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 6XG4 | pdb_00006xg4

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 (Depositor) 
  • R-Value Work: 
    0.249 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XG4

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 20.06 kDa 
  • Atom Count: 1,503 
  • Modeled Residue Count: 159 
  • Deposited Residue Count: 165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrofolate reductase165Escherichia coli K-12Mutation(s): 1 
Gene Names: folA, tmrA, b0048, JW0047
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
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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 6 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.249 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
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