Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q8LK56

- DME_ARATH

UniProt

Q8LK56 - DME_ARATH

Protein

Transcriptional activator DEMETER

Gene

DME

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 2 (13 Jun 2006)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

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

    GO - Biological processi

    1. base-excision repair Source: InterPro
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. DNA methylation Source: TAIR
    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

    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

    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 DEMETERPRO_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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

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

    Compositional bias

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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1679 – 16791Y → F in AAM77215. (PubMed:12150995)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 258258Missing in isoform 1. 1 PublicationVSP_019283Add
    BLAST
    Alternative sequencei259 – 15711313Missing in isoform 2. 2 PublicationsVSP_007455Add
    BLAST

    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

    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: October 1, 2014
    This is version 104 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