Structural Biology of Nonribosomal Peptide Synthetases

Abstract

Summary The non-ribosomal peptide synthetases are modular enzymes that catalyze synthesis of important peptide products from a variety of standard and non-proteinogenic amino acid substrates. Within a single module are multiple catalytic domains that are responsible for incorporation of a single residue. After the amino acid is activated and covalently attached to an integrated carrier protein domain, the substrates and intermediates are delivered to neighboring catalytic domains for peptide bond formation or, in some modules, chemical modification. In the final module, the peptide is delivered to a terminal thioesterase domain that catalyzes release of the peptide product. This multi-domain modular architecture raises questions about the structural features that enable this assembly line synthesis in an efficient manner. The structures of the core component domains have been determined and demonstrate insights into the catalytic activity. More recently, multi-domain structures have been determined and are providing clues to the features of these enzyme systems that govern the functional interaction between multiple domains. This chapter describes the structures of NRPS proteins and the strategies that are being used to assist structural studies of these dynamic proteins, including careful consideration of domain boundaries for generation of truncated proteins and the use of mechanism-based inhibitors that trap interactions between the catalytic and carrier protein domains.

Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

“…Nonribosomal peptide synthetases (NRPSs) 2 are fascinating modular enzymes that use an assembly line architecture to produce important peptide natural products (1)(2)(3). During synthesis, the amino acid building blocks are bound to peptidyl carrier protein (PCP) domains that migrate between catalytic active sites for the requisite steps in the biosynthetic pathway.…”

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

“…Crystallographic and NMR studies of the NRPS domains provide insight into the PCP domain and the core catalytic domains [6 • ,7]. The PCP is composed of four α-helices, a structural and functional homolog of the carrier proteins that are involved in fatty acid and polyketide synthesis [8].…”

“…Several reviews have cataloged the structures of individual NRPS domains [6 • ,7,16]. Briefly, the condensation domains are composed of two lobes that surround an active site.…”

“…In particular, structures of the PCP with thioesterase domains [31,32] or with adenylation domains [33–35] or with the auxiliary epimerization domain [36] demonstrate the importance of the residues that surround the pantetheinylation site of the carrier protein for recognition by the catalytic domains. Given the inherent flexibility of multidomain NRPSs, several strategies have been adopted to structurally characterize these proteins [6 • ]. …”

Design, Preparation of 3‐Hydroxy Isoindolinone Cyclotripeptides, and the In Vitro Antitumor Activities Against Cervical Carcinoma HeLa Cells

“…Many linear peptides showed good biological activities in vitro but poor performance in the body. The main reasons were that the flexible linear peptide bonds were easily hydrolysed by various enzymes, and the end groups without protection were also quickly metabolized . Comparing with the linear peptides, cyclopeptides show better conformational stability and high enzymatic resistivity due to the rigid structure and natural protection of the C‐terminal and N‐terminal, thus leading to high receptor affinity and better bioactivities ; consequently, cyclic peptides research has been a growing research area, and a large number of them have been isolated from different natural sources .…”