GO:0004042 acetyl-CoA:L-glutamate N-acetyltransferase activity IBA with S000004666 , PTN000559455

[ValWood]

• PTHR ID & PTN node:

GO:0004042 | acetyl-CoA:L-glutamate N-acetyltransferase activity | IBA with S000004666 , PTN000559455

• Sequences with problematic annotation (ID + gene/protein name):

https://www.pombase.org/term/GO:0004042

I have 2 genes annotated to this term ( acetyl-CoA:L-glutamate N-acetyltransferase activity for the first and fifth step in arginine biosynthesis.

acetyl-CoA:L-glutamate N-acetyltransferase activity L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H+. seems to be correct for the first step, but I think the fifth step might be glutamate N-acetyltransferase activity (GO:0004358) N(2)-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine.

based on the outputs of the previous step. @srengel could you take a look? Thanks

• Type of Issue: Erroneous source or erroneous propagation, or other issue

possibly annotation

• Add the label 'high priority' if needed. Generally high priority issues affect a lot of proteins, and annotations are incorrect (as opposed to just imprecise).

[srengel]

Hi @ValWood ARG7 is annotated to both 2.3.1.1 and 2.3.1.35, and those are the EC numbers assigned to those reactions: https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=ARGSYNBSUB-PWY&detail-level=4

[ValWood]

I still think there could be a problem.

I curated adenine biosynthesis today: http://noctua.geneontology.org/workbench/noctua-alliance-pathway-preview/?model_id=gomodel%3A6690711d00000916 (note arg3 should connect to arg12 here but the relations is not rendering in GO-CAM).

Here is a view of the S. cerevisiae pathway from https://www.researchgate.net/publication/370669123_Generation_of_a_Yeast_Cell_Model_Potentially_Useful_to_Identify_the_Mammalian_Mitochondrial_N-Acetylglutamate_Transporter/figures?lo=1

The output of ARG7 (pombe aga1) is N-acetyl L-glutamate The output of ARG2 (pombe arg6) is also N-acetyl L-glutamate but it's a cycle and the inputs from the previous step are different.

so ARG2 at the top of the pathway is Catalysis of the reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H+

and ARG7 (pombe aga1) at the bottom of the pathway returning the N-acetyl glutamate (which is also an output of ARG2).

The difference seems to be that ARG2 has acetyl COA as an input and ARG7 has N(2)-acetyl-L-ornithine as an input (they both have L-glutamate as an input). I don't see any pathway renderings where ARG7 can perform ARG2 creation.

Where were the EC's assigned?

[srengel]

the EC assignments in SGD come from Expasy https://enzyme.expasy.org/EC/2.3.1.35