7E5U

Crystal structure of Phm7

Summary for 7E5U

• Entry DOI: 10.2210/pdb7e5u/pdb
• Descriptor: Diels-Alderase, GLYCEROL, SULFATE ION, ... (5 entities in total)
• Functional Keywords: cyclase, diels-alderase, diels alder, [4+2], cycloaddition, biosynthetic protein
• Biological source: Pyrenochaetopsis sp.
• Total number of polymer chains: 3
• Total formula weight: 128229.61

Authors

Fujiyama, K.,Kato, N.,Kinugasa, K.,Hino, T.,Takahashi, S.,Nagano, S. (deposition date: 2021-02-20, release date: 2021-06-30, Last modification date: 2024-04-03)

Primary citation

Fujiyama, K.,Kato, N.,Re, S.,Kinugasa, K.,Watanabe, K.,Takita, R.,Nogawa, T.,Hino, T.,Osada, H.,Sugita, Y.,Takahashi, S.,Nagano, S.
Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.
Angew.Chem.Int.Ed.Engl., 60:22401-22410, 2021

PubMed Abstract: Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.

PubMed: 34121297
DOI: 10.1002/anie.202106186

Experimental method

X-RAY DIFFRACTION (1.62 Å)