6XG4

X-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

A trimethoprim derivative impedes antibiotic resistance evolution.

Manna, M.S.Tamer, Y.T.Gaszek, I.Poulides, N.Ahmed, A.Wang, X.Toprak, F.C.R.Woodard, D.R.Koh, A.Y.Williams, N.S.Borek, D.Atilgan, A.R.Hulleman, J.D.Atilgan, C.Tambar, U.Toprak, E.

(2021) Nat Commun 12: 2949-2949

  • DOI: https://doi.org/10.1038/s41467-021-23191-z
  • Primary Citation of Related Structures:  
    6XG4, 6XG5

  • PubMed Abstract: 

    The antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4'-desmethyltrimethoprim (4'-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments. Furthermore, antibiotic-sensitive E. coli populations acquire antibiotic resistance at a substantially slower rate when grown in the presence of 4'-DTMP than in the presence of TMP. We find that 4'-DTMP impedes evolution of resistance by selecting against resistant genotypes with the L28R mutation and diverting genetic trajectories to other resistance-conferring DHFR mutations with catalytic deficiencies. Our results demonstrate how a detailed characterization of resistance-conferring mutations in a target enzyme can help identify potential drugs against antibiotic-resistant bacteria, which may ultimately increase long-term efficacy of antimicrobial therapies by modulating evolutionary trajectories that lead to resistance.


  • Organizational Affiliation

    Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase165Escherichia coli K-12Mutation(s): 1 
Gene Names: folAtmrAb0048JW0047
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABQ4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TOP BindingDB:  6XG4 Ki: min: 3, max: 8.3 (nM) from 2 assay(s)
IC50: min: 7, max: 1.20e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.548α = 90
b = 61.548β = 90
c = 104.661γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21GM126406
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM125748

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description