6VYD | pdb_00006vyd

Terpenoid Cyclase FgGS in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium cation

• PDB DOI: https://doi.org/10.2210/pdb6VYD/pdb

• Classification: LYASE
• Organism(s): Fusarium graminearum PH-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-26 Released: 2020-07-08 
• Deposition Author(s): Herbst-Gervasoni, C.J., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Discovery of the cryptic function of terpene cyclases as aromatic prenyltransferases.

He, H., Bian, G., Herbst-Gervasoni, C.J., Mori, T., Shinsky, S.A., Hou, A., Mu, X., Huang, M., Cheng, S., Deng, Z., Christianson, D.W., Abe, I., Liu, T.

(2020) Nat Commun 11: 3958-3958

• PubMed: 32769971 
• DOI: https://doi.org/10.1038/s41467-020-17642-2
• Primary Citation Related Structures: 
  6VYD, 6W26


• PubMed Abstract: 
  

  Catalytic versatility is an inherent property of many enzymes. In nature, terpene cyclases comprise the foundation of molecular biodiversity as they generate diverse hydrocarbon scaffolds found in thousands of terpenoid natural products. Here, we report that the catalytic activity of the terpene cyclases AaTPS and FgGS can be switched from cyclase to aromatic prenyltransferase at basic pH to generate prenylindoles. The crystal structures of AaTPS and FgGS provide insights into the catalytic mechanism of this cryptic function. Moreover, aromatic prenyltransferase activity discovered in other terpene cyclases indicates that this cryptic function is broadly conserved among the greater family of terpene cyclases. We suggest that this cryptic function is chemoprotective for the cell by regulating isoprenoid diphosphate concentrations so that they are maintained below toxic thresholds.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan.
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323, USA.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104-6323, USA. [e-mail].
Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan. [e-mail].
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].
Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75 kDa 
• Atom Count: 5,471 
• Modeled Residue Count: 595 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpenoid cyclase FgGS	A, B	316	Fusarium graminearum PH-1	Mutation(s): 0  Gene Names: FGRAMPH1_01T04331 EC: 4.2.3
UniProt
Find proteins for I1RDR8 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)) Explore I1RDR8  Go to UniProtKB:  I1RDR8

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTM (Subject of Investigation/LOI)	CA [auth B], I [auth A]	N-benzyl-N,N-diethylethanaminium C13 H22 N VBQDSLGFSUGBBE-UHFFFAOYSA-N
POP	BA [auth B], H [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A], U [auth B], V [auth B], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.599	α = 90
b = 87.26	β = 90
c = 163.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Herbst-Gervasoni, C.J., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM56838

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Database references, Derived calculations
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary