PDBsum entry 1x8t

Transferase

PDB id: 1x8t

Contents

Protein chain

427 a.a. *

Ligands

RC1

FMT ×7

Waters ×468

* Residue conservation analysis

PDB id:

1x8t

Name:

Transferase

Title:

Epsps liganded with the (r)-phosphonate analog of the tetrahedral reaction intermediate

Structure:

3-phosphoshikimate 1-carboxyvinyltransferase. Chain: a. Synonym: 5-enolpyruvylshikimate-3-phosphate synthase, epsp synthase, epsps. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: aroa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.163 R-free: 0.207

Authors:

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

Key ref:

M.A.Priestman et al. (2005). Interaction of phosphonate analogues of the tetrahedral reaction intermediate with 5-enolpyruvylshikimate-3-phosphate synthase in atomic detail. Biochemistry, 44, 3241-3248. PubMed id: 15736934 DOI: 10.1021/bi048198d

Date:

18-Aug-04 Release date: 19-Apr-05

Protein chain

P0A6D3  (AROA_ECOLI) -  3-phosphoshikimate 1-carboxyvinyltransferase from Escherichia coli (strain K12)

Seq: 427 a.a.

Struc: 427 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.19 - 3-phosphoshikimate 1-carboxyvinyltransferase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3- phosphoshikimate + phosphate

3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3- phosphoshikimate (Bound ligand (Het Group name = RC1) matches with 84.00% similarity) + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi048198d

Biochemistry 44:3241-3248 (2005)

PubMed id: 15736934

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

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

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.