The Escherichia coli acid stress response allows the survival of cells over a wide range of pH challenges: down to pH 2.0 with the extreme acid stress response and down to pH 4.0 – 5.0 with the mild acid stress response. The cell employs a number of different acid stress response systems, including a number of structurally related, pyridoxal-5′-phosphate (PLP)-dependent amino acid decarboxylases, including the glutamic acid, arginine, lysine, and ornithine decarboxylases. The decarboxylases are large multi-domain enzymes that exist as homodimers or higher-order oligomers and have various activity optima at different pH values. By the proton-consuming decarboxylation of a target amino acid, these enzymes provide a response to a wide range of pH challenges. The primary focus of this work is the elucidation of the X-ray crystal structure of the inducible lysine decarboxylase LdcI, a homodecameric enzyme that has distinct 5-fold symmetry. A combination of heavy-atom derivatization, anomalous scattering and molecular replacement techniques were used to determine the X-ray structure and the model was refined to a resolution of 2.0 Å. The structure of LdcI revealed that the protein co-crystallized with the stringent response alarmone ppGpp. The stringent response is activated under nutritional and stress conditions and reorganizes cellular transcription and metabolism from exponential-phase growth into stationary phase growth. The primary target of ppGpp is the RNA polymerase, but other classes of enzymes are known to be affected. ppGpp was found to be a potent inhibitor of LdcI both in vitro and in vivo and this role provides the first evidence of a linkage between the stringent response and acid stress response. Among the decarboxylases related to LdcI (the constitutive lysine, the ornithine and arginine decarboxylases), a number of these enzymes were similarly regulated by ppGpp.

The Escherichia coli acid stress response allows the survival of cells over a wide range of pH challenges: down to pH 2.0 with the extreme acid stress response and down to pH 4.0 – 5.0 with the mild acid stress response. The cell employs a number of different acid stress response systems, including a number of structurally related, pyridoxal-5′-phosphate (PLP)-dependent amino acid decarboxylases, including the glutamic acid, arginine, lysine, and ornithine decarboxylases. The decarboxylases are large multi-domain enzymes that exist as homodimers or higher-order oligomers and have various activity optima at different pH values. By the proton-consuming decarboxylation of a target amino acid, these enzymes provide a response to a wide range of pH challenges. The primary focus of this work is the elucidation of the X-ray crystal structure of the inducible lysine decarboxylase LdcI, a homodecameric enzyme that has distinct 5-fold symmetry. A combination of heavy-atom derivatization, anomalous scattering and molecular replacement techniques were used to determine the X-ray structure and the model was refined to a resolution of 2.0 Å. The structure of LdcI revealed that the protein co-crystallized with the stringent response alarmone ppGpp. The stringent response is activated under nutritional and stress conditions and reorganizes cellular transcription and metabolism from exponential-phase growth into stationary phase growth. The primary target of ppGpp is the RNA polymerase, but other classes of enzymes are known to be affected. ppGpp was found to be a potent inhibitor of LdcI both in vitro and in vivo and this role provides the first evidence of a linkage between the stringent response and acid stress response. Among the decarboxylases related to LdcI (the constitutive lysine, the ornithine and arginine decarboxylases), a number of these enzymes were similarly regulated by ppGpp.