2GGA

CP4 EPSP synthase liganded with S3P and Glyphosate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the herbicide resistance of Roundup Ready crops.

Funke, T.Han, H.Healy-Fried, M.L.Fischer, M.Schonbrunn, E.

(2006) Proc Natl Acad Sci U S A 103: 13010-13015

  • DOI: 10.1073/pnas.0603638103
  • Primary Citation of Related Structures:  
    2GGD, 2GG6, 2GG4, 2GGA

  • PubMed Abstract: 
  • The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants ...

    The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants. Roundup Ready plants carry the gene coding for a glyphosate-insensitive form of this enzyme, obtained from Agrobacterium sp. strain CP4. Once incorporated into the plant genome, the gene product, CP4 EPSP synthase, confers crop resistance to glyphosate. Although widely used, the molecular basis for this glyphosate-resistance has remained obscure. We generated a synthetic gene coding for CP4 EPSP synthase and characterized the enzyme using kinetics and crystallography. The CP4 enzyme has unexpected kinetic and structural properties that render it unique among the known EPSP synthases. Glyphosate binds to the CP4 EPSP synthase in a condensed, noninhibitory conformation. Glyphosate sensitivity can be restored through a single-site mutation in the active site (Ala-100-Gly), allowing glyphosate to bind in its extended, inhibitory conformation.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoshikimate 1-carboxyvinyltransferaseA455Agrobacterium sp. CP4Mutation(s): 0 
Gene Names: aroA
EC: 2.5.1.19
UniProt
Find proteins for Q9R4E4 (Agrobacterium sp. (strain CP4))
Explore Q9R4E4 
Go to UniProtKB:  Q9R4E4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S3P (Subject of Investigation/LOI)
Query on S3P

Download Ideal Coordinates CCD File 
B [auth A]SHIKIMATE-3-PHOSPHATE
C7 H11 O8 P
QYOJSKGCWNAKGW-PBXRRBTRSA-N
 Ligand Interaction
GPJ (Subject of Investigation/LOI)
Query on GPJ

Download Ideal Coordinates CCD File 
C [auth A]GLYPHOSATE
C3 H9 N O5 P
XDDAORKBJWWYJS-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GPJ Binding MOAD:  2GGA Ki: 6.00e+6 (nM) from 1 assay(s)
PDBBind:  2GGA IC50: 1.10e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.086α = 90
b = 44.979β = 106.45
c = 77.251γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
CNSrefinement
CrystalCleardata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance