2E93

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-629

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 

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Literature

Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases

Guo, R.T., Cao, R., Liang, P.H., Ko, T.P., Chang, T.H., Hudock, M.P., Jeng, W.Y., Chen, C.K.-M., Zhang, Y., Song, Y., Kuo, C.J., Yin, F., Oldfield, E., Wang, A.H.-J.

(2007) Proc Natl Acad Sci U S A 104: 10022-10027

  • DOI: https://doi.org/10.1073/pnas.0702254104
  • Primary Citation of Related Structures:  
    2E8T, 2E8U, 2E8V, 2E8W, 2E8X, 2E90, 2E91, 2E92, 2E93, 2E94, 2E95, 2E98, 2E99, 2E9A, 2E9C, 2E9D

  • PubMed Abstract: 

    • Bisphosphonate drugs (e.g., Fosamax and Zometa) are thought to act primarily by inhibiting farnesyl diphosphate synthase (FPPS), resulting in decreased prenylation of small GTPases. Here, we show that some bisphosphonates can also inhibit geranylgeranyl diphosphate synthase (GGPPS), as well as undecaprenyl diphosphate synthase (UPPS), a cis-prenyltransferase of interest as a target for antibacterial therapy ...

    Bisphosphonate drugs (e.g., Fosamax and Zometa) are thought to act primarily by inhibiting farnesyl diphosphate synthase (FPPS), resulting in decreased prenylation of small GTPases. Here, we show that some bisphosphonates can also inhibit geranylgeranyl diphosphate synthase (GGPPS), as well as undecaprenyl diphosphate synthase (UPPS), a cis-prenyltransferase of interest as a target for antibacterial therapy. Our results on GGPPS (10 structures) show that there are three bisphosphonate-binding sites, consisting of FPP or isopentenyl diphosphate substrate-binding sites together with a GGPP product- or inhibitor-binding site. In UPPS, there are a total of four binding sites (in five structures). These results are of general interest because they provide the first structures of GGPPS- and UPPS-inhibitor complexes, potentially important drug targets, in addition to revealing a remarkably broad spectrum of binding modes not seen in FPPS inhibition.

    Organizational Affiliation: 

    Taiwan International Graduate Program, Institute of Biological Chemistry, Core Facility for Protein Crystallography, Academia Sinica, Taipei 115, Taiwan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetase
A, B
340Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.5.1.30 (PDB Primary Data), 2.5.1 (UniProt), 2.5.1.1 (UniProt), 2.5.1.29 (UniProt), 2.5.1.10 (UniProt)
UniProt
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12051
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B29
Query on B29
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B]		[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID
C20 H18 O8 P2
BYVXAUZOTGITQZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B29 BindingDB:  2E93 Ki: 110 (nM) from 1 assay(s)
IC50: 280 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.788α = 90
b = 115.821β = 90
c = 129.997γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance