› 2c06

Solution NMR

NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)

Released:
DOI: 10.2210/pdb2c06/pdb
PDB entry 2c06 coloured by chain, ensemble of 10 models, front view.
PDB entry 2c06 coloured by chain, ensemble of 10 models, side view.
PDB entry 2c06 coloured by chain, ensemble of 10 models, top view.
Source organism: Escherichia coli
Primary publication:
Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system.
Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Muñoz-Gómez A, van den Heuvel RH, Díaz-Orejas R, Boelens R
J Mol Biol 357 115-26 (2006)
PMID: 16413033

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146824 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Endoribonuclease PemK Chains: A, B
Molecule details ›
Chains: A, B
Length: 110 amino acids
Theoretical weight: 11.9 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P13976 (Residues: 24-133; Coverage: 83%)
Gene name: pemK
Sequence domains: PemK-like, MazF-like toxin of type II toxin-antitoxin system
Structure domains: SH3 type barrels.
5'-R(*AP*UP*AP*CP*AP)-3' Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.55 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 25%
Refinement method: HADDOCK
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Toxin-antitoxin systems in bacteria and archaea.
Yamaguchi et al. (2011)
8 more

4 mentions without citation

Structural basis of mRNA recognition and cleavage by toxin MazF and its regulation by antitoxin MazE in Bacillus subtilis.
Simanshu et al. (2013)
3 more