3HWW: Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate

Citation:
Abstract
Here we describe in detail the crystal structures of the Vitamin K(2) synthesis protein MenD, from Escherichia coli, in complex with thiamine diphosphate (ThDP) and oxoglutarate, and the effects of cofactor and substrate on its structural stability. This is the first reported structure of MenD in complex with oxoglutarate. The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure. Biospecific-interaction analysis using surface plasmon resonance (SPR) technology reveals an affinity for ThDP and oxoglutarate in the nanomolar range. Biochemical and structural analysis confirmed that MenD is highly dependent on ThDP for its structural stability. Our structural results combined with the biochemical assay reveal novel features of the enzyme that could be utilized in a program of rational structure-based drug design, as well as in helping to enhance our knowledge of the menaquinone synthesis pathway in greater detail.
PDB ID: 3HWWDownload
MMDB ID: 77833
PDB Deposition Date: 2009/6/19
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.95  Å
Source Organism:
Similar Structures:
Biological Unit for 3HWW: dimeric; determined by author and by software (PISA)
Molecular Components in 3HWW
Label Count Molecule
Proteins (2 molecules)
2
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate Synthase(Gene symbol: menD)
Molecule annotation
Chemicals (49 molecules)
1
2
2
2
3
37
4
2
5
6
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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