Shedu
Description
The Shedu antiphage system consists of a single protein, SduA, which acts as a nuclease with a conserved DUF4263 domain belonging to the PD-(D/E)XK nuclease superfamily. The system was named after an Assyrian Mythical Deity. The N-terminal domain is very diverse including diverse nucleic acid binding, enzymatic, and other domains.
Molecular Mechanism
The Shedu protein is proposed to act as a nuclease, and its N-terminal domain inhibits its activation until triggered by phage infection. The activation of the protein was described in (N/A) . In B. cereus Shedu, "a key catalytic residue in Shedu’s nuclease domain is sequestered away from the catalytic site. Activation involves a conformational change that completes the active site and promotes assembly of a homo-octamer for coordinated double-strand DNA cleavage. Removal of Shedu’s N-terminal domain ectopically activates the enzyme, suggesting that this domain allosterically inhibits Shedu in the absence of infection." The nuclease activity and specific sensing of an E. coli Shedu was described in (N/A) "The N-terminal domains of SduA form a clamp that recognizes free DNA ends. End binding positions the DNA over the PD/ExK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5’ end. The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA in vivo". In E. coli, T6 phages can escape Shedu immunity by suppressing their recombination-dependent DNA replication pathway.
Example of genomic structure
The Shedu is composed of 1 protein: SduA.
Here is an example found in the RefSeq database:
The Shedu system in Bradyrhizobium ottawaense (GCF_002278135.2, NZ_CP029425) is composed of 1 protein: SduA (WP_225004618.1)
Distribution of the system among prokaryotes
Structure
Group | Structure | Foldseek | System | Gene name | Subtype | Proteins in structure | System genes | Prediction type | N genes in sys | pLDDT | iptm+ptm | pDockQ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No data available | ||||||||||||