› 1h48

X-ray diffraction
2.3Å resolution

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

Released:
DOI: 10.2210/pdb1h48/pdb
PDB entry 1h48 coloured by chain, front view.
PDB entry 1h48 coloured by chain, side view.
PDB entry 1h48 coloured by chain, top view.
Source organism: Escherichia coli BL21
Primary publication:
The identification of isoprenoids that bind in the intersubunit cavity of Escherichia coli 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase by complementary biophysical methods.
Kemp LE, Alphey MS, Bond CS, Ferguson MA, Hecht S, Bacher A, Eisenreich W, Rohdich F, Hunter WN
Acta Crystallogr D Biol Crystallogr 61 45-52 (2005)
PMID: 15608374

Function and Biology Details

Reaction catalysed: 
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158656 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 161 amino acids
Theoretical weight: 17.16 KDa
Source organism: Escherichia coli BL21
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P62617 (Residues: 1-159; Coverage: 100%)
Gene names: JW2716, b2746, ispF, mecS, ygbB
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

5 bound ligands:
Ligand CDI 6 x CDI
Ligand ZN 6 x ZN
Ligand C5P 6 x C5P
Ligand MN 2 x MN
Ligand GPP 2 x GPP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: C2
Unit cell:
a: 198.122Å b: 150.287Å c: 57.559Å
α: 90° β: 106.52° γ: 90°
R-values:
R R work R free
0.204 0.202 0.236
Expression system: Escherichia coli BL21

Quick links

Citations

8 review citations

Biogenesis, molecular regulation and function of plant isoprenoids.
Bouvier et al. (2005)
7 more

2 mentions without citation

A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.
Ramsden et al. (2009)
1 more