5E8H

Crystal structure of geranylfarnesyl pyrophosphate synthases 2 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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This is version 1.1 of the entry. See complete history


Literature

Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants.

Wang, C.Chen, Q.Fan, D.Li, J.Wang, G.Zhang, P.

(2016) Mol Plant 9: 195-204

  • DOI: https://doi.org/10.1016/j.molp.2015.10.010
  • Primary Citation of Related Structures:  
    5E8H, 5E8K, 5E8L

  • PubMed Abstract: 

    Terpenoids are the largest and most diverse class of plant-specialized metabolites, which function in diverse physiological processes during plant development. In the biosynthesis of plant terpenoids, short-chain prenyltransferases (SC-PTs), together with terpene synthases (TPSs), play critical roles in determining terpenoid diversity. SC-PTs biosynthesize prenyl pyrophosphates with different chain lengths, and these compounds are the direct precursors of terpenoids. Arabidopsis thaliana possesses a subgroup of SC-PTs whose functions are not clearly known. In this study, we focus on 10 geranylgeranyl pyrophosphate synthase-like [GGPPSL] proteins, which are commonly thought to produce GGPP [C20]. We found that a subset of members of the Arabidopsis GGPPSL gene family have undergone neo-functionalization: GGPPSL6, 7, 9, and 10 mainly have geranylfarnesyl pyrophosphate synthase activity (C25; renamed AtGFPPS1, 2, 3, and 4), and GGPPSL8 produces even longer chain prenyl pyrophosphate (≥ C30; renamed polyprenyl pyrophosphate synthase 2, AtPPPS2). By solving the crystal structures of AtGFPPS2, AtPPPS2, and AtGGPPS11, we reveal the product chain-length determination mechanism of SC-PTs and interpret it as a "three floors" model. Using this model, we identified a novel GFPPS clade distributed in Brassicaceae plants and found that the GFPPS gene typically occurs in tandem with a gene encoding a TPS, forming a GFPPS-TPS gene cluster.


  • Organizational Affiliation

    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthase 3, chloroplastic
A, B
330Arabidopsis thalianaMutation(s): 0 
Gene Names: GGPP3At3g14550MIE1.5
EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt
Find proteins for Q9LUD9 (Arabidopsis thaliana)
Explore Q9LUD9 
Go to UniProtKB:  Q9LUD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LUD9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.245α = 90
b = 77.09β = 90
c = 114.172γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Derived calculations