6B02

Crystal structure of CfFPPS2 (apo form), a lepidopteran type-II farnesyl diphosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design.

Picard, M.E.Nisole, A.Beliveau, C.Sen, S.Barbar, A.Shi, R.Cusson, M.

(2017) Insect Biochem. Mol. Biol. 92: 84-92

  • DOI: 10.1016/j.ibmb.2017.11.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Farnesyl diphosphate synthase (FPPS) is an enzyme from the class of short chain (E)-prenyltransferases that catalyzes the condensation of two molecules of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) to generate the C1 ...

    Farnesyl diphosphate synthase (FPPS) is an enzyme from the class of short chain (E)-prenyltransferases that catalyzes the condensation of two molecules of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) to generate the C15 product FPP. In insects, FPPS plays a key role in the biosynthesis of the morphogenetic and gonadotropic "juvenile hormone" (JH). Lepidopteran genomes encode two very distinct FPPS paralogs, one of which ("type-II") is expressed almost exclusively in the JH-producing glands, the corpora allata. This paralog has been hypothesized to display structural features that enable the binding of the bulkier precursors required for the biosynthesis of lepidopteran ethyl-branched JHs. Here, we report on the first crystal structures of an insect FPPS solved to date. Apo, ligand-bound, and inhibitor-bound structures of type-II FPPS (FPPS2) from the spruce budworm, Choristoneura fumiferana (Order: Lepidoptera), were obtained. Comparison of apo and inhibitor-bound enzymes revealed differences in both inhibitor binding and structural plasticity of CfFPPS2 compared to other FPPSs. Our data showed that IPP is not essential to the closure of the C-terminal tail. Ortho-substituted pyridinium bisphosphonates, previously shown to inhibit CfFPPS2, bound to the allylic site, as predicted; however, their alkyl groups were oriented towards the homoallylic binding site, with the bulkier propyl-substituted inhibitor penetrating deeply into the IPP binding pocket. The current study sheds light on the structural basis of substrate specificity of type-II FPPS of the spruce budworm. Through a comparison with other inhibitor-bound FPPSs, we propose several approaches to improve inhibitor selectivity and potency.


    Organizational Affiliation

    Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada. Electronic address: marie-eve.picard.8@ulaval.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl diphosphate synthase
A, B
341Choristoneura fumiferanaMutation(s): 0 
Find proteins for Q1XAB1 (Choristoneura fumiferana)
Go to UniProtKB:  Q1XAB1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.679α = 90.00
b = 113.679β = 90.00
c = 131.026γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada436202

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Author supporting evidence