3IES

Firefly luciferase inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.

Auld, D.S.Lovell, S.Thorne, N.Lea, W.A.Maloney, D.J.Shen, M.Rai, G.Battaile, K.P.Thomas, C.J.Simeonov, A.Hanzlik, R.P.Inglese, J.

(2010) Proc.Natl.Acad.Sci.USA 107: 4878-4883

  • DOI: 10.1073/pnas.0909141107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Firefly luciferase (FLuc), an ATP-dependent bioluminescent reporter enzyme, is broadly used in chemical biology and drug discovery assays. PTC124 (Ataluren; (3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid) discovered in an FLuc-based assay t ...

    Firefly luciferase (FLuc), an ATP-dependent bioluminescent reporter enzyme, is broadly used in chemical biology and drug discovery assays. PTC124 (Ataluren; (3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid) discovered in an FLuc-based assay targeting nonsense codon suppression, is an unusually potent FLuc-inhibitor. Paradoxically, PTC124 and related analogs increase cellular FLuc activity levels by posttranslational stabilization. In this study, we show that FLuc inhibition and stabilization is the result of an inhibitory product formed during the FLuc-catalyzed reaction between its natural substrate, ATP, and PTC124. A 2.0 A cocrystal structure revealed the inhibitor to be the acyl-AMP mixed-anhydride adduct PTC124-AMP, which was subsequently synthesized and shown to be a high-affinity multisubstrate adduct inhibitor (MAI; K(D) = 120 pM) of FLuc. Biochemical assays, liquid chromatography/mass spectrometry, and near-attack conformer modeling demonstrate that formation of this novel MAI is absolutely dependent upon the precise positioning and reactivity of a key meta-carboxylate of PTC124 within the FLuc active site. We also demonstrate that the inhibitory activity of PTC124-AMP is relieved by free coenzyme A, a component present at high concentrations in luciferase detection reagents used for cell-based assays. This explains why PTC124 can appear to increase, instead of inhibit, FLuc activity in cell-based reporter gene assays. To our knowledge, this is an unusual example in which the "off-target" effect of a small molecule is mediated by an MAI mechanism.


    Organizational Affiliation

    NIH Chemical Genomics Center, National Institutes of Health, Bethesda, MD 20892-3370, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Luciferin 4-monooxygenase
A
551Photinus pyralisMutation(s): 0 
EC: 1.13.12.7
Find proteins for P08659 (Photinus pyralis)
Go to UniProtKB:  P08659
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M24
Query on M24

Download SDF File 
Download CCD File 
A
5'-O-[(R)-[({3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]phenyl}carbonyl)oxy](hydroxy)phosphoryl]adenosine
C25 H21 F N7 O9 P
XGTSAMZIYGBAIU-VEBYGKHWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M24IC50: 20 nM BINDINGMOAD
M24Kd: 0.12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 83.654α = 90.00
b = 83.654β = 90.00
c = 97.100γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
ADSCdata collection
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description