Molecule of the Month: EPSP Synthase and Weedkillers
The weedkiller Roundup attacks a key enzyme involved in the construction of aromatic compounds.
Exploring the Structure
Glyphosate-resistant EPSP Synthase
EPSP synthase becomes resistant to glyphosate by constricting the active site. These three structures show how this is done. The first structure (PDB entry 2pqb) shows a transition state analog bound in the active site of a glyphosate-resistant enzyme. The analog is similar to an intermediate state of the reaction, where S3P has just formed a bond to PEP, but the analog is unable to complete the reaction, so it stays in the active site and may be observed by crystallography. The second structure (PDB entry 2gga) shows how glyphosate mimics PEP, taking its place. An alanine amino acid, however, crowds the herbicide and greatly weakens its binding strength. This alanine is typically a smaller glycine in glyphosate-susceptible forms the enzyme. The third structure (PDB entry 2ggd) shows that if this change is made in the protein, glyphosate binds in a more stable, extended form, and the enzyme is effectively inhibited by the herbicide.
Topics for Further Discussion
- There are many structures of EPSP synthase from different bacteria in the PDB archive. Try using the Structure Comparison Tool to compare their similar structures.
- The PDB archive also includes many structures for different enzymes in the shikimate pathway. Try looking at shikimate kinase or shikimate dehydrogenase, two enzymes that perform steps before EPS synthase.
Related PDB-101 Resources
- Browse Biology of Plants
- Browse Biotechnology
- Browse Enzymes
- 2p1n: X Tan, LIA Calderon-Villalobos, M Sharon, C Zheng, CV Robinson, M Estelle & N Zheng (2007) Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640-645.
- 2pqb: T. Funke, ML Healy-Fried, H. Han, DG Alberg, PA Bartlett & E Schonbrunn (2007) Differential inhibition of class I and class II 5-enolpyruvylshikimate-3-phosphate synthases by tetrahedral reaction intermediate analogues. Biochemistry 46, 13344-13351.
- 2gg4, 2gga, 2ggd: T Funke, H Han, ML Healy-Fried, M Fischer & E Schonbrunn (2006) Molecular basis for the herbicide resistance of Roundup Ready crops. Proceedings of the National Academy of Sciences USA 103, 13010-13015.
February 2018, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2018_2