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-基本情報
登録情報 | データベース: SASBDB / ID: SASDGS2 |
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試料 | J-23-DNA
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引用 | ジャーナル: J Biol Chem / 年: 2019 タイトル: The domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity. 著者: Athanassios Adamopoulos / Tatjana Heidebrecht / Jeroen Roosendaal / Wouter G Touw / Isabelle Q Phan / Jos Beijnen / Anastassis Perrakis / 要旨: J-DNA-binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic ...J-DNA-binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-d-glucosyl-hydroxymethyluracil), an epigenetic modification of thymidine (T) confined to pathogenic protozoa such as and JBP1 has two known functional domains: an N-terminal T hydroxylase (TH) homologous to the 5-methylcytosine hydroxylase domain in TET proteins and a J-DNA-binding domain (JDBD) that resides in the middle of JBP1. Here, we show that removing JDBD from JBP1 results in a soluble protein (Δ-JDBD) with the N- and C-terminal regions tightly associated together in a well-ordered structure. We found that this Δ-JDBD domain retains TH activity but displays a 15-fold lower apparent rate of hydroxylation compared with JBP1. Small-angle X-ray scattering (SAXS) experiments on JBP1 and JDBD in the presence or absence of J-DNA and on Δ-JDBD enabled us to generate low-resolution three-dimensional models. We conclude that Δ-JDBD, and not the N-terminal region of JBP1 alone, is a distinct folding unit. Our SAXS-based model supports the notion that binding of JDBD specifically to J-DNA can facilitate T hydroxylation 12-14 bp downstream on the complementary strand of the J-recognition site. We postulate that insertion of the JDBD module into the Δ-JDBD scaffold during evolution provided a mechanism that synergized J recognition and T hydroxylation, ensuring inheritance of base J in specific sequence patterns following DNA replication in kinetoplastid parasites. |
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-構造の表示
-ダウンロードとリンク
-モデル
-試料
試料 | 名称: J-23-DNA / 試料濃度: 4.1 mg/ml |
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バッファ | 名称: 20 mM HEPES, 200 mM NaCl, 1 mM TCEP / pH: 7.5 |
要素 #899 | 名称: J-23-DNA / タイプ: DNA / 記述: J-DNA (23mer) / 分子量: 14.225 / 分子数: 1 配列: TCGATTTGTT CATAGACTAA TACAGCTAAA CAAGTATCTG ATTATG |
-実験情報
ビーム | 設備名称: ESRF BM29 / 地域: Grenoble / 国: France / 線源: X-ray synchrotron / 波長: 0.1 Å / スペクトロメータ・検出器間距離: 2.872 mm | ||||||||||||||||||||||||||||||
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検出器 | 名称: Pilatus 1M / タイプ: Dectris / Pixsize x: 172 mm | ||||||||||||||||||||||||||||||
スキャン | タイトル: J-23-DNA / 測定日: 2016年2月21日 / セル温度: 4 °C / 照射時間: 1 sec. / フレーム数: 31 / 単位: 1/nm /
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距離分布関数 P(R) | ソフトウェア P(R): GNOM 5.0 / ポイント数: 899 /
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結果 | カーブのタイプ: sec /
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