2AA9

EPSP synthase liganded with shikimate

• PDB DOI:  https://doi.org/10.2210/pdb2AA9/pdb

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


• Deposited: 2005-07-13 Released: 2006-02-14 
• Deposition Author(s): Priestman, M.A., Healy, M.L., Funke, T., Becker, A., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 

Literature

Molecular basis for the glyphosate-insensitivity of the reaction of 5-enolpyruvylshikimate 3-phosphate synthase with shikimate.

Priestman, M.A., Healy, M.L., Funke, T., Becker, A., Schonbrunn, E.

(2005) FEBS Lett 579: 5773-5780

• PubMed: 16225867 
• DOI: https://doi.org/10.1016/j.febslet.2005.09.066
• Primary Citation of Related Structures:  
  2AA9, 2AAY


• PubMed Abstract: 
  

The shikimate pathway enzyme 5-enolpyruvyl shikimate-3-phosphate synthase (EPSP synthase) has received attention in the past because it is the target of the broad-spectrum herbicide glyphosate. The natural substrate of EPSP synthase is shikimate-3-phosphate. However, this enzyme can also utilize shikimate as substrate. Remarkably, this reaction is insensitive to inhibition by glyphosate. Crystallographic analysis of EPSP synthase from Escherichia coli, in complex with shikimate/glyphosate at 1.5 Angstroms resolution, revealed that binding of shikimate induces changes around the backbone of the active site, which in turn impact the efficient binding of glyphosate. The implications from these findings with respect to the design of novel glyphosate-insensitive EPSP synthase enzymes are discussed.

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Organizational Affiliation: 

Department of Medicinal Chemistry, University of Kansas, 4040a Malott Hall, Lawrence, 66045, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.1 kDa 
• Atom Count: 3,867 
• Modelled Residue Count: 427 
• Deposited Residue Count: 427 
• Unique protein chains: 1

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
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
SKM	B [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-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], Q [auth A], R [auth A], S [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SKM	BindingDB:  2AA9	IC50: 9.00e+7 (nM) from 1 assay(s)
	PDBBind:  2AA9	IC50: 1.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.075	α = 90
b = 85.025	β = 90
c = 87.633	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Priestman, M.A., Healy, M.L., Funke, T., Becker, A., Schonbrunn, E.

Revision History  

• Version 1.0: 2006-02-14
  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
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description