The nitrogen regulatory protein P II and the ammonia gas channel AmtB are both found in most prokaryotes. Interaction between these two proteins has been observed in several organisms and may regulate the activities of both proteins. The regulation of their interaction is only partially understood, and we show that in Rhodospirillum rubrum one P II homolog, GlnJ, has higher affinity for an AmtB 1 -containing membrane than the other two P II homologs, GlnB and GlnK. This interaction strongly favors the nonuridylylated form of GlnJ and is disrupted by high levels of 2-ketoglutarate (2-KG) in the absence of ATP or low levels of 2-KG in the presence of ATP. ADP inhibits the destabilization of the GlnJ-AmtB 1 complex in the presence of ATP and 2-KG, supporting a role for P II as an energy sensor measuring the ratio of ATP to ADP. In the presence of saturating levels of ATP, the estimated K d of 2-KG for GlnJ bound to AmtB 1 is 340 M, which is higher than that required for uridylylation of GlnJ in vitro, about 5 M. This supports a model where multiple 2-KG and ATP molecules must bind a P II trimer to stimulate release of P II from AmtB 1 , in contrast to the lower 2-KG requirement for productive uridylylation of P II by GlnD.The ammonium channel/rhesus (Amt/Rh) family of proteins is a widely distributed group of trimeric integral membrane proteins found in all domains of life that can function as gas channels of ammonia and perhaps carbon dioxide (13,20,29,39,43). A subset of this family, the AmtB proteins, is found in bacteria, archaea, some lower eukaryotes and plants. Homologs of amtB are often found in close proximity to genes encoding P II homologs (46). P II regulatory proteins are also found in most prokaryotes and some plant chloroplasts (3). P II is a small, soluble, trimeric protein that regulates the functions of several other proteins involved in nitrogen metabolism (3,4,35,36). AmtB appears to have two roles in the cell. The first function, to act as a channel for uncharged ammonia, has been explored physiologically, structurally, and computationally (28,33,44). The second function of AmtB is to interact with P II and has only recently been described (6,9,21,22,53).AmtB proteins have been shown to interact with homologs of P II in several bacteria and in the archaeon Methanococcus jannaschii (8,10,17,18,44,45,47,50,53). The association of P II with AmtB can physically block the ammonia gas channels of AmtB under conditions of nitrogen sufficiency in the cell. In addition, the AmtB-P II complex is able to recruit at least one other protein to the membrane, dinitrogenase reductase-activating glycohydrolase (DRAG), in organisms capable of nitrogen fixation (22,48). This membrane sequestration requires both an Amt protein and a P II protein and results in the inability of DRAG to activate dinitrogenase reductase in vivo. Finally, AmtB is able to remove equimolar amounts of P II from the cytoplasm, preventing P II from interacting with at least some other proteins. Although membrane sequestration of P II has b...