Structural insight into the necessary conformational changes of modular nonribosomal peptide synthetases

Abstract

Nonribosomal peptide synthetases (NRPSs) catalyze the assembly line biosynthesis of peptide natural products that play important roles in microbial signaling and communication. These multidomain enzymes use an integrated carrier protein that delivers the growing peptide to the catalytic domains, requiring coordinated conformational changes that allow the proper sequence of synthetic steps. Recent structural studies of NRPSs have described important conformational states and illustrate the critical role of a small subdomain within the adenylation domains. This subdomain alternates between catalytic conformations and also serves as a linker domain, providing further conformational flexibility to enable the carrier to project from the core of NRPS. These studies are described along with remaining questions in the study of the structural dynamics of NRPSs.

Nonribosomal peptide synthetase biosynthetic clusters of ESKAPE pathogens

“…Because the NRPS module can adopt the conformation to catalyze simultaneously peptide bond formation in the condensation domain while also catalyzing substrate adenylation within the adenylation domain, the enzyme is able to prime the next cycle of synthesis while the PCP is engaged with the condensation domain. 51 In comparison to the the magnificent rate enhancements of many enzymes, the modular NRPS enzymes are rather slow, with turnover constants ranging from 1 to 100 turnovers per minute. 30, 83, 84 This is true for many secondary metabolites and perhaps reflects limited, or none at all, evolutionary pressure to accelerate natural product biosynthesis.…”

Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations

“…An NRPS module is defined as the set of domains that together possess all the activities required to add one acyl residue to the nascent nonribosomal peptide chain. [44][45][46][47][48] A standard elongation module includes a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP) domain arranged as C-A-PCP ( Figure 1b). (Note that, the PCP domain is equally commonly called the T domain.…”

“…59,93,94 Furthermore, the broader structural view of NRPSs is starting to take shape with several recent studies of didomains, modules, or supra-modular NRPSs showing how domains and modules coordinate in peptide synthesis. 7,34,44,45,56,57,83,85,86,90,[95][96][97][98][99][100][101][102] 2 | DEPSIPEPTIDES Nonribosomal depsipeptides are compounds with both ester and amide bonds in their structures 103 (Figure 1a). They are common natural products with a vast array of biological activities of medical and industrial relevance.…”

“…NRPSs synthesize peptides using a modular synthetic scheme that resembles an assembly line. An NRPS module is defined as the set of domains that together possess all the activities required to add one acyl residue to the nascent nonribosomal peptide chain 44–48 . A standard elongation module includes a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP) domain arranged as C‐A‐PCP (Figure 1b).…”

“…Another release strategy is reductive release, where R domains are termination domains that release the thioester peptide as an aldehyde or an alcohol using NADH or NADPH as a cofactor 59,93,94 . Furthermore, the broader structural view of NRPSs is starting to take shape with several recent studies of didomains, modules, or supra‐modular NRPSs showing how domains and modules coordinate in peptide synthesis 7,34,44,45,56,57,83,85,86,90,95–102 …”