page_title: Diaminopimelate decarboxylase
section_title: Mechanism
hierarchical_section_title: Diaminopimelate decarboxylase / Mechanism
caption_attribution_description: English: 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.
context_page_description: In enzymology, diaminopimelate decarboxylase, also known as diaminopimelic acid decarboxylase, DAPDC, meso-diaminopimelate decarboxylase, DAP-decarboxylase, and meso-2,6-diaminoheptanedioate carboxy-lyase, is an enzyme that catalyzes the cleavage of carbon-carbon bonds in meso 2,6 diaminoheptanedioate to produce CO2 and L-lysine, the essential amino acid. It employs the cofactor pyridoxal phosphate, also known as PLP, which participates in numerous enzymatic transamination, decarboxylation and deamination reactions.
  This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is meso-2,6-diaminoheptanedioate carboxy-lyase.DAP-decarboxylase catalyzes the final step in the meso-diaminopimelate/lysine biosynthetic pathway. Lysine is used for protein synthesis and used in the peptidoglycan layer of Gram-positive bacteria cell walls. This enzyme is not found in humans, but the ortholog is ornithine decarboxylase.
context_section_description: 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. The lysine residue binding PLP to the structure is replaced by diaminopimelate. DAPDC then uses the interaction of 3 residues (Arginine, Aspartate, and Glutamate) within the active site to identify the D-stereocenter. The DAP is decarboxylated and then stabilized by PLP. It is not clear which general acid protonates after decarboxylation, but there is speculation that the lysine residue is the donor.
caption: 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.
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