4M7V

Dihydrofolate reductase from Enterococcus faecalis complexed with NADP(H)and RAB-propyl

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The Structure and Competitive Substrate Inhibition of Dihydrofolate Reductase from Enterococcus faecalis Reveal Restrictions to Cofactor Docking.

Bourne, C.R., Wakeham, N., Webb, N., Nammalwar, B., Bunce, R.A., Berlin, K.D., Barrow, W.W.

(2014) Biochemistry 53: 1228-1238

  • DOI: 10.1021/bi401104t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • We are addressing bacterial resistance to antibiotics by repurposing a well-established classic antimicrobial target, the dihydrofolate reductase (DHFR) enzyme. In this work, we have focused on Enterococcus faecalis, a nosocomial pathogen that freque ...

    We are addressing bacterial resistance to antibiotics by repurposing a well-established classic antimicrobial target, the dihydrofolate reductase (DHFR) enzyme. In this work, we have focused on Enterococcus faecalis, a nosocomial pathogen that frequently harbors antibiotic resistance determinants leading to complicated and difficult-to-treat infections. An inhibitor series with a hydrophobic dihydrophthalazine heterocycle was designed from the anti-folate trimethoprim. We have examined the potency of this inhibitor series based on inhibition of DHFR enzyme activity and bacterial growth, including in the presence of the exogenous product analogue folinic acid. The resulting preferences were rationalized using a cocrystal structure of the DHFR from this organism with a propyl-bearing series member (RAB-propyl). In a companion apo structure, we identify four buried waters that act as placeholders for a conserved hydrogen-bonding network to the substrate and indicate an important role in protein stability during catalytic cycling. In these structures, the nicotinamide of the nicotinamide adenine dinucleotide phosphate cofactor is visualized outside of its binding pocket, which is exacerbated by RAB-propyl binding. Finally, homology models of the TMP(R) sequences dfrK and dfrF were constructed. While the dfrK-encoded protein shows clear sequence changes that would be detrimental to inhibitor binding, the dfrF-encoded protein model suggests the protein would be relatively unstable. These data suggest a utility for anti-DHFR compounds for treating infections arising from E. faecalis. They also highlight a role for water in stabilizing the DHFR substrate pocket and for competitive substrate inhibitors that may gain advantages in potency by the perturbation of cofactor dynamics.

    Organizational Affiliation: 

    Department of Veterinary Pathobiology, Oklahoma State University , Stillwater, Oklahoma 74078, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
175Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: folA
EC: 1.5.1.3
Find proteins for Q834R2 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q834R2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAR
Query on RAR
Download SDF File 
Download CCD File 
A
5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine
(S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-propylphthalazin-2(1H)-yl)prop-2-en-1-one
C27 H30 N6 O3
YGDVMSPWZQHNMB-NEQMZLFVSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RARKi: 4.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.254α = 90.00
b = 63.254β = 90.00
c = 97.148γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CrystalCleardata collection
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2013-08-12 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Bourne, C.R.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references