3AQ0

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1104/pp.110.168799
  • Primary Citation of Related Structures:  

  • 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-dou ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranyl diphosphate synthase
A, B, C, D, E, F, G, H
348Arabidopsis thalianaMutation(s): 4 
Gene Names: SPS3 (GPS1)
EC: 2.5.1.85
Find proteins for Q5HZ00 (Arabidopsis thaliana)
Go to UniProtKB:  Q5HZ00
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ISY
Query on ISY

Download SDF File 
Download CCD File 
A, H
3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid
Isopentyl S-Thiolodiphosphate
C5 H12 O6 P2 S
YLTQZUVQWVAPNP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C, E, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PPV
Query on PPV

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Download CCD File 
B, C, D, E, F, G
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
FPP
Query on FPP

Download SDF File 
Download CCD File 
A, B, C, E, G, H
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 115.961α = 90.00
b = 115.961β = 90.00
c = 385.874γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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