9KM6

The crystal structure of XhnM1 and its inhibitor sinefugin

Summary for 9KM6

• Entry DOI: 10.2210/pdb9km6/pdb
• Descriptor: Class I SAM-dependent methyltransferase, SINEFUNGIN, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: complex, inhibitor, sinefugin, transferase
• Biological source: Streptomyces xinghaiensis
• Total number of polymer chains: 2
• Total formula weight: 65389.38

Authors

Wu, L.,Tang, G.L. (deposition date: 2024-11-15, release date: 2025-08-20)

Primary citation

Nie, Q.Y.,Fang, S.Q.,Wu, L.,Gao, R.Q.,Hu, Y.,Ding, D.,Pan, H.X.,Pei, Z.F.,He, J.B.,Zhou, Q.,Chen, Z.H.,Hou, X.F.,Zhao, X.Q.,Tang, G.L.
Targeted Discovery and Characterization of Type-II PKS-NRPS Hybrid DNA-Alkylating Antibiotics.
Angew.Chem.Int.Ed.Engl., :e202512820-e202512820, 2025

PubMed Abstract: DNA alkylating natural products usually exhibit diverse bioactivity and serve as a crucial source of drug leads. Here, we employed genome mining guided by HTH-42 superfamily resistance gene to precisely discover a new class of DNA-alkylating antibiotics, xinghaicarcins, from Streptomyces xinghaiensis. They possess an intricate spiro-epoxide-bearing spiroketal heptacyclic scaffold fused with a pipecolic acid, assembled by a type II polyketide synthase-nonribosomal peptide synthetase hybrid system. An aminotransferase XhnB1 and a methyltransferase XhnM are identified to catalyze the formation of N-methylated pipecolic acid building block, leading to the completion of the polyketide-peptide backbone. The identification of XhnM facilitated stereochemical determination of six chiral centers in xinghaicarcins by co-crystallization. Notably, xinghaicarcins exhibit potent antibacterial activity against drug-resistant pathogens and cytotoxicity against multiple cancer cell lines. Additionally, the HTH-42 superfamily resistant protein, XhnU2, was characterized to mitigate xinghaicarcin-induced genotoxicity. This work provides comprehensive insights into structure, biosynthesis, bioactivity, and self-resistance mechanisms of xinghaicarcins, expanding diversity of DNA alkylating natural products.

PubMed: 40761108
DOI: 10.1002/anie.202512820

Experimental method

X-RAY DIFFRACTION (2.00003128301 Å)