Toward an Understanding of the Mechanistic Differences Between the Hydroxylating and Desaturating Pyridoxal 5′-Phosphate-Dependent L-Arginine Oxidases

Pyridoxal-5′-phosphate (PLP)-dependent L-arginine oxidases (PDAOs) catalyze 4-electron oxidations of L-arginine in the context of secondary metabolite biosynthesis. PDAOs are separated into two classes based on whether they hydroxylate or desaturate L-arginine. A detailed mechanistic understanding of these enzymes will extend our knowledge of natural products biosynthesis. Here, we present detailed transient kinetic analyses of representative hydroxylating and desaturating PDAOs: MppP from Streptomyces wadayamensis (SwMppP) and the Ind4 homolog from Pseudoalteromonas luteoviolacea (Plu4). While both SwMppP and Plu4 kinetics can be accurately predicted using the same kinetic model, they in fact use subtly different mechanisms. This work seeks to uncover how two enzymes that are so similar in terms of sequence, structure, and catalytic function can have different mechanisms. To this end, we determined the structure of an additional desaturating PDAO, the Ind4 homolog from Bacillus cereus (Bcer4). This brings the total number of PDAOs whose structures have been determined to four: two hydroxylases and two desaturases. Examination of the available structural data fails to point out any class-specific structural differences that could explain the mechanistic differences between the classes. The subtle mechanistic differences are likely due to differences in protein dynamics rather than structure.