8YHM
The structure of SdnG covalently binding with the cope rearrangement product
This is a non-PDB format compatible entry.
Summary for 8YHM
| Entry DOI | 10.2210/pdb8yhm/pdb |
| Descriptor | Sordarin/hypoxysordarin biosynthesis cluster protein G, (4S)-2-METHYL-2,4-PENTANEDIOL, (3aR,5R,5aR,8R,8aR,9aR)-5-methanoyl-8,9a-dimethyl-2-propan-2-yl-3,3a,4,5,5a,6,7,8,8a,9-decahydrocyclopenta[g]azulene-1-carboxylic acid, ... (4 entities in total) |
| Functional Keywords | diels alderase, norbornene, sordarin, cope rearrangement, biosynthetic protein |
| Biological source | Sordaria araneosa |
| Total number of polymer chains | 2 |
| Total formula weight | 33299.77 |
| Authors | |
| Primary citation | Sun, Z.,Zang, X.,Zhou, Q.,Ohashi, M.,Houk, K.N.,Zhou, J.,Tang, Y. Iminium Catalysis in Natural Diels-Alderase. Nat Catal, 8:218-228, 2025 Cited by PubMed Abstract: Iminium-catalyzed cycloaddition is one of the most prominent examples of organocatalysis, yet a biological counterpart has not been reported despite the wide-spread occurrence of iminium adducts in enzymes. Here, we present biochemical, structural, and computational evidence for iminium catalysis by the natural Diels-Alderase SdnG that catalyzes norbornene formation in sordarin biosynthesis. A Schiff base adduct between the ε-nitrogen of active site K127 and the aldehyde group of the enal dienophile was revealed by structural analysis and captured under catalytic conditions via borohydride reduction. This Schiff base adduct positions the substrate into near-attack conformation and decreases the transition state barrier of Diels-Alder cyclization by 8.3 kcal/mol via dienophile activation. A hydrogen bond network consisting of a catalytic triad is proposed to facilitate proton transfer required for iminium formation. This work establishes a new mode of catalysis for Diels-Alderases and points the way to the design of novel iminium based (bio)catalysts. PubMed: 40881614DOI: 10.1038/s41929-025-01294-w PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.72 Å) |
Structure validation
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