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Solution structure and small angle scattering analysis of TraI (381–569)
Author(s) -
Wright Nathan T.,
Raththagala Madushi,
Hemmis Casey W.,
Edwards Sheldon,
Curtis Joseph E.,
Krueger Susan,
Schildbach Joel F.
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24114
Subject(s) - helicase , dna , linker , biology , biophysics , binding site , cooperativity , protein structure , biochemistry , crystallography , chemistry , rna , gene , computer science , operating system
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. Proteins 2012; © 2012 Wiley Periodicals, Inc.