› 3hww

X-ray diffraction
1.95Å resolution

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate

Released:
DOI: 10.2210/pdb3hww/pdb
PDB entry 3hww coloured by chain, front view.
PDB entry 3hww coloured by chain, side view.
PDB entry 3hww coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural and functional analysis of Vitamin K2 synthesis protein MenD.
Priyadarshi A, Kim EE, Hwang KY
Biochem Biophys Res Commun 388 748-51 (2009)
PMID: 19703421

Function and Biology Details

Reaction catalysed: 
Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147868 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase Chains: A, D
Molecule details ›
Chains: A, D
Length: 556 amino acids
Theoretical weight: 61.45 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P17109 (Residues: 1-556; Coverage: 100%)
Gene names: JW5374, b2264, menD
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand AKG 2 x AKG
Ligand MG 2 x MG
Ligand NA 37 x NA
Ligand CL 2 x CL
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P41212
Unit cell:
a: 117.91Å b: 117.91Å c: 175.276Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.255
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Engineering stereoselectivity of ThDP-dependent enzymes.
Hailes et al. (2013)
2 more