6IX5

The structure of LepI complex with SAM and its substrate analogue

• PDB DOI:  https://doi.org/10.2210/pdb6IX5/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Aspergillus flavus NRRL3357
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-09 Released: 2019-07-17 
• Deposition Author(s): Cai, Y., Ohashi, M., Hai, Y., Tang, Y., Zhou, J.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.

Cai, Y., Hai, Y., Ohashi, M., Jamieson, C.S., Garcia-Borras, M., Houk, K.N., Zhou, J., Tang, Y.

(2019) Nat Chem 11: 812-820

• PubMed: 31332284 
• DOI: https://doi.org/10.1038/s41557-019-0294-x
• Primary Citation of Related Structures:  
  6IX3, 6IX5, 6IX7, 6IX8, 6IX9


• 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.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 93.97 kDa 
• Atom Count: 7,501 
• Modelled Residue Count: 778 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase lepI	A, B	405	Aspergillus flavus NRRL3357	Mutation(s): 0  Gene Names: lepI, AFLA_066940 EC: 2.1.1
UniProt
Find proteins for B8NJH3 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167)) Explore B8NJH3  Go to UniProtKB:  B8NJH3

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], V [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
B0L	D [auth A], W [auth B]	4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one C22 H25 N O3 YJRUCHHILBSMDC-GGXDDXSJSA-N
GOL	S [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	U [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	EA [auth B], FA [auth B], GA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	HA [auth B], T [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.051	α = 90
b = 62.239	β = 113.15
c = 114.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Cai, Y., Ohashi, M., Hai, Y., Tang, Y., Zhou, J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB20000000

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references
• Version 1.2: 2019-09-11
  Changes: Data collection, Database references