8A7B

PcIDS1_D319N in complex with Mg2+ and 3-Br-GPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors.

Ecker, F.Vattekkatte, A.Boland, W.Groll, M.

(2023) Nat Chem 15: 1188-1195

  • DOI: https://doi.org/10.1038/s41557-023-01235-9
  • Primary Citation of Related Structures:  
    8A6U, 8A6V, 8A6Z, 8A70, 8A73, 8A74, 8A78, 8A7A, 8A7B, 8A7C, 8A7J, 8A7K, 8A7L, 8A7R, 8A7U

  • PubMed Abstract: 

    Terpenoids account for more than 60% of all natural products, and their carbon skeletons originate from common isoprenoid units of different lengths such as geranyl pyrophosphate and farnesyl pyrophosphate. Here we characterize a metal-dependent, bifunctional isoprenyl diphosphate synthase from the leaf beetle Phaedon cochleariae by structural and functional analyses. Inter- and intramolecular cooperative effects in the homodimer strongly depend on the provided metal ions and regulate the biosynthetic flux of terpene precursors to either biological defence or physiological development. Strikingly, a unique chain length determination domain adapts to form geranyl or farnesyl pyrophosphate by altering enzyme symmetry and ligand affinity between both subunits. In addition, we identify an allosteric geranyl-pyrophosphate-specific binding site that shares similarity with end-product inhibition in human farnesyl pyrophosphate synthase. Our combined findings elucidate a deeply intertwined reaction mechanism in the P. cochleariae isoprenyl diphosphate synthase that integrates substrate, product and metal-ion concentrations to harness its dynamic potential.


  • Organizational Affiliation

    Center for Protein Assemblies, Technical University of Munich, Garching, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoprenyl diphosphate synthase
A, B
346Phaedon cochleariaeMutation(s): 1 
EC: 2.5.1.1
UniProt
Find proteins for M1JS91 (Phaedon cochleariae)
Explore M1JS91 
Go to UniProtKB:  M1JS91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1JS91
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L7X (Subject of Investigation/LOI)
Query on L7X

Download Ideal Coordinates CCD File 
J [auth A][(2Z)-3-bromanyl-7-methyl-octa-2,6-dienyl] phosphono hydrogen phosphate
C9 H17 Br O7 P2
YMIXOXPUDYECRP-TWGQIWQCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
I [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.31α = 90
b = 77.97β = 101.26
c = 88.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGR-1861/5-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description