2E95

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-675


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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: 10.1073/pnas.0702254104
  • Primary Citation of Related Structures:  
    2E8X, 2E99, 2E8W, 2E98, 2E8V, 2E8U, 2E9D, 2E9C, 2E9A, 2E8T

  • 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 geranylgera ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetaseAB340Saccharomyces 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)
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B75
Query on B75

Download CCD File 
A, B
1-HYDROXY-2-[3'-(NAPHTHALENE-2-SULFONYLAMINO)-BIPHENYL-3-YL]ETHYLIDENE-1,1-BISPHOSPHONIC ACID
C24 H23 N O9 P2 S
MZVWVRVNMXTDAK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B75Ki:  80   nM  BindingDB
B75IC50:  200   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.39α = 90
b = 116.262β = 90
c = 128.695γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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