7TQ1

Crystal structure of adaptive laboratory evolved sulfonamide-resistant Dihydropteroate Synthase (DHPS) from Escherichia coli in complex with 6-hydroxymethylpterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics.

Venkatesan, M.Fruci, M.Verellen, L.A.Skarina, T.Mesa, N.Flick, R.Pham, C.Mahadevan, R.Stogios, P.J.Savchenko, A.

(2023) Nat Commun 14: 4031-4031

  • DOI: https://doi.org/10.1038/s41467-023-39778-7
  • Primary Citation of Related Structures:  
    7S2I, 7S2J, 7S2K, 7S2L, 7S2M, 7TQ1, 8SCD

  • PubMed Abstract: 

    The sulfonamides (sulfas) are the oldest class of antibacterial drugs and inhibit the bacterial dihydropteroate synthase (DHPS, encoded by folP), through chemical mimicry of its co-substrate p-aminobenzoic acid (pABA). Resistance to sulfa drugs is mediated either by mutations in folP or acquisition of sul genes, which code for sulfa-insensitive, divergent DHPS enzymes. While the molecular basis of resistance through folP mutations is well understood, the mechanisms mediating sul-based resistance have not been investigated in detail. Here, we determine crystal structures of the most common Sul enzyme types (Sul1, Sul2 and Sul3) in multiple ligand-bound states, revealing a substantial reorganization of their pABA-interaction region relative to the corresponding region of DHPS. We use biochemical and biophysical assays, mutational analysis, and in trans complementation of E. coli ΔfolP to show that a Phe-Gly sequence enables the Sul enzymes to discriminate against sulfas while retaining pABA binding and is necessary for broad resistance to sulfonamides. Experimental evolution of E. coli results in a strain harboring a sulfa-resistant DHPS variant that carries a Phe-Gly insertion in its active site, recapitulating this molecular mechanism. We also show that Sul enzymes possess increased active site conformational dynamics relative to DHPS, which could contribute to substrate discrimination. Our results reveal the molecular foundation for Sul-mediated drug resistance and facilitate the potential development of new sulfas less prone to resistance.


  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydropteroate synthase
A, B
285Escherichia coliMutation(s): 0 
Gene Names: folPdhpSb3177JW3144
EC: 2.5.1.15
UniProt
Find proteins for P0AC13 (Escherichia coli (strain K12))
Explore P0AC13 
Go to UniProtKB:  P0AC13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC13
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.884α = 90
b = 84.571β = 90
c = 175.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

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 Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references, Structure summary
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description