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Article
Nature Structural Biology  10, 812 - 819 (2003)
Published online: 21 September 2003; | doi:10.1038/nsb983

Context and conformation dictate function of a transcription antitermination switch

Tianbing Xia1, Adam Frankel1, Terry T Takahashi1, Jinsong Ren2 & Richard W Roberts1

1  Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.

2  Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.

Correspondence should be addressed to Richard W Roberts rroberts@its.caltech.edu
In bacteriophage l, transcription elongation is regulated by the N protein, which binds a nascent mRNA hairpin (termed boxB) and enables RNA polymerase to read through distal terminators. We have examined the structure, energetics and in vivo function of a number of N−boxB complexes derived from in vitro protein selection. Trp18 fully stacks on the RNA loop in the wild-type structure, and can become partially or completely unstacked when the sequence context is changed three or four residues away, resulting in a recognition interface in which the best binding residues depend on the sequence context. Notably, in vivo antitermination activity correlates with the presence of a stacked aromatic residue at position 18, but not with N−boxB binding affinity. Our work demonstrates that RNA polymerase responds to subtle conformational changes in cis-acting regulatory complexes and that approximation of components is not sufficient to generate a fully functional transcription switch.

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Nature Structural & Molecular Biology
ISSN: 1545-9993
EISSN: 1545-9985
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