Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y

Experimental Data Snapshot

  • Resolution: 3.28 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures.

Lisnyansky, M.Kapelushnik, N.Ben-Bassat, A.Marom, M.Loewenstein, A.Khananshvili, D.Giladi, M.Haitin, Y.

(2018) Mol Pharmacol 94: 1391-1400

  • DOI: https://doi.org/10.1124/mol.118.113670
  • Primary Citation of Related Structures:  
    6G31, 6G32

  • PubMed Abstract: 

    Bisphosphonates are widely used for treating osteoporosis, a common disorder in which bone strength is reduced, increasing the risk for fractures. Rarely, bisphosphonates can paradoxically lead to atypical fractures occurring spontaneously or with trivial trauma. Recently, a novel missense mutation (D188Y) in the GGPS1 gene, encoding for geranylgeranyl diphosphate synthase (GGPPS), was associated with bisphosphonate-induced atypical fractures. However, the molecular basis for GGPPS involvement in this devastating condition remains elusive. Here, we show that while maintaining an overall unperturbed global enzyme structure, the D188Y mutation leads to ∼4-fold catalytic activity decrease. Furthermore, GGPPS-D188Y is unable to support cross-species complementation, highlighting the functional significance of the reduced catalytic activity observed in vitro. We next determined the crystal structure of apo-GGPPS-D188Y, revealing that while Y188 does not alter the protein fold, its bulky side chain sterically interferes with substrate binding. In agreement, we show that GGPPS-D188Y exhibits ∼3-fold reduction in the binding affinity of zoledronate, a commonly used bisphosphonate. However, inhibition of the mutated enzyme by zoledronate, in pharmacologically relevant concentrations, is maintained. Finally, we determined the crystal structure of zoledronate-bound GGPPS-D188Y, revealing large ligand-induced binding pocket rearrangements, revising the previous model for GGPPS-bisphosphonate interactions. In conclusion, we propose that among heterozygotes residual GGPPS activity is sufficient to support physiologic cellular function, concealing any pathologic phenotype. However, under bisphosphonate treatment, GGPPS activity is reduced below a crucial threshold for osteoclast function, leading to impaired bone remodeling and increased susceptibility to atypical fractures.

  • Organizational Affiliation

    Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthase
A, B, C, D, E
A, B, C, D, E, F
307Homo sapiensMutation(s): 1 
Gene Names: GGPS1
EC: 2.5.1 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95749 (Homo sapiens)
Explore O95749 
Go to UniProtKB:  O95749
GTEx:  ENSG00000152904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95749
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.28 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.54α = 90
b = 148.54β = 90
c = 268.23γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentIsraelIsrael Science Foundation (ISF) grant 1721/16
Other governmentIsraelIsrael Science Foundation (ISF) grant 1775/12
Other governmentIsraelIsrael Cancer Research Foundation (ICRF) grant 01214
German Research FoundationIsraelI-2425-418.13/2016

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description