› 4zdq

X-ray diffraction
2.3Å resolution

Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP

Released:
DOI: 10.2210/pdb4zdq/pdb
Model geometry
Fit model/data
PDB entry 4zdq coloured by chain, front view.
PDB entry 4zdq coloured by chain, side view.
PDB entry 4zdq coloured by chain, top view.
Source organism: Burkholderia thailandensis E264
Primary publication:
Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis.
Pierce PG, Hartnett BE, Laughlin TM, Blain JM, Mayclin SJ, Bolejack MJ, Myers JB, Higgins TW, Dranow DM, Sullivan A, Lorimer DD, Edwards TE, Hagen TJ, Horn JR, Myler PJ
Acta Crystallogr F Struct Biol Commun 80 43-51 (2024)
PMID: 38305785

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173960 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 241 amino acids
Theoretical weight: 25.82 KDa
Source organism: Burkholderia thailandensis E264
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2SWT6 (Residues: 2-236; Coverage: 100%)
Gene names: BTH_I2089, ispD
Sequence domains: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Structure domains: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Ligands and Environments

5 bound ligands:
Ligand CTP 2 x CTP
Ligand MG 2 x MG
Ligand ACT 10 x ACT
Ligand CAD 1 x CAD
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 45.9Å b: 138.95Å c: 76.92Å
α: 90° β: 101.94° γ: 90°
R-values:
R R work R free
0.207 0.205 0.257
Expression system: Escherichia coli BL21(DE3)

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