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J. Biol. Chem., Vol. 280, Issue 50, 41530-41536, December 16, 2005

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The C-terminal RpoN Domain of ⁵⁴ Forms an Unpredicted Helix-Turn-Helix Motif Similar to Domains of ^70*

Michaeleen Doucleff, Lawrence T. Malak¶, Jeffrey G. Pelton, and David E. Wemmer1

From the Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Departments of Chemistry and ^¶Molecular and Cell Biology, University of California, Berkeley, California 94720

The "" subunit of prokaryotic RNA polymerase allows gene-specific transcription initiation. Two families have been identified, ⁷⁰ and ⁵⁴, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the ⁷⁰-type factors have been well characterized structurally by x-ray crystallography, no high resolution structural information is available for the ⁵⁴-type factors. Here we present the NMR-derived structure of the C-terminal domain of ⁵⁴ from Aquifex aeolicus. This domain (Thr-323 to Gly-389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the ⁷⁰-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. The homology of this structure with other DNA-binding proteins, combined with previous biochemical data, suggests how the C-terminal domain of ⁵⁴ binds to DNA.

Received for publication, August 16, 2005 , and in revised form, October 3, 2005.

The atomic coordinates and structure factors (code 2AHQ) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by National Institutes of Health Grant GM62163 (to D. E. W.) and by a University of California fellowship (to M. D.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1 and S2 and Table S1.

¹ To whom correspondence should be addressed: Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720. Tel.: 510-486-4318; Fax: 510-486-6059; E-mail: DEWemmer{at}lbl.gov.

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