Effectors of the Stringent Response Target the Active Site ofEscherichia coli Adenylosuccinate Synthetase

Guanosine 5′-diphosphate 3′-diphosphate (ppGpp), a pleiotropic effector of the stringent response, potently inhibits adenylosuccinate synthetase from Escherichia coli as an allosteric effector and/or as a competitive inhibitor with respect to GTP. Crystals of the synthetase grown in the presence of IMP, hadacidin, NO₃⁻, and Mg²⁺, then soaked with ppGpp , reveal electron density at the GTP pocket which is consistent with guanosine 5′-diphosphate 2′:3′-cyclic monophosphate. Unlike ligand complexes of the synthetase involving IMP and GDP, the coordination of Mg²⁺ in this complex is octahedral with the side chain of Asp¹³ in the inner sphere of the cation. The cyclic phosphoryl group interacts directly with the side chain of Lys⁴⁹ and indirectly through bridging water molecules with the side chains of Asn²⁹⁵ and Arg³⁰⁵. The synthetase either directly facilitates the formation of the cyclic nucleotide or scavenges trace amounts of the cyclic nucleotide from solution. Regardless of its mode of generation, the cyclic nucleotide binds far more tightly to the active site than does ppGpp . Conceivably, synthetase activity in vivo during the stringent response may be sensitive to the relative concentrations of several effectors, which together exercise precise control over the de novosynthesis of AMP.