title: Solution structure and small angle scattering analysis of TraI (381-569).
abstract: TraI, the F plasmid-encoded nickase, is a 1756 amino acid protein essential for conjugative transfer of plasmid DNA from one bacterium to another. Although crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. The central region (between residues 306 and 1520) is known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Here, we show that the ssDNA binding site is located between residues 381 and 858, and we also present the high-resolution solution structure of the N-terminus of this region (residues 381-569). This fragment folds into a four-strand parallel β sheet surrounded by α helices, and it resembles the structure of the N-terminus of helicases such as RecD and RecQ despite little sequence similarity. The structure supports the model that F TraI resulted from duplication of a RecD-like domain and subsequent specialization of domains into the more N-terminal ssDNA binding domain and the more C-terminal domain containing helicase motifs. In addition, we provide evidence that the nickase and ssDNA binding domains of TraI are held close together by an 80-residue linker sequence that connects the two domains. These results suggest a possible physical explanation for the apparent negative cooperativity between the nickase and ssDNA binding domain.
authors.affiliation: Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Nathan T
authors.initials: NT
authors.lastname: Wright
authors.forename: Madushi
authors.initials: M
authors.lastname: Raththagala
authors.forename: Casey W
authors.initials: CW
authors.lastname: Hemmis
authors.forename: Sheldon
authors.initials: S
authors.lastname: Edwards
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Curtis
authors.forename: Susan
authors.initials: S
authors.lastname: Krueger
authors.forename: Joel F
authors.initials: JF
authors.lastname: Schildbach
mesh_terms: D001665:Binding Sites; D004265:DNA Helicases / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D053838:Scattering, Small Angle
chemical_list: D029968:Escherichia coli Proteins; C027093:TraI protein, E coli; D004265:DNA Helicases