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As pointed out here, many important co-enzymes (essential enzyme cofactors) such such acetyl-CoA and vitamin B12 contain nucleotide portions that do not function in the enzyme catalysis. They have been suggested to be relics of the RNA world, so it would appear to me that they are redundant. Suppose we were to remove these nucleotide portions of the co-enzymes, would that improve the working of the proteins (and perhaps our health) or wouldn’t it make any difference?

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  • $\begingroup$ Those aren't enzymes but rather coenzymes, and the nucleotide moiety is necessary for function. $\endgroup$ – canadianer Sep 29 '17 at 4:10
  • $\begingroup$ @canadianer — I agree that this question is based on a fallacy. Surely that point should be made in an answer or the question should be voted to be closed. The only point of a comment to the poster would seem to me to be to ask the poster to withdraw the question, which he is unlikely to do if he doesn't understand that the nucleotide part of coenzymes interact with proteins rather than provide the functionality. $\endgroup$ – David Sep 29 '17 at 8:03
  • $\begingroup$ @David Surely the point should be made in an answer. Actually I think this question is a duplicate but I cannot find the other post. $\endgroup$ – canadianer Sep 29 '17 at 14:40
  • $\begingroup$ @canadianer — Don't know about the duplicate. But, yes, probably best as an answer. Are you going to answer or me. In any case I think I'll edit it so it's more accurate and explains the problem in more detail. (I've a little time to kill while waiting for a program to run.) $\endgroup$ – David Sep 29 '17 at 15:23
  • $\begingroup$ @David I don't have the time; feel free. $\endgroup$ – canadianer Sep 29 '17 at 15:28
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The video cited in the question is to be commended and presents a number of points relevant to questions about DNA and RNA posted here previously.

The problem with the question sems to be an incomplete understanding of the role of these coenzymes/cofactors in the function of the enzyme. (The original question implied that acetyl-CoA and vitamin B12 are the enzymes.) In contemporary protein enzymes, these non-protein cofactors are bound to the protein part of the enzyme and complement it in its function. Typically, the protein will have binding sites for the substrates (the reactants) and the coenzyme will provide the sophisticated catalysis or other essential function.

The coenzyme must obviously interact with the protein, and in a way that leaves its catalytic or functional part free to operate. This is what the nucleotide portion of the coenzyme does — in fact it is performing the same role as has been suggested it played in the RNA world, but instead of interacting with an RNA enzyme (ribozyme) by base pairing, it interacts with amino acid side-chains by a variety of weak interactions. An example of this is shown for coenzyme-B12 in the enzyme, methylmalonyl-CoA mutase (my annotations in red and brown).

coenzyme-B12 in methylmalonyl-CoA mutase

To quote from the figure legend in the paper: “The lower axial ligand to the cobalt is histidine HisA610, which is in turn bound through AspA608 to LysA604. The pseudo-nucleotide tail is bound in a pocket between the sheet and the C-terminal helix.”

The situation for coenzyme-A (CoA) is slightly different, in that it is involved in the transfer of acetyl and other groups, rather than catalyis per se. However the principle is the same — there is a chemically functional portion and a nucleotide portion that binds it to the protein.

Thus, the nucleotide portion of coenzymes is not redundant and without it they could not bind to the enzyme and enable it to perform its function.

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