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Q8LK56

- DME_ARATH

UniProt

Q8LK56 - DME_ARATH

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Protein
Transcriptional activator DEMETER
Gene
DME, At5g04560/At5g04570/At5g04580, T32M21.160/T32M21.170/T32M21.180
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - 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

Cofactori

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1629 – 16291Iron-sulfur (4Fe-4S) By similarity
Metal bindingi1636 – 16361Iron-sulfur (4Fe-4S) By similarity
Metal bindingi1639 – 16391Iron-sulfur (4Fe-4S) By similarity
Metal bindingi1645 – 16451Iron-sulfur (4Fe-4S) By similarity

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. DNA N-glycosylase activity Source: TAIR
  3. DNA binding Source: UniProtKB-KW
  4. DNA-(apurinic or apyrimidinic site) lyase activity Source: TAIR
  5. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. DNA methylation Source: TAIR
  3. base-excision repair Source: InterPro
  4. embryo development ending in seed dormancy Source: TAIR
  5. regulation of gene expression by genetic imprinting Source: TAIR
  6. regulation of transcription, DNA-templated Source: UniProtKB-KW
  7. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Hydrolase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

4Fe-4S, DNA-binding, 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
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G04560.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: TAIR
  2. polar nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1562 – 15621D → N: Loss of activity and abnormal MEA imprinting. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 19871987Transcriptional activator DEMETER
PRO_0000102245Add
BLAST

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

GenevestigatoriQ8LK56.

Interactioni

Protein-protein interaction databases

BioGridi15614. 6 interactions.
MINTiMINT-8070511.

Structurei

3D structure databases

ProteinModelPortaliQ8LK56.
SMRiQ8LK56. Positions 1474-1649.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni955 – 1054100DEMETER
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi291 – 36676Lys-rich (basic)
Add
BLAST
Compositional biasi473 – 625153Gln-rich
Add
BLAST

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

eggNOGiCOG0177.
HOGENOMiHOG000112227.
InParanoidiQ8LK56.
OMAiRENCEPI.
PhylomeDBiQ8LK56.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
InterProiIPR011257. DNA_glycosylase.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR028924. Perm-CXXC.
IPR028925. RRM_DME.
[Graphical view]
PfamiPF00730. HhH-GPD. 1 hit.
PF15629. Perm-CXXC. 1 hit.
PF15628. RRM_DME. 1 hit.
[Graphical view]
SMARTiSM00525. FES. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 2 hits.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

