Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains

Seok-Yong Lee; Armando De La Torre; Dalai Yan; Sydney Kustu; B. Tracy Nixon; David E. Wemmer

doi:10.1101/gad.1125603

Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA⁺ ATPase domains

¹ Graduate Group in Biophysics, University of California, Berkeley, California 94720,USA
² Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
³ Department of Molecular Cellular Biology, University of California, Berkeley, California 94720, USA
⁴ Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
⁵ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
⁶ Department of Chemistry, University of California, Berkeley, California 94720, USA

Abstract

Transcription by σ⁵⁴ RNA polymerase depends on activators that contain ATPase domains of the AAA⁺ class. These activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. Here, we report the first crystal structures of the ATPase domain of an activator, the NtrC1 protein from the extreme thermophile Aquifex aeolicus. This domain alone, which is active, crystallized as a ring-shaped heptamer. The protein carrying both the ATPase and adjacent receiver domains, which is inactive, crystallized as a dimer. In the inactive dimer, one residue needed for catalysis is far from the active site, and extensive contacts among the domains prevent oligomerization of the ATPase domain. Oligomerization, which completes the active site, depends on surfaces that are buried in the dimer, and hence, on a rearrangement of the receiver domains upon phosphorylation. A motif in the ATPase domain known to be critical for coupling energy to remodeling of polymerase forms a novel loop that projects from the middle of an α helix. The extended, structured loops from the subunits of the heptamer localize to a pore in the center of the ring and form a surface that could contact σ⁵⁴.

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Footnotes

Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.1125603.
↵7 Corresponding author. E-MAIL dewemmer{at}lbl.gov; FAX (510) 486-6059.
- Received June 25, 2003.
- Revision received August 25, 2003.
Cold Spring Harbor Laboratory Press