Database Accession: DI1400002
Name: Doc in complex with the C-terminal peptide of Phd
PDB ID: 3dd7
Experimental method: X-ray (1.70 Å)
Source organism: Enterobacteria phage P1
Proof of disorder:
Primary publication of the structure:
Garcia-Pino A, Christensen-Dalsgaard M, Wyns L, Yarmolinsky M, Magnuson RD, Gerdes K, Loris R
Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation.
(2008) J. Biol. Chem. 283: 30821-7
PMID: 18757857
Abstract:
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
Biological process:
transcription, DNA-templated The cellular synthesis of RNA on a template of DNA.
regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: B, A
Notes: Chains C and D were removed as chains A and B represent the biologically relevant interaction.
Name: Antitoxin phd
Source organism: Enterobacteria phage P1
Length: 23 residues
Sequence:Sequence according to PDB SEQRESALDAEFASLFDTLDSTNKEMVNR
The sequence contains the following modified/non-standard residues:
• selenomethionine (M) at position 70 (PDB position: 70)
UniProtKB AC: Q06253 (positions: 51-73) Coverage: 31.5%
UniRef90 AC: UniRef90_Q06253 (positions: 51-73)
Name: Protein kinase doc
Source organism: Enterobacteria phage P1
Length: 126 residues
Sequence:Sequence according to PDB SEQRESMRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSAE
UniProtKB AC: Q06259 (positions: 1-126) Coverage: 100%
UniRef90 AC: UniRef90_Q06259 (positions: 1-126)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Chain B:
The 41-73 region described in DisProt entry DP00288 covers 100% of the sequence present in the structure.
Chain A:
The Fido domain involved in the interaction is known to adopt a stable structure in isolation (PMID: 20603017).
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). The structure can be rotated by left click and hold anywhere on the structure. Representation options can be edited by right clicking on the structure window.
Download our modified structure (.pdb)
