6IX3

The structure of LepI complex with SAM

Summary for 6IX3

• Entry DOI: 10.2210/pdb6ix3/pdb
• Descriptor: O-methyltransferase lepI, S-ADENOSYLMETHIONINE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: leporin, sam, o-methyltransferase, pericyclase, biosynthetic protein
• Biological source: Aspergillus flavus
• Total number of polymer chains: 2
• Total formula weight: 91815.70

Authors

Cai, Y.,Ohashi, M.,Hai, Y.,Tang, Y.,Zhou, J. (deposition date: 2018-12-09, release date: 2019-07-17, Last modification date: 2024-03-27)

Primary citation

Cai, Y.,Hai, Y.,Ohashi, M.,Jamieson, C.S.,Garcia-Borras, M.,Houk, K.N.,Zhou, J.,Tang, Y.
Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.
Nat.Chem., 11:812-820, 2019

PubMed Abstract: LepI is an S-adenosylmethionine (SAM)-dependent pericyclase that catalyses the formation of the 2-pyridone natural product leporin C. Biochemical characterization has shown that LepI can catalyse stereoselective dehydration to yield a reactive (E)-quinone methide that can undergo bifurcating intramolecular Diels-Alder (IMDA) and hetero-Diels-Alder (HDA) cyclizations from an ambimodal transition state, as well as a [3,3]-retro-Claisen rearrangement to recycle the IMDA product into leporin C. Here, we solve the X-ray crystal structures of SAM-bound LepI and in complex with a substrate analogue, the product leporin C, and a retro-Claisen reaction transition-state analogue to understand the structural basis for the multitude of reactions. Structural and mutational analysis reveals how nature evolves a classic methyltransferase active site into one that can serve as a dehydratase and a multifunctional pericyclase. Catalysis of both sets of reactions employs H133 and R295, two active-site residues that are not found in canonical methyltransferases. An alternative role of SAM, which is not found to be in direct contact with the substrate, is also proposed.

PubMed: 31332284
DOI: 10.1038/s41557-019-0294-x

Experimental method

X-RAY DIFFRACTION (2.13 Å)