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 IIANtr, is homologous to IIA proteins of the phosphoenolpyruvate:sugar phosphotransferase (PTS) system. IIANtr 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 IIANtr. 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.