› 1yqn

X-ray diffraction
3.11Å resolution

E. coli ispF double mutant

Released:
DOI: 10.2210/pdb1yqn/pdb
PDB entry 1yqn coloured by chain, front view.
PDB entry 1yqn coloured by chain, side view.
PDB entry 1yqn coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A double mutation of Escherichia coli2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.
Sgraja T, Kemp LE, Ramsden N, Hunter WN
Acta Crystallogr Sect F Struct Biol Cryst Commun 61 625-9 (2005)
PMID: 16511114

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-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: 161 amino acids
Theoretical weight: 17.08 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

4 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 1 x MN
Ligand CDP 1 x CDP
Ligand GPP 1 x GPP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: I213
Unit cell:
a: 143.778Å b: 143.778Å c: 143.778Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.209
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

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

2 mentions without citation

A double mutation of Escherichia coli2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.
Sgraja et al. (2005)
1 more