9P2U

Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with two AzaSAM and [4Fe-4S] cluster bound

Summary for 9P2U

• Entry DOI: 10.2210/pdb9p2u/pdb
• Descriptor: Radical S-adenosylmethionine methyltransferase NocN, S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE, IRON/SULFUR CLUSTER, ... (4 entities in total)
• Functional Keywords: radical s-adenosylmethionine enzyme nocathiacin nosiheptide, oxidoreductase
• Biological source: Nocardia sp. ATCC 202099
• Total number of polymer chains: 1
• Total formula weight: 47491.97

Authors

Wang, B.,Knox, H.L.,York, N.J.,Radle, M.I.,Silakov, A.,Booker, S.J. (deposition date: 2025-06-12, release date: 2026-06-03, Last modification date: 2026-06-24)

Primary citation

Wang, B.,Knox, H.L.,York, N.J.,Radle, M.I.,Silakov, A.,Booker, S.J.
Structural and Spectroscopic Basis for Catalysis by a Class C Radical S -Adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis.
J.Am.Chem.Soc., 148:22892-22902, 2026

PubMed Abstract: Nosiheptide (NOS) is a ribosomally synthesized and post-translationally modified peptide natural product that exhibits potent antibiotic activity against multiple bacterial pathogens. NOS features a core macrocyclic peptide containing thiazoles, dehydrated serine and threonine residues, and a 3-hydroxypyridine ring. In addition to the macrocycle, NOS possesses a side-ring system formed by a 3-methyl-2-indolic acid (MIA) bridge that connects to glutamyl and cysteinyl residues on the core peptide via ester and thioester linkages. This unique side-ring is installed by the class C radical -adenosylmethionine (SAM) methylase NosN. Here, we report three X-ray crystal structures of the NosN homologue, NocN, at resolutions of 1.40 Å, 1.84 Å, and 1.78 Å under anaerobic conditions, representing the first structural characterization of a class C radical SAM methylase. The structures reveal clear electron density for two bound SAM molecules. Remarkably, the C5' atom of SAM, which coordinates to the [FeS] cluster, lies 3.5 Å from the methyl group of SAM and is properly positioned for direct hydrogen atom abstraction. A structure containing a product mimic illustrates how NocN engages its substrate and identifies Tyr276 as a key catalytic residue. The structure further suggests that the sulfonium center of SAM may undergo epimerization to facilitate radical attack. Finally, electron paramagnetic resonance spectroscopy identifies a paramagnetic species consistent with the addition of the SAM-derived methylene radical to the MIA substrate.

PubMed: 42200415
DOI: 10.1021/jacs.6c03999

Experimental method

X-RAY DIFFRACTION (1.4 Å)