imt1 = inositol phosphorylceramide mannosyltransferase activity

[ValWood]

GO:0103064
inositol phosphorylceramide mannosyltransferase activity

SGD orthologs get this as IEA from Rhea. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558548/ useful for mammalian/fungal comparative pathways.

@dexink

[ValWood]

missing CSG2 is the regulatory subunit

[dexink]

CSG2 was the other iirc from #3244

**edit: yes see comment

[dexink]

GO:0103064 inositol phosphorylceramide mannosyltransferase activity

SGD orthologs get this as IEA from Rhea. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558548/ useful for mammalian/fungal comparative pathways.

@dexink

So if we resolve this GO activity, we may disambiguate the pathway in S. pombe?

[dexink]

Just to state it in this thread officially, there are no proteins with this specific GO term in Pombase.

Expanded context of annotations: 75 proteins, however, are annotated with its parent, "hexosyltransferase activity", GO:0016758

Within this list are several GO molecular function annotations, including one featuring imt1: mannosyltransferase activity (GO:0000030). This MF annotation list only contains 9 proteins, all of which appear restricted to the Golgi. This could have been expected, as the enzyme completing the second step in ceramide/sphingolipid biosynthesis presumed for S. pombe, 3-ketosphinganine reductase, is upstream of this activity and is fused with a pig-F orthologous domain, of which is expected to be integral to the ER membrane (SPCC1450.15).

[dexink]

missing CSG2 is the regulatory subunit

Does the complex require a distinct regulatory subunit (i.e., CSG2)? Where would imt1 fit into these pathways?

@ValWood Do we think that Aur1 (inositol phosphorylceramide synthase) could participate in this complex (i.e., the complex in which CSG2 in S. cerevisiae is expected to be the regulatory subunit)?

[dexink]

Just to state it in this thread officially, there are no proteins with this specific GO term in Pombase.

Expanded context of annotations: 75 proteins, however, are annotated with its parent, "hexosyltransferase activity", GO:0016758

Within this list are several GO molecular function annotations, including one featuring imt1: mannosyltransferase activity (GO:0000030). This MF annotation list only contains 9 proteins, all of which appear restricted to the Golgi. This could have been expected, as the enzyme completing the second step in ceramide/sphingolipid biosynthesis presumed for S. pombe, 3-ketosphinganine reductase, is upstream of this activity and is fused with a pig-F orthologous domain, of which is expected to be integral to the ER membrane (SPCC1450.15).

@ValWood do we think that the GPI complex in S. pombe is localized to the ER instead of the golgi? Or is it the other way around? Predictions among some participants or expected participants seem to conflict. (see comment in Noctua model-specific thread)

[ValWood]

Just to state it in this thread officially, there are no proteins with this specific GO term in Pombase.

imt1 is not annotated to "inositol phosphorylceramide mannosyltransferase activity" with an experimental evidence code even though it is currently only IEA, it is based on EXP. (I.e there is evidence).

I have asked SGD to make an EXP annotation since we are really only supposed to use "ISO" (inferred from ortholog) evidence code with experimental annotation. The existing annotation should be more specific.

This should updated tomorrow (in PomBAse, I pre-empted the SGD update). I don't know about the localization, but I might be inclined to go with orthology rather than the high throughput localization study.

(Imt1 came onto my radar yesterday for a completely different reason. I am assessing some orthology predictions using AlphaFold structures and imt1 is predicted to be closest structurally to human Lactosylceramide 4-alpha-galactosyltransferase A4GALT (which is LCS in the figure above)