2A0I

F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA

2A0I の概要

• エントリーDOI: 10.2210/pdb2a0i/pdb
• 関連するPDBエントリー: 1P4D
• 分子名称: F plasmid single-stranded oriT DNA, TraI protein, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: single-stranded dna, protein-dna complex, 5-strand antiparallel beta sheet, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Escherichia coli; 詳細
• 細胞内の位置: Cytoplasm : P14565
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 43352.37

構造登録者

Larkin, C.,Datta, S.,Harley, M.J.,Anderson, B.J.,Ebie, A.,Hargreaves, V.,Schildbach, J.F. (登録日: 2005-06-16, 公開日: 2005-10-25, 最終更新日: 2023-08-23)

主引用文献

Larkin, C.,Datta, S.,Harley, M.J.,Anderson, B.J.,Ebie, A.,Hargreaves, V.,Schildbach, J.F.
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase.
Structure, 13:1533-1544, 2005

PubMed Abstract: The TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack.

PubMed: 16216584
DOI: 10.1016/j.str.2005.06.013

実験手法

X-RAY DIFFRACTION (2.72 Å)