2A0I
F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA
Summary for 2A0I
Entry DOI | 10.2210/pdb2a0i/pdb |
Related | 1P4D |
Descriptor | F plasmid single-stranded oriT DNA, TraI protein, MAGNESIUM ION, ... (5 entities in total) |
Functional Keywords | single-stranded dna, protein-dna complex, 5-strand antiparallel beta sheet, hydrolase-dna complex, hydrolase/dna |
Biological source | Escherichia coli More |
Cellular location | Cytoplasm : P14565 |
Total number of polymer chains | 2 |
Total formula weight | 43352.37 |
Authors | Larkin, C.,Datta, S.,Harley, M.J.,Anderson, B.J.,Ebie, A.,Hargreaves, V.,Schildbach, J.F. (deposition date: 2005-06-16, release date: 2005-10-25, Last modification date: 2023-08-23) |
Primary citation | 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 Cited by 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: 16216584DOI: 10.1016/j.str.2005.06.013 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (2.72 Å) |
Structure validation
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