{"id":{"repo_id":"toronto-retro","oai_identifier":"oai:utoronto.scholaris.ca:1807/32786"},"canonical_url":"https://search.dev.ndltd.org/etd/toronto-retro/oai:utoronto.scholaris.ca:1807/32786","repository":{"repo_id":"toronto-retro","name":"University of Toronto","base_url":"https://utoronto.scholaris.ca/server/oai/request"},"display":{"title":"Structural and Functional Studies on the Escherichia coli Inducible Lysine Decarboxylase: Linking the Acid Stress and Stringent Responses","abstract":"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.","abstract_html":"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.","abstract_has_math":false,"creators":["Kanjee, Usheer"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Biochemistry","school":null,"contributors":[],"advisors":["Houry, Walid A."],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-08-30","date_published":"2012-08-30","updated_at":"2026-07-27T21:28:09Z","subjects":["Biochemistry","X-ray Crystallography","Acid Stress","Stringent Response","Escherichia coli","Inducible Lysine Decarboxylase","ppGpp","Alarmone"],"languages":["en_ca"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1807/32786","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Houry, Walid A."]},{"key":"dc:contributor.department","label":"Department","values":["Biochemistry"]},{"key":"dc:creator","label":"Author","values":["Kanjee, Usheer"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-06"]},{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2012-08-30T19:23:20Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["NO_RESTRICTION","2012-08-30T19:23:20Z"]},{"key":"dc:date.issued","label":"Date","values":["2012-08-30"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biochemistry","X-ray Crystallography","Acid Stress","Stringent Response","Escherichia coli","Inducible Lysine Decarboxylase","ppGpp","Alarmone"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_ca"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1807/32786"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["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."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["PhD"]},{"key":"dc:title","label":"Title","values":["Structural and Functional Studies on the Escherichia coli Inducible Lysine Decarboxylase: Linking the Acid Stress and Stringent Responses"]}]}],"canonical_facts":{"dc:contributor.advisor":["Houry, Walid A."],"dc:contributor.department":["Biochemistry"],"dc:creator":["Kanjee, Usheer"],"dc:date":["2012-06"],"dc:date.accessioned":["2012-08-30T19:23:20Z"],"dc:date.available":["NO_RESTRICTION","2012-08-30T19:23:20Z"],"dc:date.issued":["2012-08-30"],"dc:description.abstract":["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."],"dc:description.degree":["PhD"],"dc:identifier.uri":["http://hdl.handle.net/1807/32786"],"dc:language.iso":["en_ca"],"dc:subject":["Biochemistry","X-ray Crystallography","Acid Stress","Stringent Response","Escherichia coli","Inducible Lysine Decarboxylase","ppGpp","Alarmone"],"dc:title":["Structural and Functional Studies on the Escherichia coli Inducible Lysine Decarboxylase: Linking the Acid Stress and Stringent Responses"],"dc:type":["Thesis"]},"updated_at":"2026-07-27T21:28:09Z"}