SEA-PHAGES | PD-(D/E)XK endonuclease

Link to this post \| posted 26 Jul, 2021 23:40
cdshaffer	I have run across a very clean HHPRED hit to the crystal structure 2OST in phage Jada (CDS 81782 - 82135) and Bartholomune (CDS 105264 - 105620). There are two more genes in the pham group, Braelyn_205 which is annotated NKF and Racecar_217 which is currently annotated "Holiday junction resolvase" and is quite a bit larger than the other three. For Jada the protein has an HHPRED hit with 99.9% probability and 99.1% coverage to the 2OST crystal. There are secondary hits to Holiday junction resolvases but these alignments are only about 45% coverage. This Jada protein also aligns in HHPRED to the Pfam PF11645 with 98.9% prob 98% coverage. the paper associated with this crystal is here: The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. Yhis paper described a different type of endonuclease with a fold pattern and critical amino acids which is distinct from the more typical HNH endonucleases. Following the typical structure of our other endonucleases I would propose either "PD-(D/E)-XK endonuclease" based on the terms used in the above EMBO paper or the same without the dashes (i.e. PD(D/E)XK ) or the variant used with the Pfam "PD-(D/E)XK endonuclease" Note jada protein does not align to any of the other types of endonucleases (HNH, RusA, G-I-Y Y-I-G, or LAGLIDADG). Edited 26 Jul, 2021 23:50

Link to this post | posted 26 Jul, 2021 23:40

I have run across a very clean HHPRED hit to the crystal structure 2OST in phage Jada (CDS 81782 - 82135) and Bartholomune (CDS 105264 - 105620). There are two more genes in the pham group, Braelyn_205 which is annotated NKF and Racecar_217 which is currently annotated "Holiday junction resolvase" and is quite a bit larger than the other three.

For Jada the protein has an HHPRED hit with 99.9% probability and 99.1% coverage to the 2OST crystal. There are secondary hits to Holiday junction resolvases but these alignments are only about 45% coverage. This Jada protein also aligns in HHPRED to the Pfam PF11645 with 98.9% prob 98% coverage.

the paper associated with this crystal is here: The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.

Yhis paper described a different type of endonuclease with a fold pattern and critical amino acids which is distinct from the more typical HNH endonucleases. Following the typical structure of our other endonucleases I would propose either "PD-(D/E)-XK endonuclease" based on the terms used in the above EMBO paper or the same without the dashes (i.e. PD(D/E)XK ) or the variant used with the Pfam "PD-(D/E)XK endonuclease"

Note jada protein does not align to any of the other types of endonucleases (HNH, RusA, G-I-Y Y-I-G, or LAGLIDADG).

Edited 26 Jul, 2021 23:50

Link to this post \| posted 28 Jul, 2021 21:47
cdshaffer	I just found this comment in the approved list in the notes for Cas4 family exonuclease which may be why some people may remember seeing hits to this Pfam before but never using it in a functional annotation: Cas4 family exonucleases - This family of exonucleases is similar to the exonuclease domain of RecB. The Cas4 label should be used if the gene includes only the exonuclease region. IF the gene also includes a helicase domain, the RecB label should be used. Cas4 family nucleases tend to have alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others). I checked and there were a few HHPRED alignments between Cas4 and this Jada protein but they were very short (~25 aa) with scores of ~35%, so the "Cas4 family exonuclease" is not really appropriate for this small group of proteins. However, for many other proteins, with high quality alignments to both Cas4 and hits to PD-(D/E)XK, the Cas4 may be the better final annotation. Annotators should examine the lengths and qualities of the alignments to pick between all these various exonucleases.

Link to this post | posted 28 Jul, 2021 21:47

cdshaffer

I just found this comment in the approved list in the notes for Cas4 family exonuclease which may be why some people may remember seeing hits to this Pfam before but never using it in a functional annotation:

Cas4 family exonucleases - This family of exonucleases is similar to the exonuclease domain of RecB. The Cas4 label should be used if the gene includes only the exonuclease region. IF the gene also includes a helicase domain, the RecB label should be used. Cas4 family nucleases tend to have alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others).

I checked and there were a few HHPRED alignments between Cas4 and this Jada protein but they were very short (~25 aa) with scores of ~35%, so the "Cas4 family exonuclease" is not really appropriate for this small group of proteins. However, for many other proteins, with high quality alignments to both Cas4 and hits to PD-(D/E)XK, the Cas4 may be the better final annotation. Annotators should examine the lengths and qualities of the alignments to pick between all these various exonucleases.

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PD-(D/E)XK endonuclease