2AAY

EPSP synthase liganded with shikimate and glyphosate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.

(2005) Febs Lett. 579: 5773-5780

  • DOI: 10.1016/j.febslet.2005.09.066
  • Primary Citation of Related Structures:  

  • 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-ph ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoshikimate 1-carboxyvinyltransferase
A
427Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aroA
EC: 2.5.1.19
Find proteins for P0A6D3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6D3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
SKM
Query on SKM

Download SDF File 
Download CCD File 
A
(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
SHIKIMATE
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
 Ligand Interaction
GPJ
Query on GPJ

Download SDF File 
Download CCD File 
A
GLYPHOSATE
C3 H9 N O5 P
XDDAORKBJWWYJS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SKMIC50: >90000000 nM (100) BINDINGDB
GPJIC50: 1700000 nM BINDINGMOAD
SKMIC50: 1200000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.678α = 90.00
b = 84.916β = 90.00
c = 87.542γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description