7T7Q | pdb_00007t7q

R-27 In Complex with S. aureus DHFR and alpha-NADPH - Remediated for comparison with tNADPH

• PDB DOI: https://doi.org/10.2210/pdb7T7Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-15 Released: 2022-02-02 
• Deposition Author(s): Reeve, S.M., Wang, S., Donald, B.R., Wright, D.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus.

Wang, S., Reeve, S.M., Holt, G.T., Ojewole, A.A., Frenkel, M.S., Gainza, P., Keshipeddy, S., Fowler, V.G., Wright, D.L., Donald, B.R.

(2022) PLoS Comput Biol 18: e1009855-e1009855

• PubMed: 35143481 
• DOI: https://doi.org/10.1371/journal.pcbi.1009855
• Primary Citation Related Structures: 
  7T7Q, 7T7S


• PubMed Abstract: 
  

  Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates (PLAs), next generation DHFR inhibitors, are much more resilient than TMP against this F98Y variant, yet this F98Y substitution still reduces efficacy of these agents. Surprisingly, differences in the enantiomeric configuration at the stereogenic center of PLAs influence the isomeric state of the NADPH cofactor. To understand the molecular basis of F98Y-mediated resistance and how PLAs' inhibition drives NADPH isomeric states, we used protein design algorithms in the osprey protein design software suite to analyze a comprehensive suite of structural, biophysical, biochemical, and computational data. Here, we present a model showing how F98Y SaDHFR exploits a different anomeric configuration of NADPH to evade certain PLAs' inhibition, while other PLAs remain unaffected by this resistance mechanism.

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Organizational Affiliation: 
• Department of Computer Science, Duke University, Durham, North Carolina, United States of America.
Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America.
Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America.
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America.
Division of Infections Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
Department of Chemistry, University of Connecticut, Storrs, Connecticut, United States of America.
Department of Mathematics, Duke University, Durham, North Carolina, United States of America.
Department of Chemistry, Duke University, Durham, North Carolina, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.19 kDa 
• Atom Count: 1,402 
• Modeled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	157	Staphylococcus aureus	Mutation(s): 0  Gene Names: folA EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus) Explore P0A017  Go to UniProtKB:  P0A017

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDW	B [auth X]	alpha-NADPH C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-OPDHFMQKSA-N
06U	C [auth X]	6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine C22 H23 N5 O KEPLBUUTAQCZOE-AWEZNQCLSA-N
ACT	D [auth X]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.875	α = 90
b = 78.875	β = 90
c = 107.993	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Reeve, S.M., Wang, S., Donald, B.R., Wright, D.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI104841
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM078031
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118543

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references
• Version 1.2: 2023-10-18
  Changes: Refinement description