A molecular dynamics simulations investigation on the effects of Ser/Cys exchange in the Ser-cisSer-Lys catalytic triad of Malonamidase E2

The enzyme malonamidase E2 catalytically hydrolyses malonamate (MLA) into malonate and ammonia. Its active site contains an uncommon Ser-cisSer-Lys catalytic triad that is critical to its functioning. Mutations of the residues in this triad can not only provide insight into its key features but can also potentially identify how it may be influenced or adapted, i.e., decreased or increased. In this study, the effects of single and double Ser/Cys exchanges on the wildtype Ser155-cisSer131-Lys62 catalytic triad (i.e., Cys155-cisSer131-Lys62 (S155C), Ser155-cisCys131-Lys62 (S131C), and Cys155-cisCys131-Lys62 (S131C/S155C)) were examined. In particular, the dynamics and stability of the resulting substituted triads was examined along with their inter-triad residue hydrogen bonding interactions as well as those with other nearby residues and the MLA substrate. The present results suggest that some mutations are more impactful than others. Indeed, mutation of cisSer131 to cisCys131 disrupts the triad and causes inconsistent hydrogen bonding interactions among the triad residues (i.e., Ser155, Cys131, and Lys62). In contrast, in the double mutant Cys155-cisCys131-Lys62, the triad’s residues appear to exhibit greater conformation stability with more consistent hydrogen bond interactions, though not necessarily as in the wildtype.