1X8T

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

Summary for 1X8T

• Entry DOI: 10.2210/pdb1x8t/pdb
• Related: 1G6S 1G6T 1MI4 1Q36 1X8R
• Descriptor: 3-phosphoshikimate 1-carboxyvinyltransferase, [3R-[3A,4A,5B(R*)]]-5-(1-CARBOXY-1-PHOSPHONOETHOXY)-4-HYDROXY-3-(PHOSPHONOOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: inside-out alpha-beta barrel, transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : P0A6D3
• Total number of polymer chains: 1
• Total formula weight: 46869.96

Authors

Priestman, M.A.,Healy, M.L.,Becker, A.,Alberg, D.G.,Bartlett, P.A.,Schonbrunn, E. (deposition date: 2004-08-18, release date: 2005-04-19, Last modification date: 2023-08-23)

Primary citation

Priestman, M.A.,Healy, M.L.,Becker, A.,Alberg, D.G.,Bartlett, P.A.,Lushington, G.H.,Schonbrunn, E.
Interaction of phosphonate analogues of the tetrahedral reaction intermediate with 5-enolpyruvylshikimate-3-phosphate synthase in atomic detail.
Biochemistry, 44:3241-3248, 2005

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. 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.

PubMed: 15736934
DOI: 10.1021/bi048198d

Experimental method

X-RAY DIFFRACTION (1.9 Å)