› 2pmp

X-ray diffraction
2.3Å resolution

Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana

Released:
DOI: 10.2210/pdb2pmp/pdb
PDB entry 2pmp coloured by chain, front view.
PDB entry 2pmp coloured by chain, side view.
PDB entry 2pmp coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Biosynthesis of isoprenoids in plants: structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes.
Calisto BM, Perez-Gil J, Bergua M, Querol-Audi J, Fita I, Imperial S
Protein Sci 16 2082-8 (2007)
PMID: 17660251

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 analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189948 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 160 amino acids
Theoretical weight: 17.35 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9CAK8 (Residues: 72-231; Coverage: 69%)
Gene names: At1g63970, F22C12.26, ISPF, MCS, MDS, T12P18.1
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand PO4 1 x PO4
Ligand CL 1 x CL
Ligand C5P 1 x C5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I4132
Unit cell:
a: 135.795Å b: 135.795Å c: 135.795Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.251
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Mechanistic aspects of carotenoid biosynthesis.
Moise et al. (2014)
4 more

4 mentions without citation

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