Desensitizing plant EPSP synthase to glyphosate: Optimized global sequence context accommodates a glycine-to-alanine change in the active site

J Biol Chem. 2019 Jan 11;294(2):716-725. doi: 10.1074/jbc.RA118.006134. Epub 2018 Nov 13.


5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the transfer of a carboxyvinyl group from phosphoenolpyruvate (PEP) to shikimate-3-phosphate and in plants is the target of the herbicide glyphosate. EPSPSs with high catalytic efficiency and insensitivity to glyphosate are of microbial origin, including the enzyme from Agrobacterium strain CP4, in which insensitivity is conferred by an active site alanine. In the sequence context of plant EPSPSs, alanine in place of glycine at the equivalent position interferes with the binding of both glyphosate and PEP. We show here that iterative optimization of maize EPSPS containing the G101A substitution yielded variants on par with CP4 in terms of catalytic activity in the presence of glyphosate. The improvement relative to G101A alone was entirely due to reduction in Km for PEP from 333 to 18 μm, versus 9.5 μm for native maize EPSPS. A large portion of the reduction in Km was conferred by two down-sizing substitutions (L97C and V332A) within 8 Å of glyphosate, which together reduced Km for PEP to 43 μm Although the original optimization was conducted with maize EPSPS, contextually homologous substitutions conferred similar properties to the EPSPSs of other crops. We also discovered a variant having the known glyphosate-desensitizing substitution P106L plus three additional ones that reduced the Km for PEP from 47 μm, observed with P106L alone, to 10.3 μm The improvements obtained with both Ala101 and Leu106 have implications regarding glyphosate-tolerant crops and weeds.

Keywords: 5-enolpyruvylshikimate-3-phosphate synthase; biotechnology; enzyme inhibitor; glyphosate; glyphosate resistance; herbicide resistance; molecular evolution; plant EPSP synthase; plant biochemistry; protein engineering.

MeSH terms

  • 3-Phosphoshikimate 1-Carboxyvinyltransferase / chemistry
  • 3-Phosphoshikimate 1-Carboxyvinyltransferase / genetics*
  • 3-Phosphoshikimate 1-Carboxyvinyltransferase / metabolism*
  • Agrobacterium / enzymology
  • Alanine / chemistry
  • Alanine / genetics
  • Alanine / metabolism
  • Amino Acid Sequence
  • Amino Acid Substitution*
  • Catalytic Domain
  • Glycine / analogs & derivatives*
  • Glycine / chemistry
  • Glycine / genetics
  • Glycine / metabolism
  • Herbicides / metabolism*
  • Mutagenesis
  • Zea mays / drug effects
  • Zea mays / enzymology*
  • Zea mays / genetics*
  • Zea mays / metabolism


  • Herbicides
  • glyphosate
  • 3-Phosphoshikimate 1-Carboxyvinyltransferase
  • Alanine
  • Glycine

Associated data

  • PDB/1G6S
  • PDB/2GGA