› 4pu4

X-ray diffraction
3.79Å resolution

Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P21)

Released:
DOI: 10.2210/pdb4pu4/pdb
PDB entry 4pu4 coloured by chain, front view.
PDB entry 4pu4 coloured by chain, side view.
PDB entry 4pu4 coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence.
Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B, Devreese B, Savvides SN
Nucleic Acids Res 42 10134-47 (2014)
PMID: 25056321

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117986 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Serine/threonine-protein kinase toxin HipA Chains: A, B
Molecule details ›
Chains: A, B
Length: 454 amino acids
Theoretical weight: 51.17 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8EIX3 (Residues: 1-433; Coverage: 100%)
Gene names: SO_0706, hipA
Sequence domains:
Antitoxin HipB Chains: C, D
Molecule details ›
Chains: C, D
Length: 118 amino acids
Theoretical weight: 12.95 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8EIX4 (Residues: 1-78; Coverage: 100%)
Gene names: SO_0705, hipB
Sequence domains: Helix-turn-helix
Structure domains: lambda repressor-like DNA-binding domains
Operator DNA Chain: Q
Molecule details ›
Chain: Q
Length: 26 nucleotides
Theoretical weight: 8.04 KDa
Operator DNA Chain: P
Molecule details ›
Chain: P
Length: 26 nucleotides
Theoretical weight: 7.93 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1), SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 72.24Å b: 57.33Å c: 171.38Å
α: 90° β: 95.81° γ: 90°
R-values:
R R work R free
0.24 0.236 0.306
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Keeping the Wolves at Bay: Antitoxins of Prokaryotic Type II Toxin-Antitoxin Systems.
Chan et al. (2016)
4 more

5 mentions without citation

Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy.
Coussens et al. (2016)
4 more