title: Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis.
abstract: Diaminopimelate decarboxylase (DAPDC) catalyzes the final step in the diaminopimelate biosynthesis pathway of bacteria. The product of the reaction is the essential amino acid l-lysine, which is an important precursor for the synthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Accordingly, the enzyme is a promising antibacterial target. Previous structural studies demonstrate that DAPDC exists as monomers, dimers, and tetramers in the crystal state. However, the active oligomeric form has not yet been determined. We show using analytical ultracentrifugation, small angle x-ray scattering, and enzyme kinetic analyses in solution that the active form of DAPDC from Bacillus anthracis, Escherichia coli, Mycobacterium tuberculosis, and Vibrio cholerae is a dimer. The importance of dimerization was probed further by generating dimerization interface mutants (N381A and R385A) of V. cholerae DAPDC. Our studies indicate that N381A and R385A are significantly attenuated in catalytic activity, thus confirming that dimerization of DAPDC is essential for function. These findings provide scope for the development of new antibacterial agents that prevent DAPDC dimerization.
authors.affiliation: From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria 3010, and.
authors.forename: Martin G
authors.initials: MG
authors.lastname: Peverelli
authors.affiliation: From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086.
authors.forename: Tatiana P
authors.initials: TP
authors.lastname: Soares da Costa
authors.affiliation: the The Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia.
authors.forename: Nigel
authors.initials: N
authors.lastname: Kirby
authors.affiliation: From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria 3010, and M.Perugini@latrobe.edu.au.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Perugini
mesh_terms: D019943:Amino Acid Substitution; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002384:Catalysis; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020125:Mutation, Missense; D055503:Protein Multimerization
chemical_list: D029968:Escherichia coli Proteins; D002262:Carboxy-Lyases; C489812:LysA protein, E coli
keywords: analytical ultracentrifugation; diaminopimelate decarboxylase; dimerization; enzyme; enzyme kinetics; lysine biosynthesis; small-angle X-ray scattering (SAXS)