Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 7.64 kDa 
• Atom Count: 515 
• Modelled Residue Count: 56 
• Deposited Residue Count: 62 
• Unique protein chains: 1

6NXZ

Crystal structure of trimethoprim-resistant type II dihydrofolate reductase in complex with a bisbenzimidazole inhibitor

• PDB DOI: 10.2210/pdb6NXZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Eosentomon sp. 1 EDA-2008
• Mutation(s): No 


• Deposited: 2019-02-10 Released: 2019-05-29 
• Deposition Author(s): Yachnin, B.J., Berghuis, A.M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Other government, Canadian Institutes of Health Research (CIHR), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues.

Toulouse, J.L., Yachnin, B.J., Ruediger, E.H., Deon, D., Gagnon, M., Saint-Jacques, K., Ebert, M.C.C.J.C., Forge, D., Bastien, D., Colin, D.Y., Vanden Eynde, J.J., Marinier, A., Berghuis, A.M., Pelletier, J.N.

(2019) ACS Omega 4: 10056-10069

• PubMed: 31460098 
• DOI: 10.1021/acsomega.9b00640
• Primary Citation of Related Structures:  
  6NXZ, 6NY0


• PubMed Abstract: 
  

The worldwide use of the broad-spectrum antimicrobial trimethoprim (TMP) has induced the rise of TMP-resistant microorganisms. In addition to resistance-causing mutations of the microbial chromosomal dihydrofolate reductase (Dfr), the evolutionarily and structurally unrelated type II Dfrs (DfrBs) have been identified in TMP-resistant microorganisms. DfrBs are intrinsically TMP-resistant and allow bacterial proliferation when the microbial chromosomal Dfr is TMP-inhibited, making these enzymes important targets for inhibitor development. Furthermore, DfrBs occur in multiresistance plasmids, potentially accelerating their dissemination. We previously reported symmetrical bisbenzimidazoles that are the first selective inhibitors of the only well-characterized DfrB, DfrB1. Here, their diversification provides a new series of inhibitors ( K _i = 1.7-12.0 μM). Our results reveal two prominent features: terminal carboxylates and inhibitor length allow the establishment of essential interactions with DfrB1. Two crystal structures demonstrate the simultaneous binding of two inhibitor molecules in the symmetrical active site. Observations of those dimeric inhibitors inspired the design of monomeric analogues, binding in a single copy yet offering similar inhibition potency ( K _i = 1.1 and 7.4 μM). Inhibition of a second member of the DfrB family, DfrB4, suggests the generality of these inhibitors. These results provide key insights into inhibition of the highly TMP-resistant DfrBs, opening avenues to downstream development of antibiotics for combatting this emergent source of resistance.

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Organizational Affiliation: 

Département de Biochimie, Institute for Research in Immunology and Cancer (IRIC), and Département de Chimie, Université de Montréal, Montreal H3C 3J7, Quebec, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase type 2	A	62	Escherichia coli	Mutation(s): 0  EC: 1.5.1.3
UniProt
Find proteins for P00383 (Escherichia coli) Explore P00383  Go to UniProtKB:  P00383

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D49 (Subject of Investigation/LOI)	B [auth A]	2-[4-[(2~{R})-4-[4-(6-carboxy-1~{H}-benzimidazol-2-yl)phenoxy]-2-oxidanyl-butoxy]phenyl]-1~{H}-benzimidazole-5-carboxylic acid C32 H26 N4 O7 QQYJHKTWHJAQJJ-JOCHJYFZSA-N
MRD	C [auth A], D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
D49	Binding MOAD:  6NXZ	Ki: 3500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.617	α = 90
b = 67.617	β = 90
c = 51.977	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-02-10 
• Released Date: 2019-05-29 
Deposition Author(s): Yachnin, B.J., Berghuis, A.M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	227853
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	2018-04686
Other government	Canada	Canada Foundation for Innovation 11510 (www.innovation.ca)
Canadian Institutes of Health Research (CIHR)	Canada	MOP-13107
Other private	Canada	Fondation Marcel et Rolande Gosselin

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2019-09-11
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence