4H8E

Structure of S. aureus undecaprenyl diphosphate synthase in complex with FPP and sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antibacterial drug leads targeting isoprenoid biosynthesis.

Zhu, W.Zhang, Y.Sinko, W.Hensler, M.E.Olson, J.Molohon, K.J.Lindert, S.Cao, R.Li, K.Wang, K.Wang, Y.Liu, Y.L.Sankovsky, A.de Oliveira, C.A.Mitchell, D.A.Nizet, V.McCammon, J.A.Oldfield, E.

(2013) Proc Natl Acad Sci U S A 110: 123-128

  • DOI: 10.1073/pnas.1219899110
  • Primary Citation of Related Structures:  
    4H3A, 4H3C, 4H8E, 4H38, 4H2O, 4H2J, 4H2M, 3SGX, 3SH0, 3SGT

  • PubMed Abstract: 
  • With the rise in resistance to antibiotics such as methicillin, there is a need for new drugs. We report here the discovery and X-ray crystallographic structures of 10 chemically diverse compounds (benzoic, diketo, and phosphonic acids, as well as a ...

    With the rise in resistance to antibiotics such as methicillin, there is a need for new drugs. We report here the discovery and X-ray crystallographic structures of 10 chemically diverse compounds (benzoic, diketo, and phosphonic acids, as well as a bisamidine and a bisamine) that inhibit bacterial undecaprenyl diphosphate synthase, an essential enzyme involved in cell wall biosynthesis. The inhibitors bind to one or more of the four undecaprenyl diphosphate synthase inhibitor binding sites identified previously, with the most active leads binding to site 4, outside the catalytic center. The most potent leads are active against Staphylococcus aureus [minimal inhibitory concentration (MIC)(90) ∼0.25 µg/mL], and one potently synergizes with methicillin (fractional inhibitory concentration index = 0.25) and is protective in a mouse infection model. These results provide numerous leads for antibacterial development and open up the possibility of restoring sensitivity to drugs such as methicillin, using combination therapies.


    Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Undecaprenyl pyrophosphate synthaseA256Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: uppSSA1103
EC: 2.5.1.31 (PDB Primary Data), 2.5.1 (UniProt)
Find proteins for P60477 (Staphylococcus aureus (strain N315))
Explore P60477 
Go to UniProtKB:  P60477
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP

Download CCD File 
A
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.303α = 90
b = 57.303β = 90
c = 158.824γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-09-22 
  • Released Date: 2012-12-19 
  • Deposition Author(s): Zhu, W., Oldfield, E.

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references