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Protein

ATP-dependent DNA helicase DDM1

Gene

DDM1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent DNA helicase that plays a role in formation, organization, stability and heritability of heterochromatin and thus regulates several physiological traits. Binds to the nucleosome and promotes chromatin remodeling in an ATP-dependent manner; induces nucleosome repositioning on a short DNA fragment, and, possibly, could be guided to target sites (including silent transposable elements) by small interfering RNAs (siRNAs). Can bind both free and nucleosomal DNA. Required for the heritable maintenance of genome integrity and transcriptional gene silencing (TGS), including homology-dependent gene silencing (HDG silencing), via the maintenance of DNA methylation (mostly on cytosine, in both CpG and CpHpG sites, where H is A, T or C) and of histone methylation (e.g. chromatin methylation). May facilitate localization of MBD proteins at specific nuclear domains. Necessary for the maintenance of the genomic imprint at the MEA locus, especially for the silencing of paternally inherited MEA locus. Plays a major role in the inactivation maintenance of retrotransposons (e.g. Tar17, SINE, LINE, ATLN39, CAC1 (CACTAs), Athila elements, and mutator-like elements MULEs and TIR-MULEs) and the silencing of repeated genes and transgenes (e.g. T-DNA insertions). Required for KYP-dependent histone H3 'Lys-9' (H3K9me) methylation, deacetylation of histone H4 'Lys-16' (H4K16) and MET1-dependent DNA methylation. Involved in the chromatin organization of 5S rRNA genes (localized in the pericentromeric heterochromatin of chromosomes 3, 4, and 5) modifications during heterochromatin establishment. Prevents siRNA accumulation (siRNA are probably involved in epigenetic inheritance and in 5S rRNA genes regulation by silencing). Required during plant organogenesis and development, as well as during seed formation.39 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Enzyme regulationi

ATPase activity is stimulated 3-fold by DNA (both free and nucleosomal) binding.1 Publication

Kineticsi

All results where obtained at pH 8.0 and 25 degrees Celsius.
  1. KM=55 µM for ATP1 Publication
  2. KM=66 µM for ATP (in the presence of free DNA)1 Publication
  3. KM=66 µM for ATP (in the presence of chromatin)1 Publication

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi227 – 234ATPPROSITE-ProRule annotation8

    GO - Molecular functioni

    • ATPase activity Source: TAIR
    • ATP binding Source: UniProtKB-KW
    • ATP-dependent DNA helicase activity Source: UniProtKB
    • DNA binding Source: UniProtKB-KW

    GO - Biological processi

    • DNA mediated transformation Source: TAIR
    • maintenance of chromatin silencing Source: UniProtKB
    • methylation-dependent chromatin silencing Source: TAIR
    • negative regulation of histone H4 acetylation Source: UniProtKB
    • positive regulation of histone H3-K9 methylation Source: UniProtKB
    • regulation of DNA methylation Source: UniProtKB
    • regulation of gene expression by genetic imprinting Source: UniProtKB
    • transcription, DNA-templated Source: UniProtKB-KW
    • transposition, RNA-mediated Source: TAIR

    Keywordsi

    Molecular functionDNA-binding, Helicase, Hydrolase
    Biological processTranscription, Transcription regulation
    LigandATP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent DNA helicase DDM1 (EC:3.6.4.12)
    Alternative name(s):
    Protein CHROMATIN REMODELING 11 Publication
    Short name:
    AtCHR1
    Short name:
    CHR01
    Protein DECREASED DNA METHYLATION 1
    Short name:
    AtDDM1
    Protein SOMNIFEROUS 1
    SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin DDM1
    Gene namesi
    Name:DDM1
    Synonyms:CHA1, CHR11 Publication, SOM1, SOM4
    Ordered Locus Names:At5g66750
    ORF Names:MSN2.14
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 5

    Organism-specific databases

    AraportiAT5G66750.
    TAIRilocus:2173644. AT5G66750.

    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

    Disruption phenotypei

    Reactivated transcription of heavily methylated silent loci, via chromatin demethylation. Hypomethylated chromatin; gain of histone H3 'Lys-4' methylation (H3K4me) but depletion of histone H3 'Lys-9' methylation (H3K9me). Altered leaf shape, increased cauline leaf number, and delayed flowering onset (due to FWA derepression). Accumulates developmental abnormalities and transcription derepression by slowly inducing heritable lesions (hopymethylation) at unlinked loci. Derepressed paternally inherited MEA locus in male gametophytes and seeds. Reactivation of several silent retrotransposons. Smaller chromocenters with reduced heterochromatin amount. Causes a striking decondensation of centromeric heterochromatin, a redistribution of the remaining methylation of DNA, and a drastic change in the pattern of histone modification. Abnormal subcellular localization of MBD proteins (e.g. MBD2, MBD5, MBD6 and MBD7). Smaller seeds in male inherited disruption, but larger seeds in female inherited ones. The heritable and cumulative hypermethylation and silencing of BNS, leading to the bonsai phenotype, requires the hypomethylation of the flanking LINE transposon.38 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004052761 – 764ATP-dependent DNA helicase DDM1Add BLAST764

    Proteomic databases

    PaxDbiQ9XFH4.

    PTM databases

    iPTMnetiQ9XFH4.

    Expressioni

    Gene expression databases

    GenevisibleiQ9XFH4. AT.

