2E92

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-261


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 

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.Usa 104: 10022-10027

  • DOI: 10.1073/pnas.0702254104
  • Primary Citation of Related Structures:  2E8T, 2E8U, 2E8V, 2E8W, 2E8X, 2E90, 2E91, 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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl pyrophosphate synthetase
A, B
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BTS1
EC: 2.5.1.10, 2.5.1.29, 2.5.1.1, 2.5.1.-
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12051
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
M0N
Query on M0N

Download SDF File 
Download CCD File 
A, B
(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
MINODRONATE; 1-HYDROXY-2-(5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-3-YL)ETHANE-1,1-DIYLDIPHOSPONIC ACID; (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YL-ETHYLIDENE)-1,1-BISPHOSPHONIC ACID
C9 H12 N2 O7 P2
VMMKGHQPQIEGSQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M0NKi: 130 nM (100) BINDINGDB
M0NIC50: 340 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.871α = 90.00
b = 116.051β = 90.00
c = 127.733γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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