- EMDB-33835: CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: EMDB / ID: EMD-33835
タイトル
CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution
マップデータ
試料
複合体: ROS1-5mC dsDNA complex
複合体: ROS1
タンパク質・ペプチド: Sex-determining region Y protein,REPRESSOR OF SILENCING 1,DNA glycosylase/AP lyase ROS1
複合体: 5mC dsDNA
DNA: DNA (40-MER)
DNA: DNA (40-MER)
リガンド: IRON/SULFUR CLUSTER
キーワード
ROS1 / DNA glycosylase / DNA demethylation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
機能・相同性
機能・相同性情報
DNA demethylase activity / : / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / DNA N-glycosylase activity / male sex determination / defense response to fungus / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity ...DNA demethylase activity / : / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / DNA N-glycosylase activity / male sex determination / defense response to fungus / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Deactivation of the beta-catenin transactivating complex / brain development / base-excision repair / neuron differentiation / 4 iron, 4 sulfur cluster binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / positive regulation of gene expression / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能
Permuted single zf-CXXC unit / Demeter, RRM-fold domain / DNA glycosylase, plant / RRM in Demeter / Permuted single zf-CXXC unit / Transcription factor SRY / : / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix, base-excision DNA repair, C-terminal ...Permuted single zf-CXXC unit / Demeter, RRM-fold domain / DNA glycosylase, plant / RRM in Demeter / Permuted single zf-CXXC unit / Transcription factor SRY / : / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily 類似検索 - ドメイン・相同性
Sex-determining region Y protein / DNA glycosylase/AP lyase ROS1 類似検索 - 構成要素
生物種
Homo sapiens (ヒト) / Arabidopsis thaliana (シロイヌナズナ)
ジャーナル: Nat Plants / 年: 2023 タイトル: Molecular basis of the plant ROS1-mediated active DNA demethylation. 著者: Xuan Du / Zhenlin Yang / Guohui Xie / Changshi Wang / Laixing Zhang / Kaige Yan / Maojun Yang / Sisi Li / Jian-Kang Zhu / Jiamu Du / 要旨: Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly ...Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases.
分子 #1: Sex-determining region Y protein,REPRESSOR OF SILENCING 1,DNA gly...
分子
名称: Sex-determining region Y protein,REPRESSOR OF SILENCING 1,DNA glycosylase/AP lyase ROS1 タイプ: protein_or_peptide / ID: 1 詳細: Fusion protein of residues 56 to 130 of database UNP Q05066, Linker, residues 511 to 1393 of database UNP Q9SJQ6, with deletion of residues 665-835 and 1074-1109. コピー数: 1 / 光学異性体: LEVO / EC番号: DNA-(apurinic or apyrimidinic site) lyase