X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis

Non-ribosomal peptide synthetase (NRPS) mega-enzyme complexes are modular assembly lines that are involved in the biosynthesis of numerous peptide metabolites independently of the ribosome¹. The multiple interactions between catalytic domains within the NRPS machinery are further complemented by additional interactions with external enzymes, particularly focused on the final peptide maturation process. An important class of NRPS metabolites that require extensive external modification of the NRPS-bound peptide are the glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin^{2, 3}. These clinically relevant peptide antibiotics undergo cytochrome P450-catalysed oxidative crosslinking of aromatic side chains to achieve their final, active conformation^{4, 5, 6, 7, 8, 9, 10, 11, 12}. However, the mechanism underlying the recruitment of the cytochrome P450 oxygenases to the NRPS-bound peptide was previously unknown. Here we show, through in vitro studies, that the X-domain^{13, 14}, a conserved domain of unknown function present in the final module of all GPA NRPS machineries, is responsible for the recruitment of oxygenases to the NRPS-bound peptide to perform the essential side-chain crosslinking. X-ray crystallography shows that the X-domain is structurally related to condensation domains, but that its amino acid substitutions render it catalytically inactive. We found that the X-domain recruits cytochrome P450 oxygenases to the NRPS and determined the interface by solving the structure of a P450–X-domain complex. Additionally, we demonstrated that the modification of peptide precursors by oxygenases in vitro—in particular the installation of the second crosslink in GPA biosynthesis—occurs only in the presence of the X-domain. Our results indicate that the presentation of peptidyl carrier protein (PCP)-bound substrates for oxidation in GPA biosynthesis requires the presence of the NRPS X-domain to ensure conversion of the precursor peptide into a mature aglycone, and that the carrier protein domain alone is not always sufficient to generate a competent substrate for external cytochrome P450 oxygenases.




Domain labels for NRPS proteins (Tcp9–12): A, adenylation (selected amino acids indicated above the module: Hpg, 4-hydroxyphenylglycine; Dpg, 3,5-dihydroxyphenylglycine); C, condensation; E, epimerization; T, thiolation/peptidyl carrier protein (PCP); TE, thioesterase; X, domain of unknown function. Essential P450-catalysed aglycone rigidification takes place through crosslinking of aromatic side chains (OxyA–C, OxyE). Each crosslinking reaction is performed by a specific Oxy protein, with the products of each Oxy protein indicated schematically; standard ring nomenclature is indicated on the teicoplanin aglycone in red lettering.

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