2JLC

Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - native protein

Summary for 2JLC

• Entry DOI: 10.2210/pdb2jlc/pdb
• Related: 2JLA
• Descriptor: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE, THIAMINE DIPHOSPHATE, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: menaquinone biosynthesis, manganese, transferase, thiamine diphosphate cofactor, thiamine pyrophosphate
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 128653.20

Authors

Dawson, A.,Fyfe, P.K.,Hunter, W.N. (deposition date: 2008-09-08, release date: 2008-10-21, Last modification date: 2023-12-13)

Primary citation

Dawson, A.,Fyfe, P.K.,Hunter, W.N.
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-, 2008

PubMed 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.

PubMed: 18983854
DOI: 10.1016/J.JMB.2008.10.048

Experimental method

X-RAY DIFFRACTION (2.5 Å)