The structure of the P_II-ATP complex

P_II is a signal transduction protein that is part of the cellular machinery used by many bacteria to regulate the activity of glutamine synthetase and the transcription of its gene. The structure of P_II was solved using a hexagonal crystal form (form I). The more physiologically relevant form of P_II is a complex with small molecule effectors. We describe the structure of P_II with ATP obtained by analysis of two different crystal forms (forms II and III) that were obtained by co-crystallization of P_II with ATP. Both structures have a disordered recognition (T) loop and show differences at their C termini. Comparison of these structures with the form I protein reveals changes that occur on binding ATP. Surprisingly, the structure of the P_II/ATP complex differs with that of GlnK, a functional homologue. The two proteins bind the base and sugar of ATP in a similar manner but show differences in the way that they interact with the phosphates. The differences in structure could account for the differences in their activities, and these have been attributed to a difference in sequence at position 82. It has been demonstrated recently that P_II and GlnK form functional heterotrimers in vivo. We construct models of the heterotrimers and examine the junction between the subunits.