Nonribosomal peptide synthetase NRPS

As beta-lactam antibiotics continue to be a major contributor to human health preservation, research on the biosynthesis of penicillin, an almost ancient drug, continues to open up roads to new technologies and perspectives. The provision of precursor peptides to be transformed enzymatically with chemically unachieved efficiency into mono- or bicyclic antibiotics has been termed by Jack Baldwin and colleagues the irreversible commitment of metabolic carbon to the secondary metabolism [1]. The synthesis of such peptides is indeed performed by a remarkable class of synthetases which, in contrast to the protein-synthesizing machinery, have been termed a nonribosomal system or nonribosomal peptide synthetases (NRPS) [2]. These peptide synthetases have been shown to catalyze the irreversible synthesis of peptides differing both in sequence and stmctural variability, thus extending the scope of directly gene-encoded poly-... 

A similar modular type arrangement of activities is present in the nonribosomal peptide synthetases (NRPS). Several examples have been described that use a hybrid PKS-NRPS system to synthesize epothiolones,370 rifamycin,371 and C-1027372 with reviews on these hybrid systems being described.373 374... 

Fungi and bacteria produce various phytotoxic cyclic peptides using nonribosomal peptide synthetase (NRPS).308 Similar to modular organization of PKS, NRPS consists of several modules containing condensation (C), adenylation (A), and thiolation (T) domains. 

Like many other peptide antibiotics—including the lipopeptides A54145, CDA, amphomycin, laspartomycin and friulimicin daptomycin is produced by a nonribosomal peptide synthetase (NRPS) mechanism.3,6,14 It is produced in fermentation by S. roseosporus by feeding decanoic acid, which is incorporated as the fatty acid starter unit. Much has been learned about the biosynthetic process by fermentation feeding studies and by the analysis of the daptomycin biosynthetic genes.3,6,14,15... 

Fig. 9.11. Organizational overview and summary of protein engineering efforts on the poly-ketide synthetase (PKS) and nonribosomal peptide synthetase (NRPS) framework, a) In both systems, the complete synthetases consist of multiple subunits encoded on individual genes. The subunits themselves are divided in modules which each catalyze the addition of one acylbuilding block (PKS) or amino acid (NRPS). The minimal module for PKSs is made up of three domains - a keto synthase (KS), an acyl transferase (AT), and an acyl carrier protein (ACP). In addition, modules can contain up to three modifying domains to derivatize (S-carbons on the...

Several of these genes vere deduced to program for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymes as well as novel tailoring enzymes, including those that create the various unusual functional groups in jamaicamide A. 

Many important therapeutics, in use in clinics today, are biosynthesized by the nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) paradigm. For example, many of the antibiotics (penicillin, cephalosporin, vancomycin, erythromycin, etc.), immunosuppressors (cyclosporine, rapamycin), antiviral agents (luzopeptin A), antitumor agents (bleomycin), and toxins (thaxtomin) are NRPS and PKS derived.20-22 Figure 1 displays a small selection of natural products that are NRPS and PKS derived and illustrates the diversity of molecular structures generated by these biosynthetic paradigms. 

The second mechanism is performed by nonribosomal peptide synthetases (NRPS) which are multienzyme complexes consisting of four domains [2, 3]. 

Figure 6 Organization of the polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system for which ketosynthase (KS) and colinearity rule-based predictions have assisted the discovery of the thailandamides from Burkholderia thailandensis. The different proteins are highlighted in different colors and each module is boxed. The experimentally determined structure of thailandamide A is shown at the bottom of the figure.

Biochemical analyses of the assembly of the ergopeptines in C. purpurea have shown that ergopeptines are the products of an enzyme complex consisting of two nonribosomal peptide synthetase (NRPS) subunits (55). NRPSs generally exhibit modular structures, with each module responsible for the addition of an amino acid or other substituent. A typical module includes an adenylation (A-) domain, a thiolation (T-) domain (also known as a peptidyl carrier protein domain), and a condensation (C-) domain. The A-domain specifies the amino acid or other carboxylic acid substituent, and activates by it by an ATP-dependent adenylation reaction. The activated substituent then forms a thioester with the 4 -phosphopan-tetheine prosthetic group in the adjacent T-domain. Finally, the C-domain links the substituent to the next substituent in the chain. In a multimodular NRPS protein, the order in which substituents are added corresponds to the arrangement of modules from its N- to C terminus. 

The biosynthesis of pyridomycin was first studied by Ogawara. Isotope labeling studies demonstrated that it might involve the assembly of the backbone by a hybrid nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) system using 3-hydroxypicolinic acid (3-HPA) as the starting unit (Figure 6.15) [67]. 

Figure 7.60 Schematic representation of the organization of the rifamycin B gene cluster and modular organization of the rifamycin PKS leading to proansamycin X. A, T adenylation and thiolation domains of nonribosomal peptide synthetases (NRPS) AGP, acyl carrier protein KS, ketosynthase AT, acyltransferase KR, ketoreductase DH, dehydratase. An asterisk indicates nonfunctional or inactive domains.

The introduction of two dimensional (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignment is an active yet recent research topic in bioinformatics. Here we used a 2D artificial representation (four color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. 

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