› 1t0a

X-ray diffraction
1.6Å resolution

Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis

Released:
DOI: 10.2210/pdb1t0a/pdb
PDB entry 1t0a coloured by chain, front view.
PDB entry 1t0a coloured by chain, side view.
PDB entry 1t0a coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity.
Ni S, Robinson H, Marsing GC, Bussiere DE, Kennedy MA
Acta Crystallogr D Biol Crystallogr 60 1949-57 (2004)
PMID: 15502301

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-184339 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 159 amino acids
Theoretical weight: 17.16 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q8EBR3 (Residues: 1-159; Coverage: 100%)
Gene names: SO_3437, ispF
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand CO 3 x CO
Ligand FPP 1 x FPP
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591, NSLS BEAMLINE X12C
Spacegroup: P43212
Unit cell:
a: 117.088Å b: 117.088Å c: 108.937Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.174 0.193
Expression system: Escherichia coli K-12

Quick links

Citations

3 review citations

Current development in isoprenoid precursor biosynthesis and regulation.
Chang et al. (2013)
2 more

1 mention without citation

Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly amongst IspD/IspE/IspF enzymes in the MEP pathway.
Liu et al. (2018)