THE THREE-DIMENSIONAL STRUCTURE OF THE NITROGEN REGULATORY PROTEIN IIA-Ntr FROM Escheria coli

Domenico Bordo^1,*, Rob L. M. van Monfort¹, Tjaard Pijning¹, Kor H. Kalk¹, Jonathan Reizer², Milton H. Saier, Jr.² and Bauke W. Dijkstra¹

¹Laboratory of Biophysical Chemistry and BIOSON Research Institute, University of Groningen Nijenborgh 4 9747 AG Groningen, the Netherlands
²Department of Biology University of California at San Diego La Jolla, CA 92093-0116, USA
^*permanent address: Biostructure Unit, Advanced Biotechnology Center - IST Largo R. Benzi 10 16136 Genova, Italy

The bacterial rpoN operon codes for sigma-54, which is the key s factor that, under nitrogen starvation conditions, activates the transcription of genes needed to assimilate ammonia and glutamate. The rpoN operon contains several other open reading frames which are cotranscribed with sigma-54. The product of one of these, the 17.9 kDa protein IIA-Ntr, is homologous to IIA proteins of the phosphoenolpyruvate:sugar phosphotransferase (PTS) system. IIA-Ntr influences the transcription of sigma-54-dependent genes through an as yet unknown mechanism and may thereby provide a regulatory link between carbon and nitrogen metabolism. Here we describe the 2.35A X-ray structure of Escherichia coli IIANtr, obtained with the multiple isomorphous replacement technique using lead and mercury compounds as heavy atom derivatives. The enzyme displays a novel fold characterized by a central mixed parallel/anti-parallel b-sheet surrounded by six a-helices. The active site His73 is situated in a shallow depression on the protein surface.