ERCC4-ERCC1 complex and nucleotide-excision repair factor 1 complex (merge complexes, use human names?)

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ERCC4-ERCC1 complex and nucleotide-excision repair factor 1 complex (merge complexes, use human names?) #22171

Open ValWood opened 3 years ago

ValWood commented 3 years ago

GO:0070522 | ERCC4-ERCC1 complex | IBA with P07992 , PTN000297520 but we have annotated to

nucleotide-excision repair factor 1 complex (GO:0000110) One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively. [PMID:10915862]

seems to be the same thing?

pgaudet commented 3 years ago

@ValWood Is this a PAINT or an ontology issue?

ValWood commented 3 years ago

I think it probably began as an annotation issue but ended as an ontology issue...will migrate. @bmeldal can you advise?

bmeldal commented 3 years ago

We have ERCC1 in human CPX-478 ERCC1-XPF endonuclease complex, synonym: ERCC4-ERCC1 complex, and annotated to GO:0070522 ERCC4-ERCC1 complex.

We have annotated yeast CPX-1708 Nucleotide-excision repair factor 1 complex to GO:0000110 nucleotide-excision repair factor 1 complex, containing RAD1-RAD10-RAD14.

ValWood commented 3 years ago

ERCC4 = S. cerevisiae RAD16 ERCC1 = S. cerevisiae RAD10 So the GO descriptions of

Definition	Parents

A heterodimeric nucleotide-excision repair complex that has endonuclease activity specific for bubble structures characteristic of certain DNA lesions. The subunits are known as XPF/ERCC4 and ERCC1 in mammals, and Rad1p and Rad10p in S. cerevisiae.

are not consistent for the 2 species.

bmeldal commented 3 years ago

Argh!

I added the species to my previous comment to make it clearer as I missed that this afternoon.

GO, UniProt and CP seem to be consistent in which proteins they've assigned to which complex and from there it looks like:

ERCC1-ERCC4(XPF) complex = Rad1-Rad10 complex

and

nucleotide-excision repair factor 1 complex = ERCC1-ERCC4(XPF)-XPA = Rad1-Rad10-Rad14 complex

We only annotated human ERCC1-ERCC4(XPF) complex and yeast Rad1-Rad10-Rad14 complex - I can't tell you from the top of my head why we didn't annotate the reverse homologues.

While UniProt has P31244 (RAD16_YEAST): Component of the global genome repair (GGR) complex composed of at least ABF1, RAD7 and RAD16.

Another Question: Why are these endonucleases not children of GO:1905348 endonuclease complex?

ValWood commented 11 months ago

These are the same complex, we should decide which species nomenclature to use for all of these complexes, and I don't want to make that decision (but would be happy for pombe to use the human names)