STM2360 encodes a d-ornithine/d-lysine decarboxylase in Salmonella enterica serovar typhimurium

STM2360 is a gene located in a small operon of undetermined function in Salmonella enterica serovar Typhimurium LT2. The amino acid sequence of STM2360 shows significant similarity (∼30% identity) to diaminopimelate decarboxylase (DapDC), a Fold III pyridoxal-5′-phosphate (PLP) dependent enzyme involved in l-lysine biosynthesis. We have found that the protein coded by STM2360 has a previously undocumented catalytic activity, d-ornithine/d-lysine decarboxylase (DOKDC). The reaction products, cadaverine and putrescine, respectively, were identified by NMR and mass spectrometry. The substrate specificity of DOKDC is d-Lysine > d-Ornithine. This is the first pyridoxal-5′-phosphate dependent decarboxylase identified to act on d-amino acids. STM2358, located in the same operon, has ornithine racemase activity. This suggests that the physiological substrate of the decarboxylase and the operon is ornithine. Homologs of STM2360 with high sequence identity (>80%) are found in other common enterobacteria, including species of Klebsiella, Citrobacter, Vibrio and Hafnia, as well as Clostridium in the Firmicutes, and Pseudomonas. [Display omitted] •STM2360 encodes a d-ornithine/d-lysine decarboxylase.•The enzyme exhibits cooperativity, with a Hill coefficient ∼3.•STM2358 in the same operon is an ornithine racemase.•These enzymes are widely distributed in bacteria.