PDBsum entry 2ggd

Transferase

PDB id: 2ggd

Contents

Protein chain

445 a.a. *

Ligands

S3P

GPJ

Waters ×491

* Residue conservation analysis

PDB id:

2ggd

Name:

Transferase

Title:

Cp4 epsp synthase ala100gly liganded with s3p and glyphosate

Structure:

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

Source:

Agrobacterium sp.. Organism_taxid: 268951. Strain: cp4. Gene: aroa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.148 R-free: 0.174

Authors:

E.Schonbrunn,T.Funke

Key ref:

T.Funke et al. (2006). Molecular basis for the herbicide resistance of Roundup Ready crops. Proc Natl Acad Sci U S A, 103, 13010-13015. PubMed id: 16916934 DOI: 10.1073/pnas.0603638103

Date:

23-Mar-06 Release date: 22-Aug-06

Protein chain

Q9R4E4  (AROA_AGRSC) -  3-phosphoshikimate 1-carboxyvinyltransferase from Agrobacterium sp. (strain CP4)

Seq: 455 a.a.

Struc: 445 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 = S3P) matches with 76.19% similarity) + phosphate

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

reference

DOI no: 10.1073/pnas.0603638103

Proc Natl Acad Sci U S A 103:13010-13015 (2006)

PubMed id: 16916934

Molecular basis for the herbicide resistance of Roundup Ready crops.

T.Funke, H.Han, M.L.Healy-Fried, M.Fischer, E.Schönbrunn.

ABSTRACT

The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants. Roundup Ready plants carry the gene coding for a glyphosate-insensitive form of this enzyme, obtained from Agrobacterium sp. strain CP4. Once incorporated into the plant genome, the gene product, CP4 EPSP synthase, confers crop resistance to glyphosate. Although widely used, the molecular basis for this glyphosate-resistance has remained obscure. We generated a synthetic gene coding for CP4 EPSP synthase and characterized the enzyme using kinetics and crystallography. The CP4 enzyme has unexpected kinetic and structural properties that render it unique among the known EPSP synthases. Glyphosate binds to the CP4 EPSP synthase in a condensed, noninhibitory conformation. Glyphosate sensitivity can be restored through a single-site mutation in the active site (Ala-100-Gly), allowing glyphosate to bind in its extended, inhibitory conformation.

Selected figure(s)

Figure 2.
Fig. 2. Three-dimensional structure of CP4 EPSP synthase. (A) (Left) Unliganded CP4 EPSP synthase exists in an open conformation. (Right) Upon interaction with S3P, the enzyme undergoes a large conformational change to a closed state. Shown in orange is a loop spanning residues 347–358, which is highly flexible in the open conformation but becomes ordered in the closed conformation. This loop contains the strictly conserved EPSP synthase residues Glu-354 and Arg-357, which are involved in PEP/glyphosate binding. Monovalent cations may influence the conformation of this loop and facilitate binding of PEP. (B) Stereoview showing that, in the binary complex, S3P (yellow) binds to the enzyme residues shown in magenta through multiple hydrogen-bonding/electrostatic interactions (black dotted lines). In addition, the cyclohexene moiety of S3P is sandwiched between Arg-200 and Gln-175. Residues shown in light blue constitute the PEP/glyphosate binding site. Attracted by the accumulation of positive charges, a sulfate ion (shown in green) from the crystallization solution binds to the space occupied by the phosphate moiety of PEP or the phosphonate moiety of glyphosate in either ternary complex. Water molecules are shown as cyan spheres.

Figure 4.
Fig. 4. Two distinct conformations of glyphosate. Displayed are the electron densities, contoured at 3 , derived from 1F[o] – 1F[c] Fourier syntheses to 1.7-Å resolution, omitting the model of glyphosate during the refinement of the ternary complexes of CP4 EPSP synthase (Left) and Ala-100–Gly CP4 EPSP synthase (Right). (Right) The conformation of glyphosate upon interaction with the Ala-100–Gly CP4 EPSP synthase is identical to the one observed in the E. coli or Str. pneumoniae enzymes. (Left) With an Ala residue in position 100, the glyphosate molecule is 0.6 Å shorter, mainly because of a rotation around the C 4 N bond next to the carboxyl group.

Figures were selected by an automated process.