(Was: Obsoletion notice) GO:0044105 L-xylulose reductase (NAD+) activity - add RHEA x ref

[pgaudet]

EDITED

The proposal was made to obsolete GO:0044105 L-xylulose reductase (NAD+) activity - but evidence for this activity was found and a RHEA reaction was created.

Original ticket:

Please provide as much information as you can:

• GO term ID and Label

• GO:0044105 L-xylulose reductase (NAD+) activity

• Reason for deprecation ~This term was obsoleted by EC and by RHEA.~ There is no evidence that this function exists.

• "Replace by" term (ID and label) If all annotations can safely be moved to that term NA

• "Consider" term(s) (ID and label) Suggestions for reannotation

NA

• Are there annotations to this term?

• How many EXP: 0

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section) EC:1.1.1.10, but this is incorrect, as it describes the NADP reaction, which corresponds to GO:0050038 L-xylulose reductase (NADP+) activity

• Is this term in a subset? (check the AmiGO page for that term) No

• Any other information

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0044105 L-xylulose reductase (NAD+) activity. The reason for obsoletion is that there is no evidence that this activity exists. There are no annotations to this term, other than those coming from the incorrect EC mapping. This term is not in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/21874

Thanks, Pascale

[ukemi]

PMID: 20654618 Second paragraph of introduction?

[pgaudet]

@amorgat @kaxelsen This reaction is missing from RHEA and EC L-xylitol + NAD(+) <=> L-xylulose + NADH

Can it be added? If yes, I'll restore the term.

Thanks, Pascale

[alanbridge]

interesting, could be a nice TrEMBL here:

NADH L-xylulose reductase https://www.uniprot.org/uniprot/Q70FD1

[kaxelsen]

I just identified the same paper, pmid:14736891 (also in Q70FD1) from the yeast Ambrosiozyma monospora. It is more convincing than pmid:20654618 where the NADH dependent activity is only seen in crude extract. I will create the reaction.

[alanbridge]

Thanks @kaxelsen could you let @marcfeuermann know too?

[kaxelsen]

Of course

[alanbridge]

thanks, I am having a tea break from ISMB so can approve the Rhea too if needed

[pgaudet]

OK great, I'll un-obsolete the term.

[alanbridge]

this will be one more GO annotation from the Rhea2GO pipeline too...

should this reaction

https://www.rhea-db.org/rhea/48760 L-threitol + NAD(+) = H(+) + L-erythrulose + NADH

be linked to EC 1.1.1.9?

Currently that EC is only linked to

https://www.rhea-db.org/rhea/20433 NAD(+) + xylitol = D-xylulose + H(+) + NADH

but that EC number says

Also acts as an L-erythrulose reductase. https://enzyme.expasy.org/EC/1.1.1.9

I think an "L-erythrulose reductase" would be the RL form of https://www.rhea-db.org/rhea/48760, i.e.

H(+) + L-erythrulose + NADH => L-threitol + NAD(+)

(just noticed this while poking around those other reactions)

A+

[pgaudet]

Is there a reason the substrate dont have the D - ie xylitol versus D-xylitol?

[alanbridge]

It's symmetrical. Only chiral molecules have optical isomers in general.

[alanbridge]

Hi,

From @kaxelsen and now approved in Rhea

RHEA:68100 NAD+ + xylitol = H+ + L-xylulose + NADH EC 1.1.1.15 MetaCyc [RXN-11825]

SHAW DR (1956) Polyol dehydrogenases. 3. Galactitol dehydrogenase and D-iditol dehydrogenase. The Biochemical journal 64, 394-405 [PMID:13373783]

Verho R , Putkonen M , Londesborough J , Penttilä M , Richard P (2004) A novel NADH-linked l-xylulose reductase in the l-arabinose catabolic pathway of yeast. The Journal of biological chemistry 279, 14746-14751 [14736891]

Cheers, Alan

[pgaudet]

@kaxelsen Does the description for UniProt:G3YG17 need to be changed to change the NADPH to NADH ?

[pgaudet]

WRT taxon constraints, this activity exists in ~A. niger (G3YG17, PMID:20654618)~, in Ambrosiozyma monospora (PMID:17216457), and in some related species.

PMID:17627668 shows the NADH-dependent activity in Candida arabinofermentans PYCC 5603(T) and Pichia guilliermondii -

So, I will add a taxon constraint to Ascomycota. Neither of these sequences are in Panther, so I cannot be more precise.

Thanks, Pascale

[kaxelsen]

No, pmid:20654618 shows specifically that LxrA is NADPH dependent. It is when you delete that gene that a NADH dependent activity can be found in crude extracts.

[marcfeuermann]

Hello, I've annotated entry Q70FD1 corresponding to Ambrosiozyma monospora NADH L-xylulose reductase. I've added Rhea:68100. Moreover, in the same article, it is shown that AXL1 also converts D-ribulose to D-arabinitol (Rhea:17389). I've also added this reaction to the entry and associated GO:0047038 to the protein in Protein2GO. AXL1 can perform both reactions in the 2 directions and kinetic parameters have been characterized for all 4 possible substrates. Cheers, Marc.