PDBsum entry: 3bzn

Isomerase

PDB id: 3bzn

Contents

Protein chain

430 a.a. *

Ligands

SO4 ×3

Metals

_MG

Waters ×220

* Residue conservation analysis

PDB id:

3bzn

Name:

Isomerase

Title:

Crystal structure of open form of menaquinone-specific isochorismate synthase, menf

Structure:

Menaquinone-specific isochorismate synthase. Chain: a. Synonym: isochorismate mutase. Engineered: yes

Source:

Escherichia coli. Gene: menf, yfba. Expressed in: escherichia coli.

Resolution:

2.00Å R-factor: 0.206 R-free: 0.284

Authors:

J.F.Parsons,K.M.Shi,J.E.Ladner

Key ref:

J.F.Parsons et al. (2008). Structure of isochorismate synthase in complex with magnesium. Acta Crystallogr D Biol Crystallogr, 64, 607-610. PubMed id: 18453696 DOI: 10.1107/S0907444908005477

Date:

18-Jan-08 Release date: 20-May-08

Protein chain

P38051  (MENF_ECOLI) -  Menaquinone-specific isochorismate synthase

Seq: 431 a.a.

Struc: 430 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.4.2 - Isochorismate synthase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: Chorismate = isochorismate
• Cofactor: Magnesium

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

 Gene Ontology (GO) functional annotation 

• Biological process: biosynthetic process (2 terms)
• Biochemical function: isomerase activity (3 terms)

Added reference

DOI no: 10.1107/S0907444908005477

Acta Crystallogr D Biol Crystallogr 64:607-610 (2008)

PubMed id: 18453696

Structure of isochorismate synthase in complex with magnesium.

J.F.Parsons, K.M.Shi, J.E.Ladner.

ABSTRACT

The electron carrier menaquinone is one of many important bacterial metabolites that are derived from the key intermediate chorismic acid. MenF, the first enzyme in the menaquinone pathway, catalyzes the isomerization of chorismate to isochorismate. Here, an improved structure of MenF in a new crystal form is presented. The structure, solved at 2.0 angstroms resolution in complex with magnesium, reveals a well defined closed active site. Existing evidence suggests that the mechanism of the reaction catalyzed by MenF involves nucleophilic attack of a water molecule on the chorismate ring. The structure reveals a well defined water molecule located in an appropriate position for activation by Lys190 and attack on the substrate.

Selected figure(s)

Figure 1.
Figure 1 Reaction catalyzed by MenF.

Figure 2.
Figure 2 (a) Superposition of magnesium-bound MenF with apo-MenF (PDB code 2eua ), illustrating the relative positions of the secondary-structural elements that define the active-site cleft of MenF in the presence and absence of magnesium. The MenF-Mg^2+ complex is shown in blue; 2eua is shown in beige. The interaction of Arg283 with Arg406 is shown, along with the alternate conformation of Arg283 in apo-MenF. The loop containing Arg406 is poorly defined by electron density in the apo-MenF structure. (b) Superposition of the active sites of MenF with bound magnesium (shown with blue C atoms; this work) and without magnesium (PDB code 2eua ; shown in yellow), illustrating the differences in the conformations of key active-site residues in the presence and absence of magnesium. The side chain of Glu416 was not present in the 2eua structure. Water molecules coordinated to Mg^2+ are shown as green spheres. (c) The remarkable conservation among active-site residues of chorismate-utilizing enzymes suggests factors beyond the first sphere of the active-site impact catalysis and influence product distribution. A superposition of MenF (blue C atoms), anthranilate synthase (PDB code 1i7q ; green C atoms) in complex with benzoate and pyruvate and SS (PDB code 2fn1 ; yellow C atoms) in complex with salicylate and pyruvate is shown. Water molecules from MenF are shown in green; Mg^2+ ions are shown in blue. The water molecule adjacent to Lys190 is in position to attack a substrate at C2 upon activation. Sulfate ions are found in locations analogous to those of the substrate carboxylate group and the cleaved pyruvoyl group in other chorismate-utilizing enzymes.

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 607-610) copyright 2008.

Figures were selected by the author.