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The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and N interaction

Department of Biopolymers, University of Bayreuth, 95440 Bayreuth, Germany

(RECEIVED January 19, 2005; FINAL REVISION May 2, 2005; ACCEPTED May 4, 2005)

The carboxy-terminal domain of the transcription factor Escherichia coli NusA, NusACTD, interacts with the protein N of bacteriophage , N, and the carboxyl terminus of the E. coli RNA polymerase subunit, CTD. We solved the solution structure of the unbound NusACTD with high-resolution nuclear magnetic resonance (NMR). Additionally, we investigated the binding sites of N and CTD on NusACTD using NMR titrations. The solution structure of NusACTD shows two structurally similar subdomains, NusA(353–416) and NusA(431–490), matching approximately two homologous acidic sequence repeats. Further characterization of NusACTD with ¹⁵N NMR relaxation data suggests that the interdomain region is only weakly structured and that the subdomains are not interacting. Both subdomains adopt an (HhH)₂ fold. These folds are normally involved in DNA–protein and protein–protein interactions. NMR titration experiments show clear differences of the interactions of these two domains with CTD and N, in spite of their structural similarity.

Keywords: NusA; anti-termination; termination; NMR; RNA polymerase; N-protein; phage ; HhH motif

Abbreviations: CTD, carboxy-terminal domain of the subunit of the RNAP • E. coli, Escherichia coli • Het NOE, {¹H}¹⁵N heteronuclear NOE • HhH, helix hairpin helix • HSQC, heteronuclear single quantum coherence • KH, K homology • N, protein N of phage • NOESY, nuclear Overhauser spectroscopy • NusA, N utilization substance A • NusA CTD, carboxy-terminal domain of NusA • NMR, nuclear magnetic resonance, PG-SLED, pulse gradient-stimulated echo longitudinal encode-decode • RDC, residual dipolar coupling • RMSD, root mean-square deviation • RNAP, RNA polymerase • SAM, sterile motif

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051372205.

Reprint requests to: Paul Rösch, Department of Biopolymers, Universitätsstr. 30, University of Bayreuth, 95440 Bayreuth, Germany; e-mail: paul.roesch{at}uni-bayreuth.de; fax: +49-921-553544.

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