Apo form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 

Starting Model: experimental
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Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase

Hsieh, F.-L.Chang, T.-H.Ko, T.-P.Wang, A.H.-J.

(2011) Plant Physiol 155: 1079-1090

  • DOI: https://doi.org/10.1104/pp.110.168799
  • Primary Citation of Related Structures:  
    3APZ, 3AQ0

  • PubMed Abstract: 

    Prenyltransferases (PTSs) are involved in the biosynthesis of terpenes with diverse functions. Here, a novel PTS from Arabidopsis (Arabidopsis thaliana) is identified as a trans-type polyprenyl pyrophosphate synthase (AtPPPS), which forms a trans-double bond during each homoallylic substrate condensation, rather than a homomeric C10-geranyl pyrophosphate synthase as originally proposed. Biochemical and genetic complementation analyses indicate that AtPPPS synthesizes C25 to C45 medium/long-chain products. Its close relationship to other long-chain PTSs is also uncovered by phylogenetic analysis. A mutant of contiguous surface polar residues was produced by replacing four charged surface amino acids with alanines to facilitate the crystallization of the enzyme. The crystal structures of AtPPPS determined here in apo and ligand-bound forms further reveal an active-site cavity sufficient to accommodate the medium/long-chain products. The two monomers in each dimer adopt different conformations at the entrance of the active site depending on the binding of substrates. Taken together, these results suggest that AtPPPS is endowed with a unique functionality among the known PTSs.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranyl diphosphate synthase
A, B
348Arabidopsis thalianaMutation(s): 0 
Gene Names: AtNPPPSgpps
Find proteins for Q5HZ00 (Arabidopsis thaliana)
Explore Q5HZ00 
Go to UniProtKB:  Q5HZ00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HZ00
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.512α = 90
b = 150.126β = 90
c = 176.112γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description