4Q9M

Crystal structure of UPPs in complex with FPP and an allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase.

Danley, D.E.Baima, E.T.Mansour, M.Fennell, K.F.Chrunyk, B.A.Mueller, J.P.Liu, S.Qiu, X.

(2015) Protein Sci 24: 20-26

  • DOI: 10.1002/pro.2579
  • Primary Citation of Related Structures:  
    4Q9M, 4Q9O

  • PubMed Abstract: 
  • Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP) ...

    Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC50 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC90 0.4 µg mL(-1) ). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.


    Organizational Affiliation

    Worldwide Research and Development, Pfizer Inc, Groton, Connecticut, 06340.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoprenyl transferaseA, B246Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: uppSspr0240
EC: 2.5.1
Find proteins for Q8DRB3 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DRB3 
Go to UniProtKB:  Q8DRB3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP

Download Ideal Coordinates CCD File 
D [auth A], O [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
2ZW
Query on 2ZW

Download Ideal Coordinates CCD File 
C [auth A], N [auth B]3-(2-chlorophenyl)-5-methyl-N-[4-(propan-2-yl)phenyl]-1,2-oxazole-4-carboxamide
C20 H19 Cl N2 O2
WRQYTVUHKWFTAU-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2ZWKd:  66   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.85α = 90
b = 91.85β = 90
c = 155.54γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-05-01 
  • Released Date: 2014-10-15 
  • Deposition Author(s): Liu, S., Qiu, X.

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references