    Interactioni

    Subunit structurei

    Interacts with the MBD domains of MBD2, MBD5 and MBD6.1 Publication

    Protein-protein interaction databases

    BioGridi22050. 3 interactors.
    IntActiQ9XFH4. 1 interactor.
    STRINGi3702.AT5G66750.1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9XFH4.
    SMRiQ9XFH4.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini214 – 382Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST169
    Domaini528 – 695Helicase C-terminalPROSITE-ProRule annotationAdd BLAST168

    Coiled coil

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Coiled coili62 – 88Sequence analysisAdd BLAST27

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi145 – 152Nuclear localization signal 1PROSITE-ProRule annotation8
    Motifi333 – 336DEAH boxPROSITE-ProRule annotation4
    Motifi429 – 436Nuclear localization signal 2PROSITE-ProRule annotation8

    Sequence similaritiesi

    Belongs to the SNF2/RAD54 helicase family.Curated

    Keywords - Domaini

    Coiled coil, Repeat

    Phylogenomic databases

    eggNOGiKOG0385. Eukaryota.
    COG0553. LUCA.
    HOGENOMiHOG000172362.
    InParanoidiQ9XFH4.
    KOiK19001.
    OMAiKSFESWF.
    OrthoDBiEOG093603NR.
    PhylomeDBiQ9XFH4.

    Family and domain databases

    CDDicd00079. HELICc. 1 hit.
    InterProiView protein in InterPro
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR000330. SNF2_N.
    PfamiView protein in Pfam
    PF00271. Helicase_C. 1 hit.
    PF00176. SNF2_N. 1 hit.
    SMARTiView protein in SMART
    SM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    SUPFAMiSSF52540. SSF52540. 2 hits.
    PROSITEiView protein in PROSITE
    PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9XFH4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE
    60 70 80 90 100
    EILLAKNGDS SLISEAMAQE EEQLLKLRED EEKANNAGSA VAPNLNETQF
    110 120 130 140 150
    TKLDELLTQT QLYSEFLLEK MEDITINGIE SESQKAEPEK TGRGRKRKAA
    160 170 180 190 200
    SQYNNTKAKR AVAAMISRSK EDGETINSDL TEEETVIKLQ NELCPLLTGG
    210 220 230 240 250
    QLKSYQLKGV KWLISLWQNG LNGILADQMG LGKTIQTIGF LSHLKGNGLD
    260 270 280 290 300
    GPYLVIAPLS TLSNWFNEIA RFTPSINAII YHGDKNQRDE LRRKHMPKTV
    310 320 330 340 350
    GPKFPIVITS YEVAMNDAKR ILRHYPWKYV VIDEGHRLKN HKCKLLRELK
    360 370 380 390 400
    HLKMDNKLLL TGTPLQNNLS ELWSLLNFIL PDIFTSHDEF ESWFDFSEKN
    410 420 430 440 450
    KNEATKEEEE KRRAQVVSKL HGILRPFILR RMKCDVELSL PRKKEIIMYA
    460 470 480 490 500
    TMTDHQKKFQ EHLVNNTLEA HLGENAIRGQ GWKGKLNNLV IQLRKNCNHP
    510 520 530 540 550
    DLLQGQIDGS YLYPPVEEIV GQCGKFRLLE RLLVRLFANN HKVLIFSQWT
    560 570 580 590 600
    KLLDIMDYYF SEKGFEVCRI DGSVKLDERR RQIKDFSDEK SSCSIFLLST
    610 620 630 640 650
    RAGGLGINLT AADTCILYDS DWNPQMDLQA MDRCHRIGQT KPVHVYRLST
    660 670 680 690 700
    AQSIETRVLK RAYSKLKLEH VVIGQGQFHQ ERAKSSTPLE EEDILALLKE
    710 720 730 740 750
    DETAEDKLIQ TDISDADLDR LLDRSDLTIT APGETQAAEA FPVKGPGWEV
    760
    VLPSSGGMLS SLNS
    Length:764
    Mass (Da):86,638
    Last modified:November 1, 1999 - v1
    Checksum:iF7E3F91DC8E1D9F2
    GO

    Sequence cautioni

    Q9XFH4: The sequence AAX22754 differs from that shown. Reason: Erroneous gene model prediction.Curated
    Q9XFH4: The sequence AAX22755 differs from that shown. Reason: Erroneous gene model prediction.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti176I → T in AAX22754 (PubMed:15516340).Curated1
    Sequence conflicti176I → T in AAX22755 (PubMed:15516340).Curated1
    Sequence conflicti187I → M in AAX22754 (PubMed:15516340).Curated1
    Sequence conflicti187I → M in AAX22755 (PubMed:15516340).Curated1
    Sequence conflicti434C → F in AAX22754 (PubMed:15516340).Curated1
    Sequence conflicti434C → F in AAX22755 (PubMed:15516340).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF143940 Genomic DNA. Translation: AAD28303.1.
    AB018119 Genomic DNA. Translation: BAA97281.1.
    CP002688 Genomic DNA. Translation: AED98259.1.
    AY099638 mRNA. Translation: AAM20489.1.
    BT002161 mRNA. Translation: AAN72172.1.
    AY699010 Genomic DNA. Translation: AAX22754.1. Sequence problems.
    AY699011 Genomic DNA. Translation: AAX22755.1. Sequence problems.
    RefSeqiNP_201476.1. NM_126073.3.
    UniGeneiAt.28851.

    Genome annotation databases

    EnsemblPlantsiAT5G66750.1; AT5G66750.1; AT5G66750.
    GeneIDi836808.
    GrameneiAT5G66750.1; AT5G66750.1; AT5G66750.
    KEGGiath:AT5G66750.

    Similar proteinsi

    Entry informationi

    Entry nameiDDM1_ARATH
    AccessioniPrimary (citable) accession number: Q9XFH4
    Secondary accession number(s): Q5C995, Q5C996
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 8, 2011
    Last sequence update: November 1, 1999
    Last modified: October 25, 2017
    This is version 117 of the entry and version 1 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