The three-dimensional structure of the nitrogen regulatory protein IIA(Ntr) from Escherichia coli

The bacterial rpoN operon codes for σ⁵⁴, which is the key σ 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 that are cotranscribed with σ⁵⁴. 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 σ⁵⁴-dependent genes through an unknown mechanism and may thereby provide a regulatory link between carbon and nitrogen metabolism. Here we describe the 2.35 Å X-ray structure of Escherichia coli IIA(Ntr). It is the first structure of a IIA enzyme from the fructose-mannitol family of the PTS. The enzyme displays a novel fold characterized by a central mixed parallel/anti-parallel β-sheet surrounded by six α-helices. The active site His73 is situated in a shallow depression on the protein surface.