IPR003027 -> exonuclease (and SPKW)

[gocentral]

I think this mapping should be removed.There is an older paper which repoorts an exonuclease activity but according to Paul Russell nobody belives it, and it hasn't been repeated. I haven't even tracked down the original source of this as the SGD annotation is from an ISS.....does anybody know whereit was from originally?

Also not sure about DNA binding...it is loaded onto DNA but I dont think there is any covalent interaction, though I'd have to check.

val

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/32":https://sourceforge.net/p/geneontology/annotation-issues/32

[gocentral]

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The pombe gene is rad1, so S.c checkpoint clamp complex protein RAD17.

At SGD it has 3'-5'exonuclease (putative)

and a GO annotation to nuclease supported by EMBO J 16(17):5216-26 and an ISS. (I didn't look any further than this abstact which doesn't mention it) I don't know how good the ISS is but I can look in the paper to see if they provide an alignment and what they are ISS ing it to.

Original comment by: ValWood

[gocentral]

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On the DNA binding: there doesn't have to be a covalent interaction for something to bind DNA; binding should not require covalent interactions; you can have these after the fact, but they are not required (transcription factors binding DNA: no covalent interaction is involved.

For IP2GO and SPKW2Go, I think you could contact Michele Magrane magrane@ebi.ac.uk to find out how/why it was assigned?

Original comment by: hdrabkin

[gocentral]

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Hi Harold sorry, I should have said I am not sure if it binds DNA covalently or non-covalently. It is loaded by the clamp loader rad17 RFC related checkpoint protein, which is DNA binding, but I think the clamp complex encircles DNA similarly to cohesin or PCNA sliding clamps...although PCNA are Interpro annotated to DNA binding too....do you think this is correct? I'm not sure? I need to read some more on this

Original comment by: ValWood

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Ignore the second part of this. There is in vitro evidence that the complex binds to DNA.... val

Original comment by: ValWood

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Hi Val,

Let me know preface everything that follows this by saying that I don't know what determines whether a domain gets an Interpro domain ID.
And I don't know how the mapping is done. So what I'm saying may not be useful.

After looking at the Interpro page, I agree with Paul Russell. I think the data/paper listed on the Interpro page might have been retracted at some point as well. Maybe not formally in a journal but it's widely known in the repair field.

The mapping to exonuclease is a little suspect. If the domains are shared by Rad17 (scer) and Rad1 (spombe), maybe they could be assigned a different function?

The RAD17 annotation at SGD needs to be updated as well given the recently published evidence. I'll take a closer look into that.

eurie

Original comment by: eurie

[gocentral]

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thanks Eurie thats helpful, it looks like the exonuclease mapping should be removed and the description updated accordingly.

Original comment by: ValWood

[gocentral]

• milestone: --> InterPro

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> orchard

Original comment by: mah11

[gocentral]

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Hi Val IPR003027 only hits 1 protein (REC1_USTMA) plus a TrEMBL entry for the same protein, which could be merged to it.

Still an exonuclease according to Biochemistry. 1999 Oct 26;38(43):14379-86.

DNA hydrolytic activity associated with the Ustilago maydis REC1 gene product analyzed on hairpin oligonucleotide substrates.

Naureckiene S, Holloman WK.

who showed the activity experimentally, so have not changed this entry.

Are you actually talking about IPR003021 or IPR003011 - bit I cannot see this EBO ref in either of them.

Sandra

Original comment by: orchard

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yes sorry its IPR003021 Uniprot:P22193 which has exonuclease activity mapping

...if it wasn't picking up an exonuclease mapping from Interpro, it would still pick one up from the Swiss-prot keyword mapping... although the swiss-prot annotation is quite vague: "could have exonuclease activity"

Original comment by: ValWood

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Asked Kati to update the entry. Sandra

Original comment by: orchard

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Kati confirms ientries needs updating - in hand. Exonuclease activity mapping removed from IPR003011 Sandra

Original comment by: orchard

[gocentral]

• status: open --> closed

Original comment by: orchard