KormiSK

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For respecting AfD process during the List of Insaniquarium Characters deletion discussion! Dronebogus (talk) 22:01, 4 November 2021 (UTC)

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EC numbers

Hi KingisNitro

I noticed you had made this change and this one to articles I have recently edited and are on my watchlist. Your edit summary was EC numbers are for enzymes, not reactions. Your edits are unhelpful because, as Enzyme Commission number says (based on reliable sources) EC numbers do not specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. An EC number is a unique identifier for a reaction: it cannot be unique for an enzyme because the amino-acid sequence of proteins can vary considerably while not changing the function of the enzyme. There are UniProt identifiers which uniquely specify a protein by its amino acid sequence but that's not what I was using in my edits. Please go back and restore the versions of these articles and similarly revert any other such changes you have made to other articles I may not have noticed. Mike Turnbull (talk) 11:08, 16 February 2022 (UTC)

@Michael D. Turnbull: Hi there, I will not be reverting those changes. The page Enzyme Commission number, that you have linked as well, states "The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze." By definition, Enzyme Commission number defines the ENZYME that catalyzes the reaction, e.g. "alcohol dehydrogenase", not the reaction itself. The reaction is described (and classifies the enzymes) by the numbers. The fact that the enzyme can have multiple primary sequences does not mean that it is not the same enzyme (i.e., catalyzing the same reaction).

The source page for the sentence you have singled out, http://www.expasy.org/enzyme/, does not even mention the word "reaction" and I have no idea why it is linked as a "reliable" source, as it does not say whatever it is supposed to be backing up. The sentence I've picked out is linked to a source called "Enzyme nomenclature" - after all, we're naming enzymes. Same goes for Enzyme nomenclature by IUBMB - it's an enzyme nomenclature, not reaction nomenclature. I do not mind the numbers being linked on the page, but you cannot say it is "catalyzing reaction EC 1.1.1.1", as "EC 1.1.1.1" = "alcohol dehydrogenase". Also with that said, even what you said isn't true - the numbers do not mention a specific reaction, as EC 1.1.1.1 can catalyze both primary and secondary alcohols, i.e. the reaction is ambiguous. If you wish, edit all of those pages to say "it is catalyzed by [enzyme name] [EC number]". KingisNitro (talk) 11:36, 16 February 2022 (UTC)

One of the most reliable sources (the first external link in the Enzyme Commission number article) is this one, which uses the word "reaction" many times, notably to say Classification of Enzymes by the Reactions they Catalyse and Furthermore, because classification is based solely on the reaction catalysed, there are cases where proteins of very different sequences catalyse the same reaction. The point is that this is a classification scheme not a naming scheme. I think that it is perfectly reasonable to want to help readers of Wikipedia article go straight to the reliable databases of information on enzymes using the {{EC number}} template. It is true that we could use text like "X is formed from Y in the reaction catalysed by the enzyme Z EC 2.7.6.1. but I don't believe it is correct to remove the templates entirely, as you did. To your point on alcohol dehydrogenase being able to catalyse a reaction of primary or secondary alcohols that's absolutely true: in the view of an organic chemist they are the same reaction, just on different substrates, and that's precisely what the EC number suggests. Mike Turnbull (talk) 12:13, 16 February 2022 (UTC)

@Michael D. Turnbull: That sentence I am okay with. However, we're talking about substrate pages; I do not see a reason to include EC codes for the enzymes on the page of the substrate. The enzyme name is listed, if you want to know more about it and the reaction, that is why the specific page exists. It does not need all be crammed in there, esp. with the template.

As for the link, I've already sent that and it says "The complete contents of Enzyme Nomenclature, 1992 (plus subsequent supplements and other changes) are listed below in enzyme number order giving just the recommended name. Each entry provides a link to details of that enzyme. Alternatively if looking for a specific reaction used in the classification of enzymes the broad outline defined by the first two numbers are given below." It might be a classification scheme, but it still comes from enzyme nomenclature, not reaction nomenclature (as there is no such thing, to my knowledge).

The point with alcohol dehydrogenase completely invalidates the point you're making about the reactions, however. Enzymes with the same EC number catalyzing multiple different reactions (or similar reactions of different substrates) mean that you cannot use the number to define a specific reaction. At best, you can say it is a "dehydration" or "dexarboxylation", but you do not need to use the EC number for that at all. I still stand by the removal of that specific sentence and if you want, you can write them back in the format you proposed in your last reply ("X is formed from Y in the reaction catalysed by the enzyme Z EC 2.7.6.1."). Still don't see the reason to mention specific EC numbers on substrate pages, though. KingisNitro (talk) 13:36, 16 February 2022 (UTC)

OK, I'm happy with your view that the enzyme's name/page link gives readers enough information. In those cases where I think it helpful to use the template in addition (not on the specific cases you altered yesterday), I'll use the XYZ wording that we have consensus for. Mike Turnbull (talk) 13:59, 16 February 2022 (UTC)

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