› 1iv3

X-ray diffraction
1.52Å resolution

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms)

Released:
DOI: 10.2210/pdb1iv3/pdb
PDB entry 1iv3 coloured by chain, front view.
PDB entry 1iv3 coloured by chain, side view.
PDB entry 1iv3 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY
Acta Crystallogr D Biol Crystallogr 59 23-31 (2003)
PMID: 12499535

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-186024 (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: 152 amino acids
Theoretical weight: 16.6 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RQP5 (Residues: 1-152; Coverage: 100%)
Gene names: TTHA1790, ispF
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

1 bound ligand:
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P41212
Unit cell:
a: 106.179Å b: 106.179Å c: 148.811Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.202 0.257
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Biochemistry of the non-mevalonate isoprenoid pathway.
Gräwert et al. (2011)
3 more

1 mention without citation

Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction.
Tan et al. (2008)