› 2e1z

X-ray diffraction
1.98Å resolution

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP

Released:
DOI: 10.2210/pdb2e1z/pdb
PDB entry 2e1z coloured by chain, front view.
PDB entry 2e1z coloured by chain, side view.
PDB entry 2e1z coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Primary publication:
Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.
Simanshu DK, Savithri HS, Murthy MR
Proteins 70 1379-88 (2008)
PMID: 17894350

Function and Biology Details

Reaction catalysed: 
ATP + propanoate = ADP + propanoyl phosphate
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-126546 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Propionate kinase Chain: A
Molecule details ›
Chain: A
Length: 415 amino acids
Theoretical weight: 45.25 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli
UniProt:
  • Canonical: O06961 (Residues: 2-402; Coverage: 100%)
Gene names: STM3242, oxd-2, tdcD
Sequence domains: Acetokinase family
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments

2 bound ligands:
Ligand B4P 1 x B4P
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P3121
Unit cell:
a: 110.483Å b: 110.483Å c: 66.607Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.191 0.221
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Synthetic Strategies for Dinucleotides Synthesis.
Appy et al. (2019)
4 other articles

1 mention without citation

The mysterious diadenosine tetraphosphate (AP4A).
Zegarra et al. (2023)