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TitleFormation of the Diketopiperazine Moiety by a Distinct Condensation-Like Domain in Hangtaimycin Biosynthesis.
Journal, issue, pagesAngew Chem Int Ed Engl, Page e202421950, Year 2025
Publish dateFeb 25, 2025
AuthorsQing Mei / Shijuan Wu / Minghe Luo / Shunjia Ji / Jiayi Guo / Chuan Dong / Guo Sun / Jian Wang / Zixin Deng / Yi-Lei Zhao / Zhengyu Zhang / Yuhui Sun /
PubMed AbstractNon-ribosomal peptide synthetases (NRPSs) are key enzymes in pharmaceutical synthesis, with condensation (C) domains catalyzing amide bond formation between aminoacyl substrates. However, recent ...Non-ribosomal peptide synthetases (NRPSs) are key enzymes in pharmaceutical synthesis, with condensation (C) domains catalyzing amide bond formation between aminoacyl substrates. However, recent research has elucidated that the catalytic capabilities of C domains extend beyond the traditional formation of peptide bonds. In this study, we elucidate the cyclization mechanism of the NRPS-derived natural products hangtaimycin (HTM), characterized by the formation of a 2,5-diketopiperazine (DKP) moiety which involves an intramolecular vinylamide-mediated nucleophilic attack instead of an N-terminal amino group. This cyclization is catalyzed by a terminal condensation-like (C) domain within the NRPS enzyme HtmB2. We investigated the evolutionary specificity of the HtmB2-C within Streptomyces spectabilis CCTCC M2017417. Employing a multidisciplinary analytical approach, we have delineated the molecular underpinnings of DKP formation within the HTM biosynthesis. This process is facilitated by residue R2776, which modulates the formation of reactive species and stabilizes the amidate through electrostatic interactions. Besides, we found a positive correlation between the alkaline strength of the residue at position 2776 and the activity of HtmB2-C. Our study elucidates the formation mechanism of DKPs in NRPS-derived natural products, thereby bridging a critical gap in the structural and mechanistic understanding of this field.
External linksAngew Chem Int Ed Engl / PubMed:40000413
MethodsEM (single particle)
Resolution2.53 - 2.61 Å
Structure data

39711

8z0q

EMDB-39711, PDB-8z0q:
Cryo-EM structure of dimer HtmB2-CT
Method: EM (single particle) / Resolution: 2.6 Å

39713

8z0r

EMDB-39713, PDB-8z0r:
Cryo-EM structure of tetramer HtmB2-CT
Method: EM (single particle) / Resolution: 2.53 Å

39714

8z0s

EMDB-39714, PDB-8z0s:
Cryo-EM structure of trimer HtmB2-CT
Method: EM (single particle) / Resolution: 2.61 Å

Source
  • streptomyces (bacteria)
KeywordsBIOSYNTHETIC PROTEIN / Dimer of special condensation domain of NRPS / tetramer of special condensation domain of NRPS

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