1G6T

STRUCTURE OF EPSP SYNTHASE LIGANDED WITH SHIKIMATE-3-PHOSPHATE

• PDB DOI:  https://doi.org/10.2210/pdb1G6T/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-07 Released: 2001-02-07 
• Deposition Author(s): Schonbrunn, E., Eschenburg, S., Shuttleworth, W., Schloss, J.V., Amrhein, N., Evans, J.N.S., Kabsch, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.185 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 

Literature

Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail.

Schonbrunn, E., Eschenburg, S., Shuttleworth, W.A., Schloss, J.V., Amrhein, N., Evans, J.N., Kabsch, W.

(2001) Proc Natl Acad Sci U S A 98: 1376-1380

• PubMed: 11171958 
• DOI: https://doi.org/10.1073/pnas.98.4.1376
• Primary Citation of Related Structures:  
  1G6S, 1G6T


• PubMed Abstract: 
  

Biosynthesis of aromatic amino acids in plants, many bacteria, and microbes relies on the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, a prime target for drugs and herbicides. We have identified the interaction of EPSP synthase with one of its two substrates (shikimate 3-phosphate) and with the widely used herbicide glyphosate by x-ray crystallography. The two-domain enzyme closes on ligand binding, thereby forming the active site in the interdomain cleft. Glyphosate appears to occupy the binding site of the second substrate of EPSP synthase (phosphoenol pyruvate), mimicking an intermediate state of the ternary enzyme.substrates complex. The elucidation of the active site of EPSP synthase and especially of the binding pattern of glyphosate provides a valuable roadmap for engineering new herbicides and herbicide-resistant crops, as well as new antibiotic and antiparasitic drugs.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.09 kDa 
• Atom Count: 3,905 
• Modelled Residue Count: 427 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPSP SYNTHASE	A	427	Escherichia coli	Mutation(s): 0  Gene Names: aroA EC: 2.5.1.19
UniProt
Find proteins for P0A6D3 (Escherichia coli (strain K12)) Explore P0A6D3  Go to UniProtKB:  P0A6D3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S3P	C [auth A]	SHIKIMATE-3-PHOSPHATE C7 H11 O8 P QYOJSKGCWNAKGW-PBXRRBTRSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FMT	D [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], M [auth A], N [auth A], O [auth A], P [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S3P	BindingDB:  1G6T	Kd: min: 7000, max: 8000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.185 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.035	α = 90
b = 84.936	β = 90
c = 87.624	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-07 
Deposition Author(s): Schonbrunn, E., Eschenburg, S., Shuttleworth, W., Schloss, J.V., Amrhein, N., Evans, J.N.S., Kabsch, W.

Revision History  

• Version 1.0: 2001-02-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description