3DD7 image
Deposition Date 2008-06-05
Release Date 2008-09-16
Last Version Date 2024-11-06
Entry Detail
PDB ID:
3DD7
Title:
Structure of DocH66Y in complex with the C-terminal domain of Phd
Biological Source:
Source Organism:
Enterobacteria phage P1 (Taxon ID: 10678)
(Taxon ID: )
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.19
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Death on curing protein
Gene (Uniprot):doc
Mutations:H66Y, E126D
Chain IDs:A, C
Chain Length:135
Number of Molecules:2
Biological Source:Enterobacteria phage P1
Polymer Type:polypeptide(L)
Molecule:Prevent host death protein
Gene (Uniprot):phd
Mutations:L70(MSE)
Chain IDs:B, D
Chain Length:23
Number of Molecules:2
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE B MET SELENOMETHIONINE
Ligand Molecules
Primary Citation
Doc of Prophage P1 Is Inhibited by Its Antitoxin Partner Phd through Fold Complementation
J.Biol.Chem. 283 30821 30827 (2008)
PMID: 18757857 DOI: 10.1074/jbc.M805654200

Abstact

Prokaryotic toxin-antitoxin modules are involved in major physiological events set in motion under stress conditions. The toxin Doc (death on curing) from the phd/doc module on phage P1 hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation. This Phd domain is intrinsically disordered in solution and folds into an alpha-helix upon binding to Doc. The details of the interactions reveal the molecular basis for the inhibitory action of the antitoxin. The complex resembles the Fic (filamentation induced by cAMP) proteins and suggests a possible evolutionary origin for the phd/doc operon. Doc induces growth arrest of Escherichia coli cells in a reversible manner, by targeting the protein synthesis machinery. Moreover, Doc activates the endogenous E. coli RelE mRNA interferase but does not require this or any other known chromosomal toxin-antitoxin locus for its action in vivo.

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Primary Citation of related structures