Crystal Structure of D-Ornithine/D-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold Ill Decarboxylases

A newly discovered Fold III pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, D-ornithine/lysine decarboxylase (DOKDC), catalyzes decarboxylation of D-lysine and D-ornithine with inversion of stereochemistry. The X-ray crystal structure of DOKDC has been determined to 1.72 angstrom. DOKDC has a low level of sequence identity (<30%) with meso-diaminopimelate decarboxylase (DAPDC) and L-lysine/ornithine decarboxylase (LODC), but its three-dimensional structure is very similar. The distal binding site of DAPDC contains a conserved arginine that forms an ion pair with the L-carboxylate end of DAP. In both LODC and DOKDC, this distal site is modified by replacement of the arginine with aspartate, changing the substrate specificity. L-Ornithine decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a key role in the decarboxylation mechanism. We have found that both DAPDC and DOKDC have tyrosine instead of phenylalanine at this position, which precludes the binding of L-amino acids. Because the PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group responsible for protonation of the product, thus resulting in the observed retention of configuration for decarboxylation of L-amino acids and inversion for decarboxylation of D-amino acids. The reactions of DAPDC and DOKDC are likely accelerated by positive electrostatics on the re-face by the lysine epsilon-ammonium ion and on the si-face by closure of the lid over the active site, resulting in desolvation and destabilization of the D-amino acid carboxylate.