Diaminopimelate decarboxylase

DAPDC is a PLP-dependent enzyme belonging to the alanine racemase family.[4] This enzyme is generally dimeric with each monomer containing two domains.[5] The first domain is the N-terminal α/β-barrel that binds the PLP to the active site lysine residue.[3][4][5] The second domain is the C-terminal β-sandwich.[4][5] The active site is formed from residues present in both domains resulting in two active sites within the dimer.[5]

A cartoon diagram of the active site bound to PLP and the product, L-lysine. Lysine forms a Schiff base with PLP, while histidine stabilizes the formation.

DAPDC is stereochemically specific due to the opposing chiralities at each terminus of diaminopimelate.[5] In order for the L-lysine to be generated over D-lysine, decarboxylation must occur at the D-terminus. Whether DAPDC recognizes the terminus or not is dependent on the formation of a Schiff base with PLP.[5]

While the majority of DAPDC found in various species of bacteria have the same basic components, not all species follow the same structure.[3] Some species of bacteria, such as Mycobacterium tuberculosis have been observed as a tetramer.[6] The tetramer is shaped like a ring with the active sites accessible from the inside of the enzyme.[6]

A schematic of the reaction mechanism of DAPDC. DAP forms a Schiff base with PLP, reconforms so that carbon dioxide becomes a good leaving group, and then returns PLP to a lysine residue.

The first step in the mechanism is the same as for all type III PLP-dependent enzymes; the formation of a Schiff base with the substrate amino group.[5] The lysine residue binding PLP to the structure is replaced by diaminopimelate.[4][7] DAPDC then uses the interaction of 3 residues (Arginine, Aspartate, and Glutamate) within the active site to identify the D-stereocenter.[3][7] The DAP is decarboxylated and then stabilized by PLP.[4] It is not clear which general acid protonates after decarboxylation, but there is speculation that the lysine residue is the donor.[7]

DAPDC is regulated by the product L-lysine at relatively high concentrations.[3][8] Compounds that are similar to DAP in chemical complexity do not inhibit the reaction, possibly due to the residue rulers creating specific bond angles.[3] Diamines have a stronger inhibitory effect compared to dicarboxylic acids, most likely from interactions with PLP.[3]

Given that there are three pathways to convert aspartate to lysine, this is clearly an essential process for the cell, particularly in building cell walls in Gram-positive bacteria.[2][9] There is no process for producing lysine in humans, but ornithine decarboxylase shares many similarities with DAPDC.[4] Both enzymes use PLP as a cofactor and have similar structures forming the active sites.[7] However, DAPDC differs in that it decarboxylates at the D-stereocenter and is highly stereospecific.[7] These unique features make DAPDC a good candidate for antibacterial studies because potential inhibitors of such an integral step in cell viability would be unlikely to interact with necessary processes within humans.