3AQ0 | pdb_00003aq0

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

• PDB DOI: https://doi.org/10.2210/pdb3AQ0/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-24 Released: 2011-01-19 
• Deposition Author(s): Hsieh, F.-L., Chang, T.-H., Ko, T.-P., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.274 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

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

• PubMed: 21220764 
• DOI: https://doi.org/10.1104/pp.110.168799
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 307.05 kDa 
• Atom Count: 20,426 
• Modeled Residue Count: 2,551 
• Deposited Residue Count: 2,784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyl diphosphate synthase	A, B, C, D, E, F, G, H	348	Arabidopsis thaliana	Mutation(s): 4  Gene Names: AtNPPPS, gpps EC: 2.5.1.30 (PDB Primary Data), 2.5.1.85 (UniProt)
UniProt
Find proteins for Q5HZ00 (Arabidopsis thaliana) Explore Q5HZ00  Go to UniProtKB:  Q5HZ00

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPP	BA [auth G], EA [auth H], K [auth A], N [auth B], R [auth C], X [auth E]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
ISY	FA [auth H], L [auth A]	3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid C5 H12 O6 P2 S YLTQZUVQWVAPNP-UHFFFAOYSA-N
PPV	AA [auth G], M [auth B], S [auth C], T [auth D], Y [auth E], Z [auth F]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
PEG	O [auth B], U [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	CA [auth H], DA [auth H], I [auth A], J [auth A], P [auth C], Q [auth C], V [auth E], W [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.274 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.961	α = 90
b = 115.961	β = 90
c = 385.874	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Hsieh, F.-L., Chang, T.-H., Ko, T.-P., Wang, A.H.-J.

Revision History  

• 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, Derived calculations, Refinement description