Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains

Abstract

The analysis presented allows the specificity of A domains of unknown function (e.g. from polymerase chain reaction amplification or genome sequencing) to be predicted. Furthermore, it provides a rational framework for altering of A domain specificity by site-directed mutagenesis, which has significant potential for engineering the biosynthesis of novel natural products.

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

“…KS9, associated with KSs elongating chains of amino acid residues, consistent with its position C-terminal to a second NRPS module (8a), was the only other KS with predictable function. An analysis of residues lining the substrate pocket of the adenylation domain, known as the nonribosomal code (27,28), returned a perfect match to proline-activating domains (SI Appendix, Table S5). In the absence of diagnostic downstream KS domains, the portions of the polyketide generated by modules 5, 7, and 9 were predicted using classical PKS colinearity rules (29), although they often apply poorly to trans-AT PKSs.…”

Amphiphilic siderophore production by oil-associating microbes

“…The identity of the amino acid to be incorporated can be predicted based on the sequence of a ten 15 amino acid region in the adenylation domain binding pocket. 41,42 The predicted functions of the putative amphibactin biosynthetic genes are summarized in Table 2 and the biosynthetic gene map is organized in Fig. 3A.…”

Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338

“…Comparison of the NRPS sequences with those of authentic NRPSs allows the probable enzyme complement of each multienzyme to be deduced and tentative deductions to be drawn as to the likely structure of the peptide product (Supplementary Table 5 online). Our predictions are based on a structure-based ''specificity code'' 25 , which, together with later refinements 26,27 , provides useful clues to the nature of the amino acid introduced at each stage. This will certainly be useful in guiding genome mining for the natural products of the nrps genes of S. erythraea, but it is important to stress that there are now multiple examples where the compounds isolated are different from those predicted by such methods (see, for example, the recent substantial correction of the structure of the siderophore coelichelin from S. coelicolor 28 ).…”