Exploring the mechanisms and structures of N-acyl-D-Asn prodrug peptidases

Bacteria engage in chemical warfare to compete with other microorganisms in their environment. Throughout our history, we have benefited from this warfare by using the specialized metabolites produced as the basis for potent antimicrobial agents. Thus, understanding how bacteria produce these potential therapeutics and pesticides can help us increase the yields of already known metabolites, illuminate undiscovered metabolites, and even design novel metabolites based on natural ones. In this thesis, I further our understanding of a class of specialized metabolites produced by bacteria called the N-acyl-D-Asn prodrug toxins. In Chapter 1, I delve into the various prodrug mechanisms developed by bacteria with a focus on those employing N-acyl-D-Asn prodrug motifs. In Chapter 2, I present the first structural and mechanistic studies of a type II prodrug peptidase, ZmaM, revealing a unique domain arrangement and an interdependence between these modules. In Chapter 3, I further our understanding of type I prodrug peptidases by probing how the type I prodrug peptidase ClbP recognizes its substrate and exploring the possible transporter partners of ClbP. In Chapter 4, I discuss how these results apply to the broader family of prodrug peptidases and can lead to future discoveries.