› 4fwp

X-ray diffraction
2.5Å resolution

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GDP

Released:
DOI: 10.2210/pdb4fwp/pdb
PDB entry 4fwp coloured by chain, front view.
PDB entry 4fwp coloured by chain, side view.
PDB entry 4fwp coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Primary publication:
Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.
Chittori S, Simanshu DK, Banerjee S, Murthy AM, Mathivanan S, Savithri HS, Murthy MR
Biochim Biophys Acta 1834 2036-44 (2013)
PMID: 23747922

Function and Biology Details

Reaction catalysed: 
ATP + propanoate = ADP + propanoyl phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

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 str. LT2
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 EDO 2 x EDO
Ligand GDP 1 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 111.489Å b: 111.489Å c: 66.888Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.237 0.235 0.266
Expression system: Escherichia coli

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Citations

1 review citation

Manganese and microbial pathogenesis: sequestration by the Mammalian immune system and utilization by microorganisms.
Brophy et al. (2015)
3 other articles