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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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 IPR038729 #4333

Closed ValWood closed 10 months ago

ValWood commented 2 years ago

GO:0140664 | ATP-dependent DNA damage sensor activity | IEA with IPR038729

https://www.pombase.org/gene/SPAC14C4.02c

Hi, do you have a source for this? It might be correct, but a paper I read recently https://www.pombase.org/reference/PMID:30348841 implies that smc5/6 is recruited to DSB via brc1 recognising some modifies H2A to recruit the Smc 5/6 complex. This makes it seem that Smc 5/6 is not the actual sensor.

sarach06 commented 2 years ago

Dear Val, Thank you very much for pointing this out. I agree with you that members of this entry are not the sensors (see also PMID:19308707 and PMID:17698079). I replaced this term with GO:0016887 (ATP hydrolysis activity) and added GO:0006302 (DSB repair) to this entry. I added the reference you provided and the ones I mentioned. Let me know if you agree or if you consider any better mapping. The changes will be visible in InterPro 92.0. Best, Sara

ValWood commented 2 years ago

GO:0061776 topological DNA co-entrapment activity is the best term for core smc5-6 complex. It was created for condensin/cohesin, but it's essentially the same MF. I'm checking a community curated paper on this complex this morning so I'll see if I can suggest any improved biological process mappings after that.

sarach06 commented 2 years ago

Excellent, many thanks. I added GO:0061776 to this entry.

ValWood commented 2 years ago

Actually looking closer, you can't add to this InterPro entry because it also includes Rad50 (I think Rad50 might be in the sensor complex, but I am not sure it is this subunit specifically, but this explains the original mapping).

GO:0061776 could be added to any families that are specific for the Smc5/6 complex subunit.

This particular family might be a sub group of the ATPase domain (both are ATPases), I did not look closely yet...

sarach06 commented 2 years ago

I see... I'll remove it, then. Thanks.

sjm41 commented 10 months ago

It might be appropriate to add back the "GO:0140664 | ATP-dependent DNA damage sensor activity" annotation to this more rad50-specific entry?: IPR004584 DNA repair protein Rad50, eukaryotes (https://www.ebi.ac.uk/interpro/entry/InterPro/IPR004584/)

blazaropinto commented 10 months ago

Hi Steven,

Thank you for this. I am looking for evidence that Rad50 is the sensor of the MRE11-RAD50-NBS1 complex (MRN complex). In PMID: 23388631 they point to MRE11 as the sensor. The most recent review I found is PMID: 31767017, which attributes the sensor activity to the whole complex. Do you know of any other evidence?

Best,

Beatriz

sjm41 commented 10 months ago

Ah, I was making an assumption about the sensor activity being specific the Rad50 given it's the ATPase component of the complex and the previous annotation mentioned above. Given your research, it sounds like it's not appropriate to add "GO:0140664 | ATP-dependent DNA damage sensor activity" to IPR004584. So I'll re-close this ticket. Thanks for checking!