threonine, or cysteine sidechain with the amide-N, thereby forming oxazolidines 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) hydrolyzes the completed polypeptide chain from the PCP-domain of the previous module, thereby often forming cyclic amides (lactams) or cyclic esters (lactones). Also, the peptide can be released by an R-domain that 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 operons or gene clusters. Priming and deblocking To become functional, the 4'-phospho-pantetheine sidechain of acyl-CoA molecules has to be attached to the PCP-domain by 4'PP transferases (Priming) and the S-attached acyl group has to be removed by specialized associated thioesterases (TE-II) (Deblocking). Substrate specificities Most domains have a very broad substrate 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, and rational protein design has yielded methodologies to computationally switch the specificities of A-domains. 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. Computational methods, such as SANDPUMA and NRPSpredictor2, have been developed to predict substrate specificity from DNA or protein sequence data. Mixed with polyketides Due to the similarity with polyketide synthases (PKS), many secondary metabolites are, in fact, fusions of NRPs and polyketides. In essence, this occurs when PK modules follow NRP modules, and vice versa. Although there is high degree of similarity between the Carrier (PCP/ACP) domains of both types of synthetases, the mechanism of condensation is different from a chemical standpoint: PKS, carbon-carbon bond formation through Claisen condensation reaction NRPs, the C domain catalyzes the amide bond formation between the amino acid it adds to the chain (on the PCP of one module) and the nascent peptide(on the PCP of the next module). See also Epothilone Esterase Ribosomally synthesized and post-translationally modified peptides References Further reading Molecular biology Enzymes Glycopeptide antibiotics Antibiotics Peptides