2ONH

Crystal Structure of of limonene synthase with 2-fluorolinalyl diphosphate(FLPP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 

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This is version 1.4 of the entry. See complete history. 


Literature

Structure of limonene synthase, a simple model for terpenoid cyclase catalysis.

Hyatt, D.C., Youn, B., Zhao, Y., Santhamma, B., Coates, R.M., Croteau, R.B., Kang, C.

(2007) Proc Natl Acad Sci U S A 104: 5360-5365

  • DOI: https://doi.org/10.1073/pnas.0700915104
  • Primary Citation of Related Structures:  
    2ONG, 2ONH

  • PubMed Abstract: 

    • The crystal structure of (4S)-limonene synthase from Mentha spic ata, a metal ion-dependent monoterpene cyclase that catalyzes the coupled isomerization and cyclization of geranyl diphosphate, is reported at 2.7-A; resolution in two forms liganded to the substrate and intermediate analogs, 2-fluorogeranyl diphosphate and 2-fluorolinalyl diphosphate, respectively ...

    The crystal structure of (4S)-limonene synthase from Mentha spic ata, a metal ion-dependent monoterpene cyclase that catalyzes the coupled isomerization and cyclization of geranyl diphosphate, is reported at 2.7-A; resolution in two forms liganded to the substrate and intermediate analogs, 2-fluorogeranyl diphosphate and 2-fluorolinalyl diphosphate, respectively. The implications of these findings are described for domain interactions in the homodimer and for changes in diphosphate-metal ion coordination and substrate binding conformation in the course of the multistep reaction.

    Organizational Affiliation: 

    Institute of Biological Chemistry, Washingston State University, Pullman, WA 99164-6340, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4S-limonene synthase
A, B
543Mentha spicataMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3P
Query on F3P
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]		(1S)-1-[(1S)-1-FLUOROETHYL]-1,5-DIMETHYLHEXYL TRIHYDROGEN DIPHOSPHATE
C10 H23 F O7 P2
JUOIVVAWJCVSPX-AXDSSHIGSA-N		 Ligand Interaction
BTB
Query on BTB
Download Ideal Coordinates CCD File 
G [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.66α = 90
b = 198.66β = 90
c = 122.67γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
X-PLORrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-01-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description