Structural characterization of a PCP–R didomain from an archaeal nonribosomal peptide synthetase reveals novel interdomain interactions

Sandesh Deshpande¹, Eric Altermann^2,3, Vijayalekshmi Sarojini⁴, J. Shaun Lott¹, T. Verne Lee¹

School of Biological Sciences, University of Auckland, Auckland, New Zealand.

Abstract

Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that produce a wide range of bioactive peptides, such as siderophores, toxins, and antibacterial and insecticidal agents. NRPSs are dynamic proteins characterized by extensive interdomain communications as a consequence of their assembly-line mode of synthesis. Hence, crystal structures of multidomain fragments of NRPSs have aided in elucidating crucial interdomain interactions that occur during different steps of the NRPS catalytic cycle. One crucial yet unexplored interaction is that between the reductase (R) domain and the peptide carrier protein (PCP) domain. R domains are members of the short-chain dehydrogenase/reductase family and function as termination domains that catalyze the reductive release of the final peptide product from the terminal PCP domain of the NRPS. Here, we report the crystal structure of an archaeal NRPS PCP–R didomain construct. This is the first NRPS R domain structure to be determined together with the upstream PCP domain and is also the first structure of an archaeal NRPS to be reported. The structure reveals that a novel helix–turn–helix motif, found in NRPS R domains but not in other short-chain dehydrogenase/reductase family members, plays a major role in the interface between the PCP and R domains. The information derived from the described PCP–R interface will aid in gaining further mechanistic insights into the peptide termination reaction catalyzed by the R domain and may have implications in engineering NRPSs to synthesize novel peptide products.

Keywords: nonribosomal peptide synthetase, reductase domain, peptide carrier protein domain, short-chain dehydrogenase/reductase, X-ray crystallography, structure–function, protein–protein interaction, archaea, peptide biosynthesis.