Protein: ATP-dependent DNA helicase DDM1 (EC 3.6.4.12) (Protein CHROMATIN REMODELING 1) (AtCHR1) (CHR01) (Protein DECREASED DNA METHYLATION 1) (AtDDM1) (Protein SOMNIFEROUS 1) (SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin DDM1) (Q9XFH4)
Organism: Arabidopsis thaliana (Mouse-ear cress)
Function: 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.
Subcellular location: Nucleus {ECO:0000250, ECO:0000255|PROSITE-ProRule:PRU00768}. Note=Closely associated with pericentric heterochromatin. {ECO:0000250}.
Sequence: MVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKNGDSSLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFLLEKMEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETINSDLTEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNKLLLTGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVVSKLHGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRGQGWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFANNHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLKRAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLDRLLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS
InterPro domains: - IPR000330: SNF2, N-terminal (domain) [205-502]
- IPR049730: SNF2/RAD5-like, C-terminal helicase domain (domain) [514-648]
- IPR038718: SNF2-like, N-terminal domain superfamily (homologous_superfamily) [203-432]
- IPR027417: P-loop containing nucleoside triphosphate hydrolase (homologous_superfamily) [184-735]
- IPR014001: Helicase superfamily 1/2, ATP-binding domain (domain) [198-393]
- IPR044753: HELLS, N-terminal (domain) [199-433]
- IPR001650: Helicase, C-terminal domain-like (domain) [525-695]
Interaction partners: - DNA
- Histone H3-like centromeric protein CENH3
- DNA
- DNA
- Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
- DNA-directed RNA polymerase IV subunit 1
- Histone H3.1
- DNA-directed RNA polymerase V subunit 1
- Histone H3-like 5
- Histone H3.3
Gene Ontology annotations:
Molecular Function (MF): GO:0003674 (molecular function), GO:0005488 (binding), GO:0005515 (protein binding)
Biological Process (BP): GO:0008150 (biological process), GO:0008152 (metabolic process), GO:0009987 (cellular process), GO:0050896 (response to stimulus), GO:0051716 (cellular response to stimulus), GO:0009628 (response to abiotic stimulus), GO:0006950 (response to stress), GO:0044237 (cellular metabolic process), GO:0071704 (organic substance metabolic process), GO:0044238 (primary metabolic process), GO:0006807 (nitrogen compound metabolic process), GO:0006725 (cellular aromatic compound metabolic process), GO:1901360 (organic cyclic compound metabolic process), GO:0034641 (cellular nitrogen compound metabolic process), GO:0006139 (nucleobase-containing compound metabolic process), GO:0044260 (cellular macromolecule metabolic process), GO:0043170 (macromolecule metabolic process), GO:0046483 (heterocycle metabolic process), GO:0009314 (response to radiation), GO:0033554 (cellular response to stress), GO:0006259 (DNA metabolic process), GO:0009416 (response to light stimulus), GO:0090304 (nucleic acid metabolic process), GO:0006974 (cellular response to DNA damage stimulus), GO:0006281 (DNA repair), GO:0009411 (response to UV), GO:0010224 (response to UV-B)
Cellular Component (CC): GO:0005575 (cellular component), GO:0110165 (cellular anatomical entity), GO:0005622 (intracellular anatomical structure), GO:0043226 (organelle), GO:0043229 (intracellular organelle), GO:0043227 (membrane-bounded organelle), GO:0043231 (intracellular membrane-bounded organelle), GO:0005634 (nucleus)