1X8T

EPSPS liganded with the (R)-phosphonate analog of the tetrahedral reaction intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Interaction of phosphonate analogues of the tetrahedral reaction intermediate with 5-enolpyruvylshikimate-3-phosphate synthase in atomic detail.

Priestman, M.A.Healy, M.L.Becker, A.Alberg, D.G.Bartlett, P.A.Lushington, G.H.Schonbrunn, E.

(2005) Biochemistry 44: 3241-3248

  • DOI: 10.1021/bi048198d
  • Primary Citation of Related Structures:  
    1X8T, 1X8R

  • PubMed Abstract: 
  • The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway and is the target of the broad-spectrum herbicide glyphosate. Since the functionality of the shikimate pathway is vital not only for plants but also for microorganisms, EPSPS is considered a prospective target for the development of novel antibiotics ...

    The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway and is the target of the broad-spectrum herbicide glyphosate. Since the functionality of the shikimate pathway is vital not only for plants but also for microorganisms, EPSPS is considered a prospective target for the development of novel antibiotics. We have kinetically analyzed and determined the crystal structures of Escherichia coli EPSPS inhibited by (R)- and (S)-configured phosphonate analogues of the tetrahedral reaction intermediate. Both diastereomers are competitive inhibitors with respect to the substrates of the EPSPS reaction, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). Remarkably, the (S)-phosphonate (K(iS3P) = 750 nM), whose configuration corresponds to that of the genuine tetrahedral intermediate, is a much weaker inhibitor than the (R)-phosphonate analogue (K(iS3P) = 16 nM). The crystal structures of EPSPS liganded with the (S)- and (R)-phosphonates, at 1.5 and 1.9 A resolution, respectively, revealed that binding of the (R)-phosphonate induces conformational changes of the strictly conserved residues Arg124 and Glu341 within the active site. This appears to give rise to substantial structural alterations in the amino-terminal globular domain of the enzyme. By contrast, binding of the (S)-phosphonate renders the enzyme structure unchanged. Thus, EPSPS may facilitate the tight binding of structurally diverse ligands through conformational flexibility. Molecular docking calculations did not explain why the (R)-phosphonate is the better inhibitor. Therefore, we propose that the structural events during the open-closed transition of EPSPS are altered as a result of inhibitor action.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-phosphoshikimate 1-carboxyvinyltransferaseA427Escherichia coliMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RC1 (Subject of Investigation/LOI)
Query on RC1

Download Ideal Coordinates CCD File 
B [auth A][3R-[3A,4A,5B(R*)]]-5-(1-CARBOXY-1-PHOSPHONOETHOXY)-4-HYDROXY-3-(PHOSPHONOOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID
C10 H16 O13 P2
HUOJJMMXOWLGJU-QGOVLLJGSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RC1 PDBBind:  1X8T Ki: 16 (nM) from 1 assay(s)
Binding MOAD:  1X8T Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.16α = 90
b = 84.5β = 90
c = 88.24γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description