query squalene synthase or farnesyl-diphosphate farnesyltransferase activity

[gocentral]

erg9 (SGD) is described as Farnesyl-diphosphate farnesyl transferase (squalene synthase),

but GO has GO:0004310 Catalysis of the reaction: 2 farnesyl diphosphate = diphosphate + presqualene diphosphate.

Comment Note that the two reactions performed by EC:2.5.1.21 are represented in GO by 'farnesyl-diphosphate farnesyltransferase activity ; GO:0004310' and 'squalene synthase activity ; GO:0051996'.

and Catalysis of the reaction: presqualene diphosphate + NADPH = squalene + NADP+ + diphosphate.

Note that the two reactions performed by EC:2.5.1.21 are represented in GO by 'farnesyl-diphosphate farnesyltransferase activity ; GO:0004310' and 'squalene synthase activity ; GO:0051996'.

BUT EC:2.5.1.21 is described http://enzyme.expasy.org/EC/2.5.1.21 Farnesyl-diphosphate farnesyltransferase. Farnesyltransferase. Presqualene synthase. Presqualene-diphosphate synthase. Squalene synthetase.

2 farnesyl diphosphate + NAD(P)H <=> squalene + 2 diphosphate + NAD(P)(+)

(only a single reaction, both names)

shoudn't this be a single term?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/11152

[gocentral]

I see, its a 2-step reaction (performed by a single gene).Is it normal to split these we could just do one term for the 2 steps?

http://www.genome.jp/dbget-bin/www_bget?rn:R06223

kind of easier for curators...

Original comment by: ValWood

[gocentral]

On the one hand, GO_molecular_function classifies by function so if one protein has several it gets several mf labels. On the other, there's a fuzzy boundary: one could divide the multiple steps of a reaction mechanism but GO doesn't. What's the comparative biology here - are these two reactions ever catalyzed by different proteins?

Original comment by: deustp01

[gocentral]

As far as I can tell both steps are always catalysed by a single protein the Erg9/FDFT family http://www.pantherdb.org/panther/family.do?clsAccession=PTHR11626

(annotated very inconsistently at present)

On 12/09/2014 14:00, Peter D'Eustachio wrote:

On the one hand, GO_molecular_function classifies by function so if one protein has several it gets several mf labels. On the other, there's a fuzzy boundary: one could divide the multiple steps of a reaction mechanism but GO doesn't. What's the comparative biology here

• are these two reactions ever catalyzed by different proteins?

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[ontology-requests:#11152] http://sourceforge.net/p/geneontology/ontology-requests/11152 query squalene synthase or farnesyl-diphosphate farnesyltransferase activity

Status: open Group: PomBase Created: Thu Sep 11, 2014 01:44 PM UTC by Valerie Wood Last Updated: Thu Sep 11, 2014 01:47 PM UTC Owner: nobody

erg9 (SGD) is described as Farnesyl-diphosphate farnesyl transferase (squalene synthase),

but GO has GO:0004310 Catalysis of the reaction: 2 farnesyl diphosphate = diphosphate + presqualene diphosphate.

Comment Note that the two reactions performed by EC:2.5.1.21 are represented in GO by 'farnesyl-diphosphate farnesyltransferase activity ; GO:0004310' and 'squalene synthase activity ; GO:0051996'.

and Catalysis of the reaction: presqualene diphosphate + NADPH = squalene

• NADP+ + diphosphate.

Note that the two reactions performed by EC:2.5.1.21 are represented in GO by 'farnesyl-diphosphate farnesyltransferase activity ; GO:0004310' and 'squalene synthase activity ; GO:0051996'.

BUT EC:2.5.1.21 is described http://enzyme.expasy.org/EC/2.5.1.21 Farnesyl-diphosphate farnesyltransferase. Farnesyltransferase. Presqualene synthase. Presqualene-diphosphate synthase. Squalene synthetase.

2 farnesyl diphosphate + NAD(P)H <=> squalene + 2 diphosphate + NAD(P)(+)

(only a single reaction, both names)

shoudn't this be a single term?

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Original comment by: ValWood

[gocentral]

The current thinking for these types of multi-step reactions, as outlined here:

http://wiki.geneontology.org/index.php/Curator_Guide:_Enzymes_and_Reactions#Multi-Step_Enzyme_Reactions

is to have an over-arching reaction, with the sub-reactions as has_parts to it. So in this case we have the sub-reactions, but not the top term.

I think we can replicate what KEGG have in this case wrt naming and reactions:

http://www.kegg.jp/dbget-bin/www_bget?reaction+R00702+R02872+R06223

Note to self - check we're in line with RHEA with these.

Original comment by: jl242

[gocentral]

• labels: --> enzymes
• assigned_to: Jane Lomax

Original comment by: jl242

[gocentral]

Jane's plan sounds right. The GO curator guide notes that KEGG isn't always consistent about enumerating steps in these one enzyme : more than one reaction cases. For completeness, neither is Reactome. Taking RHEA as a standard sounds right.

Original comment by: deustp01

[gocentral]

Yep having the individual parts as has_parts sounds good to me. Val

Original comment by: ValWood

[gocentral]

• status: open --> closed-works-for-me

Original comment by: ValWood