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“Hydrolase” or “NKF” for hits to LAGLIDADG endonuclease, homing endonuclease, HNH endonuclease?

| posted 15 Jul, 2022 21:44
Phage Skinny gene at 63560-63949 bp hits several LAGLIDADG endonuclease, homing endonuclease, HNH endonuclease, with low similarity (less than 60%). Wondering whether to call it with the general “Hydrolase” or “NKF”? The amino acid sequence is:
I have also attached the relevant BLASTp and HHPred data:
| posted 20 Jul, 2022 23:35
Hi Fred,

I recently investigated a similar gene in clusters AZ and EH; Eraser_30 is an example. Your Skinny gene product has similar HHPred results, with many strong hits with >95% probability and >90% query coverage. Looking at the PDB hits, the query sequence aligns to almost the entire crystal sequence, so these are good matches (see attached file). The hits include descriptions like homing endonuclease, LADLIDADG domain, hydrolase, some of which are describing different levels of specificity (LADLIDADG is a type of homing endonucleases, which are all hydrolases).

The LADLIDADG endonucleases are one family of homing endonucleases (others are HNH endonucleases and G-I-Y Y-I-G endonucleases). The name refers to the consensus sequence of a motif in the DNA binding site. The conserved features of LADLIDADG endonucleases include:

- Approximately 100 amino acids with Alpha-beta-beta-alpha-beta-beta-alpha secondary structure
- LADLIGADG motif starting in the first alpha helix
- Aromatic amino acid right before the motif
The Skinny gene product meets these criteria, and has good alignment to the target sequence throughout, so I would recommend calling it LAGLIDADG endonuclease. Other approved functions that are accurate include endonuclease or nuclease or hydrolase, but I think there is enough evidence for the more specific call. I note that HNH endonuclease has been called for some of these genes, but those endonucleases have different structural features, and there is no evidence for HNH endonuclease here.

It is also interesting to note that Skinny is the only cluster M phage genome that has this pham!

Edited 20 Jul, 2022 23:36
| posted 21 Jul, 2022 18:29
Thank you Karen!
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