Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.76 kDa 
• Atom Count: 1571 
• Residue Count: 161 
• Unique protein chains: 1

3M08

Wild Type Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1

• DOI: 10.2210/pdb3M08/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-02 Released: 2010-07-14 
• Deposition Author(s): Bourne, C.R., Barrow, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.213 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 

Literature

Inhibition of Antibiotic-Resistant Staphylococcus aureus by the Broad-Spectrum Dihydrofolate Reductase Inhibitor RAB1.

Bourne, C.R., Barrow, E.W., Bunce, R.A., Bourne, P.C., Berlin, K.D., Barrow, W.W.

(2010) Antimicrob Agents Chemother 54: 3825-3833

• PubMed: 20606069 
• DOI: 10.1128/AAC.00361-10
• Primary Citation of Related Structures:  
  3M08, 3M09


• PubMed Abstract: 
  

The bacterial burden on human health is quickly outweighing available therapeutics. Our long-term goal is the development of antimicrobials with the potential for broad-spectrum activity. We previously reported phthalazine-based inhibitors of dihydrofolate reductase (DHFR) with potent activity against Bacillus anthracis, a major component of Project BioShield. The most active molecule, named RAB1, performs well in vitro and, in a cocrystal structure, was found deep within the active site of B. anthracis DHFR. We have now examined the activity of RAB1 against a panel of bacteria relevant to human health and found broad-spectrum applicability, particularly with regard to gram-positive organisms. RAB1 was most effective against Staphylococcus aureus, including methicillin- and vancomycin-resistant (MRSA/VRSA) strains. We have determined the cocrystal structure of the wild-type and trimethoprim-resistant (Phe 98 Tyr) DHFR enzyme from S. aureus with RAB1, and we found that rotational freedom of the acryloyl linker region allows the phthalazine moiety to occupy two conformations. This freedom in placement also allows either enantiomer of RAB1 to bind to S. aureus, in contrast to the specificity of B. anthracis for the S-enantiomer. Additionally, one of the conformations of RAB1 defines a unique surface cavity that increases the strength of interaction with S. aureus. These observations provide insights into the binding capacity of S. aureus DHFR and highlight atypical features critical for future exploitation in drug development.

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Related Citations: 

• Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity
  Bourne, C.R., Bunce, R.A., Bourne, P.C., Berlin, K.D., Barrow, E.W., Barrow, W.W.
  (2009) Antimicrob Agents Chemother 53: 3065

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Organizational Affiliation: 

Department of Veterinary Pathobiology, 250 McElroy Hall, Oklahoma State University, Stillwater, OK 74078, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	161	Staphylococcus aureus	Mutation(s): 0  Gene Names: folA EC: 1.5.1.3
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
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
RAR	A	5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine C27 H30 N6 O3 YGDVMSPWZQHNMB-NEQMZLFVSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RAR	IC50:  2.9000000953674316   nM  BindingDB
RAR	IC50:  12.5   nM  BindingDB
RAR	Ki:  2.799999952316284   nM  Binding MOAD
RAR	Ki:  0.8999999761581421   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.213 
• R-Value Work: 0.175 
• R-Value Observed: 0.179 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.18	α = 90
b = 79.18	β = 90
c = 107.89	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-02 
• Released Date: 2010-07-14 
Deposition Author(s): Bourne, C.R., Barrow, W.W.

Revision History 

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance