2E9C

E. coli undecaprenyl pyrophosphate synthase in complex with BPH-675


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 

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:  

  • 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
Undecaprenyl pyrophosphate synthetase
A, B
253Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ispU (rth, uppS, yaeS)
EC: 2.5.1.31
Find proteins for P60472 (Escherichia coli (strain K12))
Go to UniProtKB:  P60472
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B75
Query on B75

Download SDF File 
Download CCD File 
A, B
1-HYDROXY-2-[3'-(NAPHTHALENE-2-SULFONYLAMINO)-BIPHENYL-3-YL]ETHYLIDENE-1,1-BISPHOSPHONIC ACID
(1-HYDROXY-2-{3'-[(2-NAPHTHYLSULFONYL)AMINO]BIPHENYL-3-YL}ETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
C24 H23 N O9 P2 S
MZVWVRVNMXTDAK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B75IC50: 1100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.543α = 90.00
b = 68.693β = 90.00
c = 110.030γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction

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