Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.24 kDa 
• Atom Count: 3,771 
• Modelled Residue Count: 427 
• Deposited Residue Count: 427 
• Unique protein chains: 1

 2PQ9

E. coli EPSPS liganded with (R)-difluoromethyl tetrahedral reaction intermediate analog

• PDB DOI:  https://doi.org/10.2210/pdb2PQ9/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-01 Released: 2008-03-11 
• Deposition Author(s): Healy-Fried, M.L., Funke, T., Han, H., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.166 
• R-Value Observed: 0.191 

Literature

Differential inhibition of class I and class II 5-enolpyruvylshikimate-3-phosphate synthases by tetrahedral reaction intermediate analogues.

Funke, T., Healy-Fried, M.L., Han, H., Alberg, D.G., Bartlett, P.A., Schonbrunn, E.

(2007) Biochemistry 46: 13344-13351

• PubMed: 17958399 
• DOI: https://doi.org/10.1021/bi701095u
• Primary Citation of Related Structures:  
  2PQ9, 2PQB, 2PQC, 2PQD


• PubMed Abstract: 
  

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase or EPSPS) is best known as the target of the herbicide glyphosate. EPSPS is also considered an attractive target for the development of novel antibiotics since the pathogenicity of many microorganisms depends on the functionality of the shikimate pathway. Here, we have investigated the inhibitory potency of stable fluorinated or phosphonate-based analogues of the tetrahedral reaction intermediate (TI) in a parallel study utilizing class I (glyphosate-sensitive) and class II (glyphosate-tolerant) EPSPS. The (R)-difluoromethyl and (R)-phosphonate analogues of the TI are the most potent inhibitors of EPSPS described to date. However, we found that class II EPSPS are up to 400 times less sensitive to inhibition by these TI analogues. X-ray crystallographic data revealed that the conformational changes of active site residues observed upon inhibitor binding to the representative class I EPSPS from Escherichia coli do not occur in the prototypical class II enzyme from Agrobacterium sp. strain CP4. It appears that because the active sites of class II EPSPS do not possess the flexibility to accommodate these TI analogues, the analogues themselves undergo conformational changes, resulting in less favorable inhibitory properties. Since pathogenic microorganisms such as Staphylococcus aureus utilize class II EPSPS, we conclude that the rational design of novel EPSPS inhibitors with potential as broad-spectrum antibiotics should be based on the active site structures of class II EPSP synthases.

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Organizational Affiliation: 

Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoshikimate 1-carboxyvinyltransferase	A	427	Escherichia coli K-12	Mutation(s): 0  Gene Names: aroA, b0908, JW0891 EC: 2.5.1.19
UniProt
Find proteins for P0A6D3 (Escherichia coli (strain K12)) Explore P0A6D3  Go to UniProtKB:  P0A6D3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GG9	B [auth A]	(3R,4S,5R)-5-[(1R)-1-CARBOXY-2,2-DIFLUORO-1-(PHOSPHONOOXY)ETHOXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID C10 H14 F2 O14 P2 OHXHNRRSMKIHDJ-VFWNUGQXSA-N
FMT	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GG9	Binding MOAD:  2PQ9	Ki: 7.8 (nM) from 1 assay(s)
	PDBBind:  2PQ9	Ki: 7.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.166 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.157	α = 90
b = 85.101	β = 90
c = 87.644	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Healy-Fried, M.L., Funke, T., Han, H., Schonbrunn, E.

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance