3KH2: Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386

Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phd antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.
PDB ID: 3KH2Download
MMDB ID: 155906
PDB Deposition Date: 2009/10/29
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.71  Å
Source Organism:
Similar Structures:
Biological Unit for 3KH2: tetrameric; determined by author and by software (PISA)
Molecular Components in 3KH2
Label Count Molecule
Proteins (4 molecules)
Death on Curing Protein(Gene symbol: doc)
Molecule annotation
Prevent Host Death Protein(Gene symbol: phd)
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB