Merge GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity

[pgaudet]

Hello,

Following up on #17822, I checked the PAINT annotations and a few references. According to reaction in Figure 1 in PMID: 19081061

I think O:0034604 pyruvate dehydrogenase (NAD+) activity should be merged into GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity.

We could perhaps merge or obsolete GO:0034603 pyruvate dehydrogenase [NAD(P)+] activity (no annotations; inaccurately assigned to EC:1.2.1.51 , as reported in #17822).

Thanks, Pascale

[ValWood]

I was just looking at this because in SGD and hence in pombase the E1 subunits are annotated with pyruvate dehydrogenase (acetyl-transferring) activity even though they produce Co2 and NADH.

It would be useful to resolve this.

CC @rozaru

[ValWood]

For reference The PDH complex composed of three main enzyme components:

E1 (Pyruvate dehydrogenase enzyme): It catalyzes the decarboxylation of pyruvate, releasing CO and forming a hydroxyethyl-TPP intermediate. E2 (Dihydrolipoyl transacetylase): This enzyme transfers the acetyl group from the hydroxyethyl-TPP intermediate to coenzyme A, forming acetyl-CoA. E3 (Dihydrolipoyl dehydrogenase): It regenerates the oxidized form of the lipoamide and reduces NAD to NADH in the process.

[ValWood]

closing https://github.com/geneontology/go-ontology/issues/24350 is much more comprehensive

[sjm41]

The PDH E1 subunits ought to be annotated as follows:

contributes_to pyruvate dehydrogenase (NAD+) activity(GO:0034604) = EC:1.2.1.104 (i.e. the overall activity of the PDH complex)

contributes_to pyruvate dehydrogenase (acetyl-transferring) activity(GO:0004739) = EC:1.2.4.1 (i.e. the specific activity of E1, which requires two subunits a and b)

Definitely don't want to merge GO:0034604 and GO:0004739

[ValWood]

~Got it. Will ask SGD to make the missing annotations. @edwong57 could SGD co-annotate pda1 and pdb1 the e1 subunits to pyruvate dehydrogenase (NAD+) activity(GO:0034604) = EC:1.2.1.104~

~Also, some of the descriptions seem to be slightly wrong. For example PDA1 has Pyruvate dehydrogenase (acetyl-transferring) subunit of the mitochondrial pyruvate dehydrogenase complex~ ignore this part!

Actually @edwong57 I think you can ignore this.

[sjm41]

Sorry, entered my previous comment too quickly and made some errors - now edited and corrected!

[ValWood]

@sjm41 do you agree that we can close this one as a duplicate?