2AA9

EPSP synthase liganded with shikimate


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 

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.Schonbrunn, E.

(2005) FEBS Lett 579: 5773-5780

  • DOI: 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-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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoshikimate 1-carboxyvinyltransferaseA427Escherichia coliMutation(s): 0 
Gene Names: aroA
EC: 2.5.1.19
Find proteins for P0A6D3 (Escherichia coli (strain K12))
Explore P0A6D3 
Go to UniProtKB:  P0A6D3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SKM
Query on SKM

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

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SKMIC50:  90000000   nM  BindingDB
SKMIC50 :  1200000   nM  PDBBind
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 = 58.075α = 90
b = 85.025β = 90
c = 87.633γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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