6IX7 | pdb_00006ix7

The structure of LepI C52A in complex with SAH and substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb6IX7/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Aspergillus flavus NRRL3357
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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, National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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 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: 
• State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.
Department of Chemistry and Biochemistry, Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA.
Department of Chemistry and Biochemistry, Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA. [e-mail].
State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. [e-mail].
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  (Explore in 3D)
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: 93.06 kDa 
• Atom Count: 7,055 
• Modeled 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): 1  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], J [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
B0L	D [auth A], K [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	G [auth A], H [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.281	α = 90
b = 62.133	β = 113.66
c = 113.591	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	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
National Science Foundation (China)	China	91856202

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
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description