2JLA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).

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

(2008) J.Mol.Biol. 384: 1353

  • DOI: 10.1016/j.jmb.2008.10.048
  • Primary Citation of Related Structures:  

  • 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-su ...

    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.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
A, B, C, D
558Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: menD
EC: 2.2.1.9
Find proteins for P17109 (Escherichia coli (strain K12))
Go to UniProtKB:  P17109
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.169 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 95.830α = 90.00
b = 95.830β = 90.00
c = 463.170γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SOLVEphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance