› 1x3n

X-ray diffraction
2.3Å resolution

Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium

Released:
DOI: 10.2210/pdb1x3n/pdb
PDB entry 1x3n coloured by chain, front view.
PDB entry 1x3n coloured by chain, side view.
PDB entry 1x3n coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Primary publication:
Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily.
Simanshu DK, Savithri HS, Murthy MR
J Mol Biol 352 876-92 (2005)
PMID: 16139298

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 BL21(DE3)
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 1 x EDO
Ligand ANP 1 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 111.275Å b: 111.275Å c: 66.813Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.197 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate.
Simanshu et al. (2007)
18 other articles

1 mention without citation

Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases.
Diao et al. (2009)