5HXN

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M and E75A mutants) from the Wild Tomato Solanum habrochaites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure and Potential Head-to-Middle Condensation Function of aZ,Z-Farnesyl Diphosphate Synthase.

Chan, Y.T.Ko, T.P.Yao, S.H.Chen, Y.W.Lee, C.C.Wang, A.H.

(2017) ACS Omega 2: 930-936

  • DOI: https://doi.org/10.1021/acsomega.6b00562
  • Primary Citation of Related Structures:  
    5HXN, 5HXO, 5HXP

  • PubMed Abstract: 

    Plants produce a wide variety of secondary metabolites in response to adverse environmental factors. Z , Z -Farnesyl diphosphate ( Z , Z -FPP), synthesized by Z , Z -farnesyl diphosphate synthase ( z FPS), supports the formation of phytochemicals in wild tomatoes. Here, the crystal structure of N-terminal truncated z FPS (Δ z FPS) was determined. Irregular products including lavandulyl diphosphate and an unknown compound were surprisingly found. Apart from the truncated N-terminus as a functional regulator, structure-based analysis and mutagenesis assays revealed a residue H103 in Δ z FPS as one of the key elements to this irregular function. A series of substrate-enzyme complex structures were obtained from Δ z FPS-H103Y by co-crystallizing with isopentenyl diphosphate, dimethylallyl thiolodiphosphate, or both. Various substrate-binding modes were revealed. The catalytic mechanisms of both the head-to-tail and head-to-middle reactions in Δ z FPS were proposed. Functional switch between the two mechanisms in this enzyme and the essential role played by the flexible C-terminus were elucidated as well.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic233Solanum habrochaitesMutation(s): 1 
Gene Names: ZFPS
EC: 2.5.1.92
UniProt
Find proteins for B8XA40 (Solanum habrochaites)
Explore B8XA40 
Go to UniProtKB:  B8XA40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8XA40
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.891α = 90
b = 51.891β = 90
c = 173.286γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description