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X-ray diffraction
1.82Å resolution

CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+

Released:
DOI: 10.2210/pdb1ini/pdb
PDB entry 1ini coloured by chain, front view.
PDB entry 1ini coloured by chain, side view.
PDB entry 1ini coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis.
Richard SB, Bowman ME, Kwiatkowski W, Kang I, Chow C, Lillo AM, Cane DE, Noel JP
Nat Struct Biol 8 641-8 (2001)
PMID: 11427897

Function and Biology Details

Reaction catalysed: 
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175156 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Chain: A
Molecule details ›
Chain: A
Length: 236 amino acids
Theoretical weight: 25.77 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46893 (Residues: 1-236; Coverage: 100%)
Gene names: JW2717, b2747, ispD, ygbP
Sequence domains: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Structure domains: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand CDM 1 x CDM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: C2
Unit cell:
a: 129.99Å b: 46.764Å c: 38.387Å
α: 90° β: 92.64° γ: 90°
R-values:
R R work R free
0.222 0.222 0.273
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

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

5 mentions without citation

Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae.
Baur et al. (2009)
4 more