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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: carotenoid isomerooxygenase activity #23234

Closed sjm41 closed 2 years ago

sjm41 commented 2 years ago
sjm41 commented 2 years ago

Should also review if any other existing terms should be moved to be children of GO:0010436 carotenoid dioxygenase activity. Current tree looks like this (only showing relevant terms):

oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
|__9-cis-10'-apo-beta-carotenal cleavage oxygenase activity
|__9-cis-beta-carotene 9',10'-cleavage oxygenase activity
|__all-trans-8'-apo-beta-carotenal 15,15'-oxygenase
|__all-trans-beta-apo-10'-carotenal cleavage oxygenase activity
|__beta,beta-carotene-9',10'-cleaving oxygenase activity
|__beta-carotene 15,15'-dioxygenase activity
|__beta-carotene oxygenase activity
|__carotenoid dioxygenase activity
    |__9,10 (9', 10')-carotenoid-cleaving dioxygenase activity
    |__9-cis-epoxycarotenoid dioxygenase activity

I just noticed that all-trans-8'-apo-beta-carotenal 15,15'-oxygenase is missing 'activity' in term name. Fixed.

hdrabkin commented 2 years ago

+[Term] +id: GO:0106422 +name: carotenoid isomerooxygenase activity +namespace: molecular_function +def: "Catalysis of the reaction: Zeaxanthin + O(2) <=> (3R)-11-cis-3-hydroxyretinal + (3R)-all-trans-3-hydroxyretinal." [PMID:19020100, PMID:19889630, RHEA:33931] +comment: The enzyme can use various all-trans carotenoids, including beta- carotene, alpha-carotene and lutein, and catalyzes the symmetrical cleavage of the carotenoid and simultaneous isomerization of only one of the products to a cis configuration. +xref: EC:1.13.11.65 +xref: RHEA:33931 +is_a: GO:0010436 ! carotenoid dioxygenase activity +property_value: creation_date 2022-04-29T17:37:22Z xsd:dateTime +created_by: hjd

sjm41 commented 2 years ago

Thanks Harold. Do you think any existing terms should be moved to be children of GO:0010436 carotenoid dioxygenase activity too (see my second comment above)?

hdrabkin commented 2 years ago

Hi Steve Not my area of expertise; maybe this one for sure _beta-carotene 15,15'-dioxygenase activity

But, I'm going through looking at the defs for the others. From my understadning, a dioxygenase should have both atoms of O2 incorporated, wherease an oxygenase will have ONE atom incorporated into substrate and the other ending up in H20. so, 9-cis-beta-carotene 9',10'-cleavage oxygenase activity does not have H20 as a product, so I'm wondering if it is really a dioxygenase BUT I see that it's mapped to EC 1.13.11.68, which IS named diooxygenase. THus should be moved IMHO. I will look at the others this afternoon

pgaudet commented 2 years ago

wherease an oxygenase will have ONE atom incorporated

Isn't that a 'monooxygenase'? I thought an 'oxygenase' was less specific about the number of oxygen atoms incorporated.

hdrabkin commented 2 years ago

From here https://www.tocris.com/pharmacology/oxygenases-and-oxidases I pulled this:Dioxygenases incorporate both oxygen atoms into the substrate, whilst monooxygenases incorporate a single oxygen atom as a hydroxyl group into the substrate and the second oxygen atom is reduced to water. But I think if the original term was using the EC id as def ref, it is clear that at least in the case above, it is a dioxygenease as water is not a product.

hdrabkin commented 2 years ago

I may need to remove the comment from the new term The definition is specific to Zeaxanthin , whereas the comment says "can use various all-trans carotenoids, including beta- carotene, alpha-carotene and lutein".
Do you by chance know what the exact CHEBI term the new RHEA is using? Is it CHEBI:27547? That CHEBI has a parent term caratenoid. I don't think we want to make terms for each beta- carotene, alpha-carotene and lutein? (sibs). Yet. @ukemi thought the comment makes this confusing, especially

If the term name was carotenoid (CHEBI:23044) isomerooxygenase activity with the appropriate text and RHEA def, then the comment would be ok (because these are all types of carotenoids).

sjm41 commented 2 years ago

Hi @hdrabkin The comment is ad verbatim from the corresponding EC entry here: https://enzyme.expasy.org/EC/1.13.11.65. RHEA maps 1.13.11.65 to RHEA:33931

Yes, the RHEA pages says the ChEBI for "all-trans-zeaxanthin" is CHEBI:27547

So I see the problem, but this ought to be fixed at the EC end.

The earlier fly papers (PMID:10766819, PMID:11158606) said that the ninaB enzyme used beta-carotene, but the later paper (PMID:19889630) said that zeaxanthin is used: Previously, it has been shown that β-carotene is converted via cryptoxanthin into zeaxanthin when fed to larvae, indicating that hydroxylated carotenoids are the direct precursor for chromophore (35). However, tests for enzymatic activity with zeaxanthin and recombinant NinaB failed in a previous study (17). We therefore applied the modified test conditions that were recently established for Galleria NinaB (25). We confirmed that recombinant Galleria NinaB efficiently converts zeaxanthin to 3-hydroxy-retinal (Fig. 4, A and B). Recombinant Drosophila NinaB proved to be less active, but mass spectrometry revealed that 3-hydroxy-retinal was produced (Fig. 4C). Thus, β-carotene is first converted to zeaxanthin and then cleaved by NinaB to directly yield 3-hydroxy-retinal.

So, I think it would be OK if you decided to keep the single new GO term with zeaxanthin as the substrate and remove the comment, and I could still use that to annotate all the fly papers.

hdrabkin commented 2 years ago

Will do now. EC is not just describing a reaction like RHEA (and GO). EC is describing the enzyme. So the comment is really about the property of an enzyme, which may be loosey-goosey with substrate selection

sjm41 commented 2 years ago

Got it, thanks.