Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.10 kDa 
• Atom Count: 3912 
• Residue Count: 427 
• Unique protein chains: 1

1X8R

EPSPS liganded with the (S)-phosphonate analog of the tetrahedral reaction intermediate

• DOI: 10.2210/pdb1X8R/pdb

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


• Deposited: 2004-08-18 Released: 2005-04-19 
• Deposition Author(s): Priestman, M.A., Healy, M.L., Becker, A., Alberg, D.G., Bartlett, P.A., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Literature

Interaction of phosphonate analogues of the tetrahedral reaction intermediate with 5-enolpyruvylshikimate-3-phosphate synthase in atomic detail.

Priestman, M.A., Healy, M.L., Becker, A., Alberg, D.G., Bartlett, P.A., Lushington, G.H., Schonbrunn, E.

(2005) Biochemistry 44: 3241-3248

• PubMed: 15736934 
• DOI: 10.1021/bi048198d
• Primary Citation of Related Structures:  
  1X8T, 1X8R


• PubMed Abstract: 
  

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway and is the target of the broad-spectrum herbicide glyphosate. Since the functionality of the shikimate pathway is vital not only for plants but also for microorganisms, EPSPS is considered a prospective target for the development of novel antibiotics. We have kinetically analyzed and determined the crystal structures of Escherichia coli EPSPS inhibited by (R)- and (S)-configured phosphonate analogues of the tetrahedral reaction intermediate. Both diastereomers are competitive inhibitors with respect to the substrates of the EPSPS reaction, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). Remarkably, the (S)-phosphonate (K(iS3P) = 750 nM), whose configuration corresponds to that of the genuine tetrahedral intermediate, is a much weaker inhibitor than the (R)-phosphonate analogue (K(iS3P) = 16 nM). The crystal structures of EPSPS liganded with the (S)- and (R)-phosphonates, at 1.5 and 1.9 A resolution, respectively, revealed that binding of the (R)-phosphonate induces conformational changes of the strictly conserved residues Arg124 and Glu341 within the active site. This appears to give rise to substantial structural alterations in the amino-terminal globular domain of the enzyme. By contrast, binding of the (S)-phosphonate renders the enzyme structure unchanged. Thus, EPSPS may facilitate the tight binding of structurally diverse ligands through conformational flexibility. Molecular docking calculations did not explain why the (R)-phosphonate is the better inhibitor. Therefore, we propose that the structural events during the open-closed transition of EPSPS are altered as a result of inhibitor action.

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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	Mutation(s): 0  Gene Names: aroA EC: 2.5.1.19
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
SC1	A	[3R-[3A,4A,5B(S*)]]-5-(1-CARBOXY-1-PHOSPHONOETHOXY)-4-HYDROXY-3-(PHOSPHONOOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID C10 H16 O13 P2 HUOJJMMXOWLGJU-JQCUSGDOSA-N
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SC1	Kd:  15   nM  BindingDB
SC1	Ki:  2900   nM  Binding MOAD
SC1	Ki:  15   nM  BindingDB
SC1	Ki :  750   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.73	α = 90
b = 85.17	β = 90
c = 87.49	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-18 
• Released Date: 2005-04-19 
Deposition Author(s): Priestman, M.A., Healy, M.L., Becker, A., Alberg, D.G., Bartlett, P.A., Schonbrunn, E.

Revision History 

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description