2a0i
From Proteopedia
F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA
Overview
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.
About this Structure
2A0I is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase., Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF, Structure. 2005 Oct;13(10):1533-44. PMID:16216584 Page seeded by OCA on Sat May 3 18:27:16 2008
