SEA-PHAGES | Third type of Holiday junction resolvase

Link to this post \| posted 15 Dec, 2017 20:40
cdshaffer	Analysis of protein OzzyJ_38 draft annotation. When we run an HHPRED analysis at the original site, the top hit is to a crystal structure with 99.18% probability and an e-score of 2.6x10-12 to pdb crystal structure 2WCW which is described as a Holiday junction resolvase from Archaeoglobus fulgidus. At this point looking into the issue of it was a "RusA" or "RuvC" type of resolvase we looked at the 4th best HHPRED hit (which actually had an associated published paper) with a probability of 98.81% and e of 4.9x10-10 to the pdb crystal structure for 1GEF. This is also described as a Holiday junction resolvase but was from the hyperthermophilic archaeon Pyrococcus furiosus. The paper describing these results (Structure. 2001 Mar 7;9(3):197-204) describes this structure as "The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known." Instead the overall structure is described to be similar to type II restriction endonucleases. For now, we have submitted this protein with the simple annotation of "holliday junction resolvase" since it is neither a RusA or RuvC type. However, if adding a type was preferred, adding a descriptor like "Archaeal" or some indication of its similarity to type II RE enzymes might be appropriate. Follow on thoughts appreciated.

Link to this post | posted 15 Dec, 2017 20:40

Analysis of protein OzzyJ_38 draft annotation. When we run an HHPRED analysis at the original site, the top hit is to a crystal structure with 99.18% probability and an e-score of 2.6x10-12 to pdb crystal structure 2WCW which is described as a Holiday junction resolvase from Archaeoglobus fulgidus.

At this point looking into the issue of it was a "RusA" or "RuvC" type of resolvase we looked at the 4th best HHPRED hit (which actually had an associated published paper) with a probability of 98.81% and e of 4.9x10-10 to the pdb crystal structure for 1GEF. This is also described as a Holiday junction resolvase but was from the hyperthermophilic archaeon Pyrococcus furiosus. The paper describing these results (Structure. 2001 Mar 7;9(3):197-204) describes this structure as "The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known." Instead the overall structure is described to be similar to type II restriction endonucleases.

For now, we have submitted this protein with the simple annotation of "holliday junction resolvase" since it is neither a RusA or RuvC type. However, if adding a type was preferred, adding a descriptor like "Archaeal" or some indication of its similarity to type II RE enzymes might be appropriate.

Follow on thoughts appreciated.

Link to this post \| posted 18 Dec, 2017 16:50
welkin	Thanks Chris. I think we will have to meditate on this one a bit and get back to you.

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Third type of Holiday junction resolvase