2Q80

Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding

Kavanagh, K.L.Dunford, J.E.Bunkoczi, G.Russell, R.G.Oppermann, U.

(2006) J.Biol.Chem. 281: 22004-22012

  • DOI: 10.1074/jbc.M602603200

  • PubMed Abstract: 
  • Modification of GTPases with isoprenoid molecules derived from geranylgeranyl pyrophosphate or farnesyl pyrophosphate is an essential requisite for cellular signaling pathways. The synthesis of these isoprenoids proceeds in mammals through the mevalo ...

    Modification of GTPases with isoprenoid molecules derived from geranylgeranyl pyrophosphate or farnesyl pyrophosphate is an essential requisite for cellular signaling pathways. The synthesis of these isoprenoids proceeds in mammals through the mevalonate pathway, and the final steps in the synthesis are catalyzed by the related enzymes farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase. Both enzymes play crucial roles in cell survival, and inhibition of farnesyl pyrophosphate synthase by nitrogen-containing bisphosphonates is an established concept in the treatment of bone disorders such as osteoporosis or certain forms of cancer in bone. Here we report the crystal structure of human geranylgeranyl pyrophosphate synthase, the first mammalian ortholog to have its x-ray structure determined. It reveals that three dimers join together to form a propeller-bladed hexameric molecule with a mass of approximately 200 kDa. Structure-based sequence alignments predict this quaternary structure to be restricted to mammalian and insect orthologs, whereas fungal, bacterial, archaeal, and plant forms exhibit the dimeric organization also observed in farnesyl pyrophosphate synthase. Geranylgeranyl pyrophosphate derived from heterologous bacterial expression is tightly bound in a cavity distinct from the chain elongation site described for farnesyl pyrophosphate synthase. The structure most likely represents an inhibitory complex, which is further corroborated by steady-state kinetics, suggesting a possible feedback mechanism for regulating enzyme activity. Structural comparisons between members of this enzyme class give deeper insights into conserved features important for catalysis.


    Organizational Affiliation

    Structural Genomics Consortium, Botnar Research Centre, University of Oxford, United Kingdom. kate.kavanagh@sgc.ox.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl pyrophosphate synthetase
A, B, C, D, E, F
301Homo sapiensMutation(s): 0 
Gene Names: GGPS1
EC: 2.5.1.-
Find proteins for O95749 (Homo sapiens)
Go to Gene View: GGPS1
Go to UniProtKB:  O95749
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GRG
Query on GRG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GRGKi: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.248α = 90.00
b = 141.248β = 90.00
c = 211.705γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2012-12-05
    Type: Structure summary