Diaminopimelate decarboxylase (DAPDC) plays a critical role in the lysine biosynthesis pathway of bacteria and plants. The enzyme catalyses the final step in the pathway, namely, the decarboxylation of meso-diaminopimelate to form l-lysine. Both the substrate and product are important building blocks of the bacterial cell wall. Since the pathway is absent in humans, and that the enzyme is the product of an essential gene, the enzyme is a potential antimicrobial target.
The crystal structure of the enzyme has been characterised from several bacterial species, including, Escherichia coli, Thermotoga maritima, Vibrio cholerae, and Mycobacterium tuberculosis. Different oligomeric structures are evidenced between species. Specifically, DAPDC from the Gram-negative eubacteria E. coli and T. maritima is monomeric, while the enzyme from the Gram-negative eubacterium V. cholerae is dimeric, and the eubacterium M. tuberculosis produces DAPDC as a tetramer in the crystal form. Contrastingly, the program PISA (Proteins, Interfaces, Structures, and Assemblies) predicts that the enzymes are dimeric in solution by default, with only thermophilic bacteria predicted to form tetramers.
Accordingly, we hypothesise that the diversity of the enzyme’s quaternary structure is linked to species diversity and/or the environment in which the enzyme functions. The aim of this study is to characterise the quaternary structure of DAPDC in solution and thus compare them with the crystal structures from these diverse eubacterial species. We have subsequently expressed and purified DAPDC from Bacillus anthracis, Psychromonas ingrahamii, T. maritima, V. cholerae, E. coli, and M. tuberculosis and are in the process of conducting structural and kinetic studies to ascertain the relationship between quaternary structure and catalytic function. Additionally, to further address the involvement of quaternary structure in enzyme function, dimer attenuated V. cholerae DAPDC mutants have been created through site-directed mutagenesis and subsequently characterised.