ntr: collective parent for small protein ligases.

[gocentral]

During discussions with SGD, it emerged the difficulty in distinguishing between SUMO and ubiquitin ligases based on sequence similairty.

Although usually, ubiquitin ligases are RING fingers (or PHD fingers) and SUMO ligases are zf-MIZ, some S. cerevisiae data indicates that some which appear to be RING are in fact SUMO ligaes (the 2 families are related).

The only way round this is to annotate to their commetn parent amino-acid ligase activity which loses some info for this functioannly related group.

So can we have a new common parent for SUMO ligase activity ubiquitin-protein ligase activity NEDD8 ligase activity

(something like small conjugating protein ligase activity? perhaps somebody can think of better wording...

I also wonder if we need the term ubiquitin-like-protein ligase activity (undefined) as this appears to just mean it isn't a ubiquitin ligase?

also ubiquitin-calmodulin ligase activity isn't this just a ubiquitin ligase?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/3480":https://sourceforge.net/p/geneontology/ontology-requests/3480

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Hi,

Val's suggestions all seem quite reasonable to me, and I can't think of a better wording than 'small conjugating protein ligase activity' either.

-Karen

Original comment by: krchristie

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Given that we have 'ubiquitin-like-protein ligase activity' (GO:0019787), it's undefined, and it's only used for a few annotations, how about renaming it? The whopping 6 (count 'em, 6) annotations would still be correct, as would the existing children (and their annotations), and we could move ubiquitin- protein ligase activity under it as well. (I also haven't thought of anything better than 'small conjugating protein ligase'.)

I have moved ubiquitin-calmodulin ligase activity (GO:0050372) down to be is_a ubiquitin-protein ligase activity (GO:0004842).

m

Original comment by: mah11

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yes, i think renaming the existing term is fine

Val

Original comment by: ValWood

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hmmm, there is also

ubiquitin-like-protein-specific protease activity ubiquitin-like hydroalse activty ubiquitin-lie activating activity and ubiquitin-like conjugating activity

perhaps these should be treated similarly

Val

Original comment by: ValWood

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Midori's suggestion to rename the existing term 'ubiquitin-like-protein ligase activity' (GO:0019787)' seems good to me. Val's suggestions that perhaps the other places where we deal with ubiquitin-like __ activities should be dealt with in the same way also seem reasonable.

-Karen

Original comment by: krchristie

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I'm very tempted to make these obsolete:

-ubiquitin-like hydrolase activity GO:0019790 -[i] APG12 hydrolase activity GO:0019792 -[i] FAT10 hydrolase activity GO:0019791 -[i] Hub1 hydrolase activity GO:0042291 -[i] Urm1 hydrolase activity GO:0042290

They're not defined, as of mid-June nothing was annotated to them, I can't find much about their history, and I can't tell what, if anything, they mean. (PubMed searches for APG12 hydrolase, etc., proved unenlightening.) I suspect the 'x protease' terms -- which are defined -- will do for annotations. Any objections (or other comments)?

In other news, I followed the renaming plan for two terms: GO:0019783 now small conjugating protein-specific protease activity GO:0019787 now small conjugating protein ligase activity (and defined)

moved 'ubiquitin' terms down to be is_a renamed terms (old wording as narrow synonym): GO:0004843 is_a GO:0019783 GO:0004842 is_a GO:0019787

For the other two terms Val listed, there were already generic 'small protein' terms, so I merged pairs: GO:0008640 merged into GO:0008639 GO:0008642 merged into GO:0008641 note - changed synonym scope to narrow

m

Original comment by: mah11

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sounds good, i'd go with the obsoletions too as we have no idea what they are...I doubt anybody else will know if they aren't used, so safer to kill

Original comment by: ValWood

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No comment on those obsoletions other than to say I have no idea what they are for either.

For a completely different reason, I am curating another paper that describes a completely different SUMO ligase than the one with bad GO annots that prompted Val to ask SGD to check on.

It seems that I need a term for something like 'SUMO-conjugate binding'. I notice that we have the terms:

.protein binding ..ubiquitin binding ...polyubiquitin binding

but we don't have any terms at all for SUMO binding. I was wondering if we should make similar parallel changes for binding terms as we're suggesting for the process terms.

As a further note, the paper I'm reading makes the distinction between "Smt3-conjugated products" and "Smt3 monomers", but I think the former could be appropriately be described as "polySUMO" or "SUMO polymers"

-Karen

Original comment by: krchristie

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Trying to clarify yesterday's comment, I wonder if we should implement a parallel structure for these binding terms, as we are suggesting for the process terms.

Secondly, I need to request 2 new terms, which could be

.protein binding ..SUMO binding ; GO:new ...SUMO polymer binding ; GO:new

For the second one, 'SUMO polymer binding', this wording seems wierd, but so does 'polySUMO binding'. The paper I was reading actually referred to 'Smt3-conjugate binding', which might be appropriate as a synonym, but definitely not as the main term name.

-Karen

Original comment by: krchristie

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OK, I've added: small conjugating protein binding GO:0032182 SUMO binding GO:0032183 (exact synonym Smt3 binding) SUMO polymer binding GO:0032184 (exact synonym Smt3 polymer binding; related synonym Smt3-conjugate binding)

... and made ubiquitin binding is_a GO:0032182. Are the synonym scopes OK?

Do you want to add more children to GO:0032182 now, or just wait until the need arises?

m

Original comment by: mah11

[gocentral]

• labels: --> New term request
• milestone: --> 224410
• assigned_to: nobody --> gomidori

Original comment by: mah11

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Hi Midori,

> OK, I've added: > small conjugating protein binding GO:0032182 > SUMO binding GO:0032183 (exact synonym Smt3 binding) > SUMO polymer binding GO:0032184 > - exact synonym Smt3 polymer binding > - related synonym Smt3-conjugate binding > > ... and made ubiquitin binding is_a GO:0032182. Are the synonym > scopes OK?

This all looks good to me :)

> Do you want to add more children to GO:0032182 now, or just wait > until the need arises?

Personally, I'd wait till the need arises, because suggesting what else should be represented by a child term would require more research!

So, I think we could close this item.

Thanks,

-Karen

Original comment by: krchristie

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HI again,

I've just gone back to the paper I was reading to recheck something for the annotation I was reading. I think they may be using the phrase 'Smt- conjugated proteins' to refer to proteins that have been sumoylated, thus the smt3-conjugate would be a combination of 2 different proteins, Sumo + something else where there might be more than 1 copy of SUMO.

This might impact the "Smt3-conjugate binding" synonym. It probably shouldn't be a synonym for "SUMO polymer binding". It might be most appropriate to make a separate term for this, but I don't really need it right now. They also showed that Zip1 (the protein I'm annotating) binds directly to polymeric SUMO, so I can just use the 'SUMO polymer binding' term and we could add the other term if it becomes clear that we need it.

thanks,

-Karen

Original comment by: krchristie

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OK, to be on the safe side I've removed the synonym 'Smt3-conjugate binding' from GO:0032184.

I've also made those inscrutable terms obsolete: ubiquitin-like hydrolase activity GO:0019790 -[i] APG12 hydrolase activity GO:0019792 -[i] FAT10 hydrolase activity GO:0019791 -[i] Hub1 hydrolase activity GO:0042291 -[i] Urm1 hydrolase activity GO:0042290

... so I'll close this, and people can open new items if they need more terms later.

m

Original comment by: mah11

[gocentral]

• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11