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Sometimes I get confused about why this or that enzyme was named in this or that particular way.

1) TCA: Why was not isocitrate dehydrogenase named isocitrate decarboxylase?

Wouldn't it have been at least as accurate to name the enzyme in question isocitrate decarboxylase as to call it isocitrate dehydrogenase? It does remove the -COOH, doesn't it?

2) Glycolysis: PEP (phosphoenolpyruvate) carboxykinase. Why isn't it oxaloacetate carboxykinase? Isn't it agreed upon that enzyme substrate be used in the name of enzyme?

3) Why name enzymes by reverse reactions (especially when the reaction is irreversible)? Pyruvatekinase makes pyruvate from PEP. Why not use another name, PEP phosphatase, for example?

I understand that this is the way the enzymes were named and I just have to accept it. But I would also like to understand the logic behind these names.

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    $\begingroup$ I don't have a proof for this right now, but since the enzymes usually work in both directions (although under physiological conditions only one direction usually is happening), it is possible that the (for the physiological pathway) reverse reaction was classified and analyzed first. $\endgroup$ – Chris Aug 22 '16 at 19:37
  • $\begingroup$ Sonic Hedgehog, and his arch nemesis, robotnikinin. $\endgroup$ – CKM Aug 22 '16 at 21:09
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As @Chris commented, when assayed in vitro with a single substrate (which may not even be the physiological one) most enzymes can catalyse a reaction in either direction. And enzymes such as pyruvate kinase were discovered before the pathways they are constituents of were worked out in full. Furthermore, the ways of naming enzymes only became more sophisticated as more were discovered and characterized. (Try googling for ‘old yellow enzyme’.)

Let us take pyruvate kinase as an example. The name kinase is clearly not chemically descriptive but was applied to any reaction using ATP. But, never mind, go to the Wikipedia page for pyruvate kinase and click on the EC (Enzyme Commission) number — 2.7.1.40 — in the box on the right. You will come to a page where you will see that, like TS Eliot’s cat, the enzyme has three different names:

Accepted Name: pyruvate kinase
(because that’s what everyone uses and is in all the text books)

Other names: phosphoenolpyruvate kinase; phosphoenol transphosphorylase pyruvate kinase (phosphorylating); fluorokinase; fluorokinase (phosphorylating); pyruvic kinase; pyruvate phosphotransferase
(note these include naming it for the reverse reaction)

Systematic name ATP:pyruvate 2-O-phosphotransferase

So why is that the systematic name? If you click back from this page to the group EC 2.7.1 to which this belongs, you will find that this group is of ‘Phosphotransferases with an Alcohol Group as Acceptor’, itself a subgroup of phosphotransferases.

So, to summarize, there is a systematic name that have been arrived at after long and careful deliberation and appears in the introductory paragraphs of scientific publications. Thereafter the common name is used, which although sometimes now recognized as a misnomer, seemed most appropriate at the time.

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