Developing crosslinkers specific for epimerization domain in NRPS initiation modules to evaluate mechanism

• Published in: RSC chemical biology 2022-03, Vol.3 (3), p.312-319
• Main Authors: Kim, Woojoo E, Ishikawa, Fumihiro, Re, Rebecca N, Suzuki, Takehiro, Dohmae, Naoshi, Kakeya, Hideaki, Tanabe, Genzoh, Burkart, Michael D
• Format: Article
• Language: English
• Subjects: Chemistry
• ISSN: 2633-0679; 2633-0679
• DOI: 10.1039/d2cb00005a

Nonribosomal peptide synthetases (NRPSs) are complex multi-modular enzymes containing catalytic domains responsible for the loading and incorporation of amino acids into natural products. These unique molecular factories can produce peptides with nonproteinogenic d -amino acids in which the epimerization (E) domain catalyzes the conversion of l -amino acids to d -amino acids, but its mechanism remains not fully understood. Here, we describe the development of pantetheine crosslinking probes that mimic the natural substrate l -Phe of the initiation module of tyrocidine synthetase, TycA, to elucidate and study the catalytic residues of the E domain. Mechanism-based crosslinking assays and MALDI-TOF MS were used to identify both H743 and E882 as the crosslinking site residues, demonstrating their roles as catalytic bases. Mutagenesis studies further validated these results and allowed the comparison of reactivity between the catalytic residues, concluding that glutamate acts as the dominant nucleophile in the crosslinking reaction, resembling the deprotonation of the C α -H of amino acids in the epimerization reaction. The crosslinking probes employed in these studies provide new tools for studying the molecular details of E domains, as well as the potential to study C domains. In particular, they would elucidate key information for how these domains function and interact with their substrates in nature, further enhancing the knowledge needed to assist combinatorial biosynthetic efforts of NRPS systems to produce novel compounds. Epimerization (E) domain mechanism in initiaion modules of NRPSs studied using pantetheine analog crosslinking probes containing sulfonyl warheads that target domain's catalytic residues (His and Glu).