2QFQ

E. coli EPSP synthase Pro101Leu liganded with S3P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of glyphosate tolerance resulting from mutations of Pro101 in Escherichia coli 5-enolpyruvylshikimate-3-phosphate synthase.

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

(2007) J.Biol.Chem. 282: 32949-32955

  • DOI: 10.1074/jbc.M705624200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glyphosate, the world's most used herbicide, is a massive success because it enables efficient weed control with minimal animal and environmental toxicity. The molecular target of glyphosate is 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), whi ...

    Glyphosate, the world's most used herbicide, is a massive success because it enables efficient weed control with minimal animal and environmental toxicity. The molecular target of glyphosate is 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which catalyzes the sixth step of the shikimate pathway in plants and microorganisms. Glyphosate-tolerant variants of EPSPS constitute the basis of genetically engineered herbicide-tolerant crops. A single-site mutation of Pro(101) in EPSPS (numbering according to the enzyme from Escherichia coli) has been implicated in glyphosate-resistant weeds, but this residue is not directly involved in glyphosate binding, and the basis for this phenomenon has remained unclear in the absence of further kinetic and structural characterization. To probe the effects of mutations at this site, E. coli EPSPS enzymes were produced with glycine, alanine, serine, or leucine substituted for Pro(101). These mutant enzymes were analyzed by steady-state kinetics, and the crystal structures of the substrate binary and substrate.glyphosate ternary complexes of P101S and P101L EPSPS were determined to between 1.5- and 1.6-A resolution. It appears that residues smaller than leucine may be substituted for Pro(101) without decreasing catalytic efficiency. Any mutation at this site results in a structural change in the glyphosate-binding site, shifting Thr(97) and Gly(96) toward the inhibitor molecule. We conclude that the decreased inhibitory potency observed for glyphosate is a result of these mutation-induced long-range structural changes. The implications of our findings concerning the development and spread of glyphosate-resistant weeds are discussed.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 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): 1 
Gene Names: aroA
EC: 2.5.1.19
Find proteins for P0A6D3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6D3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S3P
Query on S3P

Download SDF File 
Download CCD File 
A
SHIKIMATE-3-PHOSPHATE
C7 H11 O8 P
QYOJSKGCWNAKGW-PBXRRBTRSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S3PKd: 7000 - 8000 nM (99) BINDINGDB
S3PIC50: 66000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.572α = 90.00
b = 85.180β = 90.00
c = 87.987γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata scaling
XDSdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance