2QK8

Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase

• PDB DOI: https://doi.org/10.2210/pdb2QK8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus anthracis str. Sterne
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-10 Released: 2007-08-28 
• Deposition Author(s): Bennett, B.C., Xu, H., Simmerman, R.F., Lee, R.E., Dealwis, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 

Literature

Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase.

Bennett, B.C., Xu, H., Simmerman, R.F., Lee, R.E., Dealwis, C.G.

(2007) J Med Chem 50: 4374-4381

• PubMed: 17696333 
• DOI: https://doi.org/10.1021/jm070319v
• Primary Citation of Related Structures:  
  2QK8


• PubMed Abstract: 
  

  Spores of Bacillus anthracis are the infectious agent of anthrax. Current antibiotic treatments are limited due to resistance and patient age restrictions; thus, additional targets for therapeutic intervention are needed. One possible candidate is dihydrofolate reductase (DHFR), a biosynthetic enzyme necessary for anthrax pathogenicity. We determined the crystal structure of DHFR from B. anthracis (baDHFR) in complex with methotrexate (MTX; 1) at 2.4 Angstrom resolution. The structure reveals the crucial interactions required for MTX binding and a putative molecular basis for how baDHFR has natural resistance to trimethoprim (TMP; 2). The structure also allows insights for designing selective baDHFR inhibitors that will have weak affinities for the human enzyme. Additionally, we have found that 5-nitro-6-methylamino-isocytosine (MANIC; 3), which inhibits another B. anthracis folate synthesis enzyme, dihydropteroate synthase (DHPS), can also inhibit baDHFR. This provides a starting point for designing multi-target inhibitors that are less likely to induce drug resistance.

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Organizational Affiliation: 

Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.6 kDa 
• Atom Count: 1,428 
• Modelled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	162	Bacillus anthracis str. Sterne	Mutation(s): 0  Gene Names: dfrA EC: 1.5.1.3
UniProt
Find proteins for Q81R22 (Bacillus anthracis) Explore Q81R22  Go to UniProtKB:  Q81R22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX	B [auth A]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTX	BindingDB:  2QK8	IC50: min: 12.2, max: 24 (nM) from 4 assay(s)
	Binding MOAD:  2QK8	IC50: 20 (nM) from 1 assay(s)
	PDBBind:  2QK8	IC50: 12.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.697	α = 90
b = 41.236	β = 119.2
c = 67.032	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BioCARS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Bennett, B.C., Xu, H., Simmerman, R.F., Lee, R.E., Dealwis, C.G.

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description