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

MNSRADPGDR YFRVPLENQT QQEFMGSWIP FTPKKPRSSL MVDERVINQD     50
LNGFPGGEFV DRGFCNTGVD HNGVFDHGAH QGVTNLSMMI NSLAGSHAQA 100
WSNSERDLLG RSEVTSPLAP VIRNTTGNVE PVNGNFTSDV GMVNGPFTQS 150
GTSQAGYNEF ELDDLLNPDQ MPFSFTSLLS GGDSLFKVRQ YGPPACNKPL 200
YNLNSPIRRE AVGSVCESSF QYVPSTPSLF RTGEKTGFLE QIVTTTGHEI 250
PEPKSDKSMQ SIMDSSAVNA TEATEQNDGS RQDVLEFDLN KTPQQKPSKR 300
KRKFMPKVVV EGKPKRKPRK PAELPKVVVE GKPKRKPRKA ATQEKVKSKE 350
TGSAKKKNLK ESATKKPANV GDMSNKSPEV TLKSCRKALN FDLENPGDAR 400
QGDSESEIVQ NSSGANSFSE IRDAIGGTNG SFLDSVSQID KTNGLGAMNQ 450
PLEVSMGNQP DKLSTGAKLA RDQQPDLLTR NQQCQFPVAT QNTQFPMENQ 500
QAWLQMKNQL IGFPFGNQQP RMTIRNQQPC LAMGNQQPMY LIGTPRPALV 550
SGNQQLGGPQ GNKRPIFLNH QTCLPAGNQL YGSPTDMHQL VMSTGGQQHG 600
LLIKNQQPGS LIRGQQPCVP LIDQQPATPK GFTHLNQMVA TSMSSPGLRP 650
HSQSQVPTTY LHVESVSRIL NGTTGTCQRS RAPAYDSLQQ DIHQGNKYIL 700
SHEISNGNGC KKALPQNSSL PTPIMAKLEE ARGSKRQYHR AMGQTEKHDL 750
NLAQQIAQSQ DVERHNSSTC VEYLDAAKKT KIQKVVQENL HGMPPEVIEI 800
EDDPTDGARK GKNTASISKG ASKGNSSPVK KTAEKEKCIV PKTPAKKGRA 850
GRKKSVPPPA HASEIQLWQP TPPKTPLSRS KPKGKGRKSI QDSGKARGPS 900
GELLCQDSIA EIIYRMQNLY LGDKEREQEQ NAMVLYKGDG ALVPYESKKR 950
KPRPKVDIDD ETTRIWNLLM GKGDEKEGDE EKDKKKEKWW EEERRVFRGR 1000
ADSFIARMHL VQGDRRFSPW KGSVVDSVIG VFLTQNVSDH LSSSAFMSLA 1050
ARFPPKLSSS REDERNVRSV VVEDPEGCIL NLNEIPSWQE KVQHPSDMEV 1100
SGVDSGSKEQ LRDCSNSGIE RFNFLEKSIQ NLEEEVLSSQ DSFDPAIFQS 1150
CGRVGSCSCS KSDAEFPTTR CETKTVSGTS QSVQTGSPNL SDEICLQGNE 1200
RPHLYEGSGD VQKQETTNVA QKKPDLEKTM NWKDSVCFGQ PRNDTNWQTT 1250
PSSSYEQCAT RQPHVLDIED FGMQGEGLGY SWMSISPRVD RVKNKNVPRR 1300
FFRQGGSVPR EFTGQIIPST PHELPGMGLS GSSSAVQEHQ DDTQHNQQDE 1350
MNKASHLQKT FLDLLNSSEE CLTRQSSTKQ NITDGCLPRD RTAEDVVDPL 1400
SNNSSLQNIL VESNSSNKEQ TAVEYKETNA TILREMKGTL ADGKKPTSQW 1450
DSLRKDVEGN EGRQERNKNN MDSIDYEAIR RASISEISEA IKERGMNNML 1500
AVRIKDFLER IVKDHGGIDL EWLRESPPDK AKDYLLSIRG LGLKSVECVR 1550
LLTLHNLAFP VDTNVGRIAV RMGWVPLQPL PESLQLHLLE LYPVLESIQK 1600
FLWPRLCKLD QRTLYELHYQ LITFGKVFCT KSRPNCNACP MRGECRHFAS 1650
AYASARLALP APEERSLTSA TIPVPPESYP PVAIPMIELP LPLEKSLASG 1700
APSNRENCEP IIEEPASPGQ ECTEITESDI EDAYYNEDPD EIPTIKLNIE 1750
QFGMTLREHM ERNMELQEGD MSKALVALHP TTTSIPTPKL KNISRLRTEH 1800
QVYELPDSHR LLDGMDKREP DDPSPYLLAI WTPGETANSA QPPEQKCGGK 1850
ASGKMCFDET CSECNSLREA NSQTVRGTLL IPCRTAMRGS FPLNGTYFQV 1900
NELFADHESS LKPIDVPRDW IWDLPRRTVY FGTSVTSIFR GLSTEQIQFC 1950
FWKGFVCVRG FEQKTRAPRP LMARLHFPAS KLKNNKT 1987
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 CAB85562.1 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.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 258258Missing in isoform 1.
VSP_019283Add
BLAST
Alternative sequencei259 – 15711313Missing in isoform 2.
VSP_007455Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1679 – 16791Y → F in AAM77215. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
AK117994 mRNA. Translation: BAC42629.1.
BT005357 mRNA. Translation: AAO63421.1.
PIRiT48452.
T48453.
T48454.
RefSeqiNP_001078527.1. NM_001085058.1. [Q8LK56-3]
NP_196076.2. NM_120538.2. [Q8LK56-1]
UniGeneiAt.33104.

Genome annotation databases

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

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
AK117994 mRNA. Translation: BAC42629.1 .
BT005357 mRNA. Translation: AAO63421.1 .
PIRi T48452.
T48453.
T48454.
RefSeqi NP_001078527.1. NM_001085058.1. [Q8LK56-3 ]
NP_196076.2. NM_120538.2. [Q8LK56-1 ]
UniGenei At.33104.

3D structure databases

ProteinModelPortali Q8LK56.
SMRi Q8LK56. Positions 1474-1649.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 15614. 6 interactions.
MINTi MINT-8070511.

Proteomic databases

PaxDbi Q8LK56.
PRIDEi Q8LK56.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G04560.2 ; AT5G04560.2 ; AT5G04560 . [Q8LK56-3 ]
GeneIDi 830335.
KEGGi ath:AT5G04560.

Organism-specific databases

TAIRi AT5G04560.

Phylogenomic databases

eggNOGi COG0177.
HOGENOMi HOG000112227.
InParanoidi Q8LK56.
OMAi RENCEPI.
PhylomeDBi Q8LK56.

Gene expression databases

Genevestigatori Q8LK56.

Family and domain databases

Gene3Di 1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
InterProi IPR011257. DNA_glycosylase.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR028924. Perm-CXXC.
IPR028925. RRM_DME.
[Graphical view ]
Pfami PF00730. HhH-GPD. 1 hit.
PF15629. Perm-CXXC. 1 hit.
PF15628. RRM_DME. 1 hit.
[Graphical view ]
SMARTi SM00525. FES. 1 hit.
[Graphical view ]
SUPFAMi SSF48150. SSF48150. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.
    , 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. 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.
    , 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.

Entry informationi

Entry nameiDME_ARATH
AccessioniPrimary (citable) accession number: Q8LK56
Secondary accession number(s): Q1WEY5
, Q84TL4, Q9LZ67, Q9LZ68, Q9LZ69
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.

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

External Data

Dasty 3

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