PTS(Ntr) is a regulatory phosphotransferase system in many bacteria. Mutation of the PTS(Ntr) enzymes causes pleiotropic growth phenotypes, dry colony morphology and a posttranslational inactivation of ABC transporters in Rhizobium leguminosarum 3841. The PTS(Ntr) proteins EI(Ntr) and 2 copies of EIIA(Ntr) have been described previously. Here we identify the intermediate phosphocarrier protein NPr and show its phosphorylation by EI(Ntr) in vitro. Furthermore we demonstrate that phosphorylation of EI(Ntr) and NPr is required for ABC transport activation and that the N-terminal GAF domain of EI(Ntr) is not required for autophosphorylation. Previous studies have shown that non-phosphorylated EIIA(Ntr) is able to modulate the transcriptional activation of the high affinity potassium transporter KdpABC. In R. leguminosarum 3841 kdpABC expression strictly depends on EIIA(Ntr). Here we demonstrate that under strong potassium limitation ABC transport is inactivated, presumably by non-phosphorylated EIIA(Ntr). This is to our knowledge the first report where PTS(Ntr) dictates an essential cellular function. This is achieved by the inverse regulation of two important ATP dependent transporter classes.