Mechanism of 2-oxoglutarate signaling by the <i>Synechococcus elongatus</i> P _II signal transduction protein

<jats:p> P <jats:sub>II</jats:sub> proteins control key processes of nitrogen metabolism in bacteria, archaea, and plants in response to the central metabolites ATP, ADP, and 2-oxoglutarate (2-OG), signaling cellular energy and carbon and nitrogen abundance. This metabolic information is integrated by P <jats:sub>II</jats:sub> and transmitted to regulatory targets (key enzymes, transporters, and transcription factors), modulating their activity. In oxygenic phototrophs, the controlling enzyme of arginine synthesis, <jats:italic>N</jats:italic> -acetyl-glutamate kinase (NAGK), is a major P <jats:sub>II</jats:sub> target, whose activity responds to 2-OG via P <jats:sub>II</jats:sub> . Here we show structures of the <jats:italic>Synechococcus elongatus</jats:italic> P <jats:sub>II</jats:sub> protein in complex with ATP, Mg <jats:sup>2+</jats:sup> , and 2-OG, which clarify how 2-OG affects P <jats:sub>II</jats:sub> –NAGK interaction. P <jats:sub>II</jats:sub> trimers with all three sites fully occupied were obtained as well as structures with one or two 2-OG molecules per P <jats:sub>II</jats:sub> trimer. These structures identify the site of 2-OG located in the vicinity between the subunit clefts and the base of the T loop. The 2-OG is bound to a Mg <jats:sup>2+</jats:sup> ion, which is coordinated by three phosphates of ATP, and by ionic interactions with the highly conserved residues K58 and Q39 together with B- and T-loop backbone interactions. These interactions impose a unique T-loop conformation that affects the interactions with the P <jats:sub>II</jats:sub> target. Structures of P <jats:sub>II</jats:sub> trimers with one or two bound 2-OG molecules reveal the basis for anticooperative 2-OG binding and shed light on the intersubunit signaling mechanism by which P <jats:sub>II</jats:sub> senses effectors in a wide range of concentrations. </jats:p>