Nonribosomal peptide 1118963 207353297 2008-04-22T13:28:43Z 212.201.75.102 /* Examples */ '''Nonribosomal peptide'''s (NRP) are a class of [[peptide]] [[secondary metabolites]], usually produced by [[microorganism]]s like [[bacterium|bacteria]] and [[fungi]]. Nonribosomal peptides are also found in higher organisms, such as [[nudibranch]]s, but are thought to be made by bacteria [[commensurism|inside]] these organisms.{{Fact|date=December 2007}} While there exist a wide range of peptides that are not synthesized by [[ribosome]]s, the term ''nonribosomal peptide'' typically refers to a very specific set of these as discussed in this article. Nonribosomal peptides are synthesized by '''nonribosomal peptide synthetases''', which, unlike the [[ribosome]]s, are independent of [[messenger RNA]]. Each nonribosomal peptide synthetase can synthesize only one type of peptide. Nonribosomal peptides often have a [[cyclic compound|cyclic]] and/or branched structures, can contain non-[[proteinogenic]] [[amino acid]]s including <small>D</small>-amino acids, carry modifications like ''[[Nitrogen|N]]''-methyl and ''N''-formyl groups, or are [[Glycosylation|glycosylated]], [[Acylation|acylated]], [[Halogenation|halogenated]], or [[Hydroxylation|hydroxylated]]. Cyclization of amino acids against the peptide "backbone" is often performed, resulting in [[oxazoline]]s and [[thiazoline]]s; these can be further oxidized or reduced. On occasion, dehydration is performed on [[serine]]s, resulting in [[dehydroalanine]]. This is just a sampling of the various manipulations and variations that nonribosomal peptides can perform. Nonribosomal peptides are often [[dimer]]s or [[trimer]]s of identical sequences chained together or cyclized, or even branched. Nonribosomal peptides are a very diverse family of natural products with an extremely broad range of biological activities and pharmacological properties. They are often toxins, [[siderophore]]s, or [[pigment]]s. Nonribosomal peptide [[antibiotic]]s, [[cytostatic]]s, and [[immunosuppressant]]s are in commercial use. ==Examples== * [[Antibiotic]]s ** [[Actinomycin]] ** [[Bacitracin]] ** [[Vancomycin]] ** [[Tyrocidine]] ** [[Gramicidin]] ** [[Thiostrepton]] * [[Antibiotic]] precursors ** [[Penicillin|ACV-Tripeptide]] * [[Cytostatic]]s ** [[Epothilone]] ** [[Bleomycin]] * [[Immunosuppressant]]s ** [[Ciclosporin]] (Cyclosporine A) * [[Siderophore]]s ** [[Enterobactin]] ** [[Myxochelin A]] * [[Pigment]]s ** [[Indigodin]] * [[Toxin]]s ** [[Microcystin]]s and ** [[Nodularin]]s, [[cyanotoxin]]s from [[cyanobacteria]]. ** [[Alpha-amanitin|α-amanitine]] from ''[[Death Cap|Amanita phalloides]]'' (Death Cap) * Nitrogen storage polymers ** [[Cyanophycin]] - produced by some [[cyanobacteria]] == Biosynthesis == Nonribosomal peptides are synthesized by one or more specialized nonribosomal peptide-synthetase (NRPS) [[enzyme]]s. The NRPS genes for a certain peptide are usually organized in one [[operon]] in bacteria and in [[gene cluster]]s in [[eukaryote]]s. The enzymes are organized in modules that are responsible for the introduction of one additional amino acid. Each module consists of several [[Domain (biology)|domain]]s with defined functions, separated by short spacer regions of about 15 amino acids. The [[biosynthesis]] of nonribosomal peptides shares characteristics with the [[polyketide]] and [[fatty acid]] biosynthesis. Due to these structural and mechanistic similarities, some nonribosomal peptide synthetases contain [[polyketide|polyketide synthase]] modules for the insertion of [[acetate]] or [[propionic acid|propionate]]-derived subunits into the peptide chain. === Modules === The order of modules and domains of a complete nonribosomal peptide synthetase is as follows: * ''Initiation'' or ''Starting'' module: [F/NMe]-A-PCP- * ''Elongation'' or ''Extending'' modules: -(C/Cy)-[NMe]-A-PCP-[E]- * ''Termination'' or ''Releasing'' module: -(TE/R) (Order: [[N-terminus]] to [[C-terminus]]; ''[]'': optionally; ''()'': alternatively) === Domains === * F: Formylation (optional) * A: Adenylation (required in a module) * PCP: Thiolation and Peptide Carrier Protein with attached 4'-phospho-pantethein (required in a module) * C: Condensation forming the amide bond (required in a module) * Cy: Cylization into thiazoline or oxazolines (optional) * Ox: Oxidation of thiazolines or oxazolines to thiazoles or oxazoles (optional) * Red: Reduction of thiazolines or oxazolines to thiazolidines or oxazolidines (optional) * E: Epimerization into D-amino acids (optional) * TE: Termination by a thio-esterase (only found once in a NRPS) * R: Reduction to terminal aldehyde or alcohol (optional) === Starting stage === * Loading: The first amino acid is activated with [[adenosine triphosphate|ATP]] as a mixed [[acyl]]-[[phosphoric acid]] [[anhydride]] with [[adenosine monophosphate|AMP]] by the A-domain and loaded onto the [[serine]]-attached 4'-phospho-[[pantethein]] (4'PP) sidechain of the PCP-domain catalyzed by the PCP-domain (thiolation) . * Sometimes the amino group of the bound amino acid is [[Formylation|formylated]] by an F-domain or [[Methylation|methylated]] by an NMe-domain. ===Elongation stages=== * Loading: Analogous to the starting stage, each module loads its specific amino acid onto its PCP-domain. * [[Condensation]]: The C-domain catalyzes the [[amide]] [[Chemical bond|bond]] formation between the [[thioester]] group of the growing peptide chain from the previous module with the amino group of the current module. The extended peptide is now attached to the current PCP-domain. * [[Condensation]]-[[Cyclization]]: Sometimes the C-domain is replaced by a Cy-domain, which, in addition to the amide bond formation, catalyzes the reaction of the [[serine]], [[threonine]], or [[cysteine]] sidechain with the amide-''[[Nitrogen|N]]'', thereby forming [[oxazolidine]]s and [[thiazolidine]], respectively. * [[Epimerization]]: Sometimes an E-domain epimerizes the innermost amino acid of the peptide chain into the [[D-configuration]]. * This cycle is repeated for each elongation module. === Termination stage === * Termination: The TE-domain (thio-esterase domain) [[Hydrolysis|hydrolyzes]] the completed polypeptide chain from the ACP-domain of the previous module, thereby often forming cyclic amides ([[lactam]]s) or cyclic [[ester]]s ([[lactone]]s). * Also, the peptide can be released by an R-domain that [[Redox|reduces]] the thioester bond to terminal [[aldehyde]] or [[alcohol]]. === Processing=== The final peptide is often modified, e.g., by [[glycosylation]], [[acylation]], [[halogenation]], or [[hydroxylation]]. The responsible enzymes are usually associated to the synthetase complex and their genes are organized in the same [[operon]]s or [[gene cluster]]s. ===Priming and Deblocking=== To become functional, the 4'-phospho-pantethein sidechain of [[CoA|acyl-CoA]] molecules has to be attached to the PCP-domain by 4'PP transferases (Priming) and the [[Sulfur|S]]-attached [[acyl]] group has to be removed by specialized associated thioesterases (TE-II) (Deblocking). === Substrate specificities === Most domains have a very broad [[substrate (biochemistry)|substrate]] [[Specificity (tests) |specificity]] and usually only the A-domain determines which amino acid is incorporated in a module. Ten amino acids that control substrate specificity and can be considered the '[[codons]]' of nonribosomal peptide synthesis have been identified. The condensation C-domain is also believed to have substrate specificity, especially if located behind an epimerase E-domain-containing module where it functions as a 'filter' for the epimerized [[isomer]]. == Mixed with Polyketides == Due to the similarity with polyketide synthetases (PKS), many secondary metabolites are, in fact, fusions of NRPs and polyketides. In essencce, this occurs when PK modules follow NRP modules, and vice versa. Although there is high degree of similarity between the PCP domains of both types of sythetases, the mechanism of condensation is different from a chemical standpoint (claisen vs. transamidation). * [[Epothilone]] == See also == * [[Esterase]] * [[Polyketide]] == Literature == * "Nonribosomal peptides: from genes to products" by Dirk Schwarzer, Robert Finking, and Mohamed A. Marahiel in ''Nat. Prod. Rep.'' 20(3):275-287 (2003) [http://dx.doi.org/10.1039/b111145k DOI: 10.1039/b111145k] * "Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis" by Mohamed A. Marahiel, Torsten Stachelhaus, and Henning D. Mootz in ''Chem. Rev.'' 97(7):2651-2673 (1997) [http://dx.doi.org/10.1021/cr960029e DOI: 10.1021/cr960029e] [[Category:Molecular biology]] [[Category:Enzymes]] [[Category:Glycopeptide antibiotics]] [[Category:Antibiotics]] [[Category:Peptides]] [[ja:非リボソームペプチド]] [[pl:Peptyd nierybosomalny]]