E. coli EPSP synthase (T97I) liganded with S3P and glyphosate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 

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This is version 1.4 of the entry. See complete history


Structural Basis of Glyphosate Resistance Resulting from the Double Mutation Thr97 -> Ile and Pro101 -> Ser in 5-Enolpyruvylshikimate-3-phosphate Synthase from Escherichia coli.

Funke, T.Yang, Y.Han, H.Healy-Fried, M.Olesen, S.Becker, A.Schonbrunn, E.

(2009) J Biol Chem 284: 9854-9860

  • DOI: https://doi.org/10.1074/jbc.M809771200
  • Primary Citation of Related Structures:  
    3FJX, 3FJZ, 3FK0, 3FK1

  • PubMed Abstract: 

    The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the target of the broad spectrum herbicide glyphosate. The genetic engineering of EPSPS led to the introduction of glyphosate-resistant crops worldwide. The genetically engineered corn lines NK603 and GA21 carry distinct EPSPS enzymes. CP4 EPSPS, expressed in NK603 corn and transgenic soybean, cotton, and canola, belongs to class II EPSPS, glyphosate-insensitive variants of this enzyme isolated from certain Gram-positive bacteria. GA21 corn, on the other hand, was created by point mutations of class I EPSPS, such as the enzymes from Zea mays or Escherichia coli, which are sensitive to low glyphosate concentrations. The structural basis of the glyphosate resistance resulting from these point mutations has remained obscure. We studied the kinetic and structural effects of the T97I/P101S double mutation, the molecular basis for GA21 corn, using EPSPS from E. coli. The T97I/P101S enzyme is essentially insensitive to glyphosate (K(i) = 2.4 mm) but maintains high affinity for the substrate phosphoenolpyruvate (PEP) (K(m) = 0.1 mm). The crystal structure at 1.7-A resolution revealed that the dual mutation causes a shift of residue Gly(96) toward the glyphosate binding site, impairing efficient binding of glyphosate, while the side chain of Ile(97) points away from the substrate binding site, facilitating PEP utilization. The single site T97I mutation renders the enzyme sensitive to glyphosate and causes a substantial decrease in the affinity for PEP. Thus, only the concomitant mutations of Thr(97) and Pro(101) induce the conformational changes necessary to produce catalytically efficient, glyphosate-resistant class I EPSPS.

  • Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoshikimate 1-carboxyvinyltransferase427Escherichia coli K-12Mutation(s): 1 
Gene Names: aroAb0908JW0891
Find proteins for P0A6D3 (Escherichia coli (strain K12))
Explore P0A6D3 
Go to UniProtKB:  P0A6D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6D3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on S3P

Download Ideal Coordinates CCD File 
C7 H11 O8 P
Query on GPF

Download Ideal Coordinates CCD File 
C [auth A]N-(phosphonomethyl)glycine
C3 H8 N O5 P
Query on SER

Download Ideal Coordinates CCD File 
B [auth A]SERINE
C3 H7 N O3
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [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]
C H2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
GPF Binding MOAD:  3FJZ Ki: 9.00e+4 (nM) from 1 assay(s)
PDBBind:  3FJZ Ki: 9.00e+4 (nM) from 1 assay(s)
BindingDB:  3FJZ Ki: 160 (nM) from 1 assay(s)
Kd: 160 (nM) from 1 assay(s)
IC50: 2000 (nM) from 1 assay(s)
S3P BindingDB:  3FJZ Kd: min: 7000, max: 8000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.58α = 90
b = 85.38β = 90
c = 87.78γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description