6CLV

Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Structural and Functional Basis for Recurring Sulfa Drug Resistance Mutations inStaphylococcus aureusDihydropteroate Synthase.

Griffith, E.C.Wallace, M.J.Wu, Y.Kumar, G.Gajewski, S.Jackson, P.Phelps, G.A.Zheng, Z.Rock, C.O.Lee, R.E.White, S.W.

(2018) Front Microbiol 9: 1369-1369

  • DOI: https://doi.org/10.3389/fmicb.2018.01369
  • Primary Citation of Related Structures:  
    6CLU, 6CLV

  • PubMed Abstract: 

    Staphylococcal species are a leading cause of bacterial drug-resistant infections and associated mortality. One strategy to combat bacterial drug resistance is to revisit compromised targets, and to circumvent resistance mechanisms using structure-assisted drug discovery. The folate pathway is an ideal candidate for this approach. Antifolates target an essential metabolic pathway, and the necessary detailed structural information is now available for most enzymes in this pathway. Dihydropteroate synthase (DHPS) is the target of the sulfonamide class of drugs, and its well characterized mechanism facilitates detailed analyses of how drug resistance has evolved. Here, we surveyed clinical genetic sequencing data in S. aureus to distinguish natural amino acid variations in DHPS from those that are associated with sulfonamide resistance. Five mutations were identified, F17L, S18L, T51M, E208K, and KE257_dup. Their contribution to resistance and their cost to the catalytic properties of DHPS were evaluated using a combination of biochemical, biophysical and microbiological susceptibility studies. These studies show that F17L, S18L, and T51M directly lead to sulfonamide resistance while unexpectedly increasing susceptibility to trimethoprim, which targets the downstream enzyme dihydrofolate reductase. The secondary mutations E208K and KE257_dup restore trimethoprim susceptibility closer to wild-type levels while further increasing sulfonamide resistance. Structural studies reveal that these mutations appear to selectively disfavor the binding of the sulfonamides by sterically blocking an outer ring moiety that is not present in the substrate. This emphasizes that new inhibitors must be designed that strictly stay within the substrate volume in the context of the transition state.


  • Organizational Affiliation

    Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydropteroate synthase
A, B, C, D
291Staphylococcus aureusMutation(s): 2 
Gene Names: folPdpsA
EC: 2.5.1.15
UniProt
Find proteins for O05701 (Staphylococcus aureus)
Explore O05701 
Go to UniProtKB:  O05701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05701
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6MB
Query on 6MB

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C]
4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide
C18 H18 N8 O4 S
JJZFSJXETRBCPR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.212 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.75α = 90
b = 79.75β = 90
c = 175.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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 StatesR01 AI070721-08
St. Jude Children's Research Hospital (ALSAC)United States--
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references