PDBsum entry 2jlc

Transferase

PDB id: 2jlc

Contents

Protein chains

554 a.a. *

Ligands

TPP ×2

Metals

_MN ×2

Waters ×246

* Residue conservation analysis

PDB id:

2jlc

Name:

Transferase

Title:

Crystal structure of e.Coli mend, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - native protein

Structure:

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene -1- carboxylate synthase. Chain: a, b. Synonym: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase, menaquinone biosynthesis protein mend. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.211 R-free: 0.293

Authors:

A.Dawson,P.K.Fyfe,W.N.Hunter

Key ref:

A.Dawson et al. (2008). Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase). J Mol Biol, 384, 1353-1368. PubMed id: 18983854 DOI: 10.1016/j.jmb.2008.10.048

Date:

08-Sep-08 Release date: 21-Oct-08

Protein chains

P17109  (MEND_ECOLI) -  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase from Escherichia coli (strain K12)

Seq: 556 a.a.

Struc: 554 a.a.

Enzyme reactions

• Enzyme class: E.C.2.2.1.9 - 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid
• Reaction: isochorismate + 2-oxoglutarate + H⁺ = 5-enolpyruvoyl-6-hydroxy-2- succinyl-cyclohex-3-ene-1-carboxylate + CO2
• Cofactor: Mg(2+)

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

reference

DOI no: 10.1016/j.jmb.2008.10.048

J Mol Biol 384:1353-1368 (2008)

PubMed id: 18983854

Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase).

A.Dawson, P.K.Fyfe, W.N.Hunter.

ABSTRACT

The thiamine diphosphate (ThDP) and metal-ion-dependent enzyme 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase, or MenD, catalyze the Stetter-like conjugate addition of alpha-ketoglutarate with isochorismate to release 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate and carbon dioxide. This reaction represents the first committed step for biosynthesis of menaquinone, or vitamin K2, a key cofactor for electron transport in bacteria and a metabolite for posttranslational modification of proteins in mammals. The medium-resolution structure of MenD from Escherichia coli (EcMenD) in complex with its cofactor and Mn2+ has been determined in two related hexagonal crystal forms. The subunit displays the typical three-domain structure observed for ThDP-dependent enzymes in which two of the domains bind and force the cofactor into a configuration that supports formation of a reactive ylide. The structures reveal a stable dimer-of-dimers association in agreement with gel filtration and analytical ultracentrifugation studies and confirm the classification of MenD in the pyruvate oxidase family of ThDP-dependent enzymes. The active site, created by contributions from a pair of subunits, is highly basic with a pronounced hydrophobic patch. These features, formed by highly conserved amino acids, match well to the chemical properties of the substrates. A model of the covalent intermediate formed after reaction with the first substrate alpha-ketoglutarate and with the second substrate isochorismate positioned to accept nucleophilic attack has been prepared. This, in addition to structural and sequence comparisons with putative MenD orthologues, provides insight into the specificity and reactivity of MenD and allows a two-stage reaction mechanism to be proposed.

Selected figure(s)

Figure 7.
Fig. 7. A stereoview of the model for substrates binding to EcMenD. The post-decarboxylation covalent adduct of ThDP and α-ketoglutarate (ThDP asterisk ) is shown, and the reactive C atoms of this intermediate and isochorismate are 1.6 Å apart. This separation is indicated by a magenta broken line. The polypeptide main chain is shown as a gray ribbon and atomic positions are colored as in the previous figures except that the C atoms of the second substrate, isochorismate, are yellow. A calculated electrostatic surface potential (blue, positive; red, negative; white, neutral) showing the active-site cleft. The figure was produced using PyMOL^1 with Adaptive Poisson–Boltzmann Solver^39 with electrostatic potential isocontours set at + 5 kT/e (blue) and − 5 kT/e (red).

Figure 8.
Fig. 8. A two-stage mechanism for catalysis by EcMenD. An asterisk marks the isochorismate C2, which is attacked by the carbanion intermediate.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 1353-1368) copyright 2008.

Figures were selected by the author.