHDL NLAQQIAQSQ DVERHNSSTC VEYLDAAKKT 

       790        800        810        820        830        840 
KIQKVVQENL HGMPPEVIEI EDDPTDGARK GKNTASISKG ASKGNSSPVK KTAEKEKCIV 

       850        860        870        880        890        900 
PKTPAKKGRA GRKKSVPPPA HASEIQLWQP TPPKTPLSRS KPKGKGRKSI QDSGKARGPS 

       910        920        930        940        950        960 
GELLCQDSIA EIIYRMQNLY LGDKEREQEQ NAMVLYKGDG ALVPYESKKR KPRPKVDIDD 

       970        980        990       1000       1010       1020 
ETTRIWNLLM GKGDEKEGDE EKDKKKEKWW EEERRVFRGR ADSFIARMHL VQGDRRFSPW 

      1030       1040       1050       1060       1070       1080 
KGSVVDSVIG VFLTQNVSDH LSSSAFMSLA ARFPPKLSSS REDERNVRSV VVEDPEGCIL 

      1090       1100       1110       1120       1130       1140 
NLNEIPSWQE KVQHPSDMEV SGVDSGSKEQ LRDCSNSGIE RFNFLEKSIQ NLEEEVLSSQ 

      1150       1160       1170       1180       1190       1200 
DSFDPAIFQS CGRVGSCSCS KSDAEFPTTR CETKTVSGTS QSVQTGSPNL SDEICLQGNE 

      1210       1220       1230       1240       1250       1260 
RPHLYEGSGD VQKQETTNVA QKKPDLEKTM NWKDSVCFGQ PRNDTNWQTT PSSSYEQCAT 

      1270       1280       1290       1300       1310       1320 
RQPHVLDIED FGMQGEGLGY SWMSISPRVD RVKNKNVPRR FFRQGGSVPR EFTGQIIPST 

      1330       1340       1350       1360       1370       1380 
PHELPGMGLS GSSSAVQEHQ DDTQHNQQDE MNKASHLQKT FLDLLNSSEE CLTRQSSTKQ 

      1390       1400       1410       1420       1430       1440 
NITDGCLPRD RTAEDVVDPL SNNSSLQNIL VESNSSNKEQ TAVEYKETNA TILREMKGTL 

      1450       1460       1470       1480       1490       1500 
ADGKKPTSQW DSLRKDVEGN EGRQERNKNN MDSIDYEAIR RASISEISEA IKERGMNNML 

      1510       1520       1530       1540       1550       1560 
AVRIKDFLER IVKDHGGIDL EWLRESPPDK AKDYLLSIRG LGLKSVECVR LLTLHNLAFP 

      1570       1580       1590       1600       1610       1620 
VDTNVGRIAV RMGWVPLQPL PESLQLHLLE LYPVLESIQK FLWPRLCKLD QRTLYELHYQ 

      1630       1640       1650       1660       1670       1680 
LITFGKVFCT KSRPNCNACP MRGECRHFAS AYASARLALP APEERSLTSA TIPVPPESYP 

      1690       1700       1710       1720       1730       1740 
PVAIPMIELP LPLEKSLASG APSNRENCEP IIEEPASPGQ ECTEITESDI EDAYYNEDPD 

      1750       1760       1770       1780       1790       1800 
EIPTIKLNIE QFGMTLREHM ERNMELQEGD MSKALVALHP TTTSIPTPKL KNISRLRTEH 

      1810       1820       1830       1840       1850       1860 
QVYELPDSHR LLDGMDKREP DDPSPYLLAI WTPGETANSA QPPEQKCGGK ASGKMCFDET 

      1870       1880       1890       1900       1910       1920 
CSECNSLREA NSQTVRGTLL IPCRTAMRGS FPLNGTYFQV NELFADHESS LKPIDVPRDW 

      1930       1940       1950       1960       1970       1980 
IWDLPRRTVY FGTSVTSIFR GLSTEQIQFC FWKGFVCVRG FEQKTRAPRP LMARLHFPAS 


KLKNNKT 

« Hide

Isoform 1 [UniParc].

Checksum: D4A3EA9C65AD1FE2
Show »

FASTA1,729192,905
Isoform 2 [UniParc].

Checksum: 74F337BA8947ACB6
Show »

FASTA67475,340

References

« Hide 'large scale' references
[1]"DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis."
Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., Fischer R.L.
Cell 110:33-42(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, CHARACTERIZATION.
Strain: cv. Columbia.
Tissue: Flower.
[2]"DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases."
Morales-Ruiz T., Ortega-Galisteo A.P., Ponferrada-Marin M.I., Martinez-Macias M.I., Ariza R.R., Roldan-Arjona T.
Proc. Natl. Acad. Sci. U.S.A. 103:6853-6858(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION.
Strain: cv. Columbia.
[3]"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. expand/collapse author list , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[4]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[5]"Functional annotation of a full-length Arabidopsis cDNA collection."
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K.
Science 296:141-145(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Strain: cv. Columbia.
[6]"Empirical analysis of transcriptional activity in the Arabidopsis genome."
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. expand/collapse author list , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Strain: cv. Columbia.
[7]"An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene."
Choi Y., Harada J.J., Goldberg R.B., Fischer R.L.
Proc. Natl. Acad. Sci. U.S.A. 101:7481-7486(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF ASP-1562.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
AK117994 mRNA. Translation: BAC42629.1.
BT005357 mRNA. Translation: AAO63421.1.
PIRT48452.
T48453.
T48454.
RefSeqNP_001078527.1. NM_001085058.1. [Q8LK56-3]
NP_196076.2. NM_120538.2. [Q8LK56-1]
UniGeneAt.33104.

3D structure databases

ProteinModelPortalQ8LK56.
SMRQ8LK56. Positions 1474-1649.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid15614. 6 interactions.
MINTMINT-8070511.

Proteomic databases

PaxDbQ8LK56.
PRIDEQ8LK56.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G04560.2; AT5G04560.2; AT5G04560. [Q8LK56-3]
GeneID830335.
KEGGath:AT5G04560.

Organism-specific databases

TAIRAT5G04560.

Phylogenomic databases

eggNOGCOG0177.
HOGENOMHOG000112227.
InParanoidQ8LK56.
OMARENCEPI.
PhylomeDBQ8LK56.

Gene expression databases

GenevestigatorQ8LK56.

Family and domain databases

Gene3D1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
InterProIPR011257. DNA_glycosylase.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR028924. Perm-CXXC.
IPR028925. RRM_DME.
[Graphical view]
PfamPF00730. HhH-GPD. 1 hit.
PF15629. Perm-CXXC. 1 hit.
PF15628. RRM_DME. 1 hit.
[Graphical view]
SMARTSM00525. FES. 1 hit.
[Graphical view]
SUPFAMSSF48150. SSF48150. 2 hits.
ProtoNetSearch...

Entry information

Entry nameDME_ARATH
AccessionPrimary (citable) accession number: Q8LK56
Secondary accession number(s): Q1WEY5 expand/collapse secondary AC list , Q84TL4, Q9LZ67, Q9LZ68, Q9LZ69
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: June 13, 2006
Last modified: May 14, 2014
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names