5ER8

Crystal structure of cyclization domain of Phomopsis amygdali fusicoccadiene synthase complexed with manganese ions and neridronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase.

Chen, M.Chou, W.K.Toyomasu, T.Cane, D.E.Christianson, D.W.

(2016) Acs Chem.Biol. 11: 889-899

  • DOI: 10.1021/acschembio.5b00960
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fusicoccin A is a diterpene glucoside phytotoxin generated by the fungal pathogen Phomopsis amygdali that causes the plant disease constriction canker, first discovered in New Jersey peach orchards in the 1930s. Fusicoccin A is also an emerging new l ...

    Fusicoccin A is a diterpene glucoside phytotoxin generated by the fungal pathogen Phomopsis amygdali that causes the plant disease constriction canker, first discovered in New Jersey peach orchards in the 1930s. Fusicoccin A is also an emerging new lead in cancer chemotherapy. The hydrocarbon precursor of fusicoccin A is the tricyclic diterpene fusicoccadiene, which is generated by a bifunctional terpenoid synthase. Here, we report X-ray crystal structures of the individual catalytic domains of fusicoccadiene synthase: the C-terminal domain is a chain elongation enzyme that generates geranylgeranyl diphosphate, and the N-terminal domain catalyzes the cyclization of geranylgeranyl diphosphate to form fusicoccadiene. Crystal structures of each domain complexed with bisphosphonate substrate analogues suggest that three metal ions and three positively charged amino acid side chains trigger substrate ionization in each active site. While in vitro incubations reveal that the cyclase domain can utilize farnesyl diphosphate and geranyl diphosphate as surrogate substrates, these shorter isoprenoid diphosphates are mainly converted into acyclic alcohol or hydrocarbon products. Gel filtration chromatography and analytical ultracentrifugation experiments indicate that full-length fusicoccadiene synthase adopts hexameric quaternary structure, and small-angle X-ray scattering data yield a well-defined molecular envelope illustrating a plausible model for hexamer assembly.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusicoccadiene synthase
A, B
363Phomopsis amygdaliMutation(s): 0 
Gene Names: PaFS (orf1)
Find proteins for A2PZA5 (Phomopsis amygdali)
Go to UniProtKB:  A2PZA5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NRD
Query on NRD

Download SDF File 
Download CCD File 
A, B
(6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid
C6 H17 N O7 P2
PUUSSSIBPPTKTP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.601α = 90.00
b = 142.601β = 90.00
c = 117.632γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SHELXCDphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references