› 1knj

X-ray diffraction
2.8Å resolution

Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+

Released:
DOI: 10.2210/pdb1knj/pdb
PDB entry 1knj coloured by chain, front view.
PDB entry 1knj coloured by chain, side view.
PDB entry 1knj coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway.
Richard SB, Ferrer JL, Bowman ME, Lillo AM, Tetzlaff CN, Cane DE, Noel JP
J Biol Chem 277 8667-72 (2002)
PMID: 11786530

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 Chain: A
Molecule details ›
Chain: A
Length: 159 amino acids
Theoretical weight: 17.11 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
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

3 bound ligands:
Ligand MN 1 x MN
Ligand C5P 1 x C5P
Ligand CDI 1 x CDI
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A, ESRF BEAMLINE ID14-1
Spacegroup: I213
Unit cell:
a: 144.254Å b: 144.254Å c: 144.254Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.286 0.241 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Molecular recognition in chemical and biological systems.
Persch et al. (2015)
10 more

1 mention without citation

New Insight into Isoprenoids Biosynthesis Process and Future Prospects for Drug Designing in Plasmodium.
Saggu et al. (2016)