4Q67

Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protein design algorithms predict viable resistance to an experimental antifolate.

Reeve, S.M.Gainza, P.Frey, K.M.Georgiev, I.Donald, B.R.Anderson, A.C.

(2015) Proc.Natl.Acad.Sci.USA 112: 749-754

  • DOI: 10.1073/pnas.1411548112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates. In this study, a structure-based protein design algorithm (K* in the OSPREY suit ...

    Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates. In this study, a structure-based protein design algorithm (K* in the OSPREY suite) was used to prospectively identify single-nucleotide polymorphisms that confer resistance to an experimental inhibitor effective against dihydrofolate reductase (DHFR) from Staphylococcus aureus. Four of the top-ranked mutations in DHFR were found to be catalytically competent and resistant to the inhibitor. Selection of resistant bacteria in vitro reveals that two of the predicted mutations arise in the background of a compensatory mutation. Using enzyme kinetics, microbiology, and crystal structures of the complexes, we determined the fitness of the mutant enzymes and strains, the structural basis of resistance, and the compensatory relationship of the mutations. To our knowledge, this work illustrates the first application of protein design algorithms to prospectively predict viable resistance mutations that arise in bacteria under antibiotic pressure.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269; and amy.anderson@uconn.edu brd+dhfr14@cs.duke.edu.,Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269; and.,Departments of Computer Science and Biochemistry, Duke University, Durham, NC 27708 amy.anderson@uconn.edu brd+dhfr14@cs.duke.edu.,Departments of Computer Science and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
160N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.260α = 90.00
b = 79.260β = 90.00
c = 107.420γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
StructureStudiodata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references