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.Keywords: ATP binding protein; GlnK; P II ; signal transduction; X-ray structure.P II is a signal transduction protein found in a variety of organisms. It is best characterized in Escherichia coli in which it indicates the nitrogen status of the cell. In many bacteria the level of available nitrogen is closely coupled to the level of glutamine synthetase (GS) activity. P II is involved in the regulation of GS and the transcription of its gene [1±4]. In brief, the nitrogen status of the cell is monitored by the uridylyl transferase/uridylyl removing enzyme (UT/URase). It uridylylates P II at Tyr51 to form P II ±UMP [5±7] under conditions of limiting ammonia and catalyses the removal of UMP under conditions of excess ammonia. The uridylylation status of P II reflects the nitrogen status of the cell. P II dictates the direction of the enzymatic regulation of GS through its interaction with adenylyl transferase (ATase). The transcriptional regulation of GS is mediated by P II and the nitrogen regulatory proteins I and II (NRI and NRII) also known as NtrC and NtrB, respectively. Although the regulation of GS has been studied for many years, much remains to be learnt about this system in the light of some recent discoveries. For example, it is now apparent that many organisms possess two P II -like proteins. The second protein in E. coli is known as GlnK [8,9]. The physical properties of GlnK are very similar to those of P II and under some circumstances GlnK can substitute for P II . When the cell is grown in nitrogen-poor conditions, P II and GlnK form heterotrimers [10] to fine-tune the regulation of GS [11]. The fine regulation of the nitrogen signal cascade by functional heterotrimers of P II and GlnK introduces a new level of complexity to ...
