SB C/P #35

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JG19
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Joined: Sun Jul 28, 2019 6:28 pm

SB C/P #35

Post by JG19 » Sun Jul 28, 2019 6:36 pm

Hello! Can someone please explain what is going on in this mechanism and why the deprotonation causes the water molecule to be more nucleophillic? Were they talking about a specific amino acid or molecule in this question?
NS_Tutor_Mathias
Posts: 264
Joined: Sat Mar 30, 2019 8:39 pm

Re: SB C/P #35

Post by NS_Tutor_Mathias » Mon Jul 29, 2019 12:55 pm

Deprotonated water is just hydroxide (and for reference: protonated water is just hydronium). Hydroxide is, especially in biological reactions, probably the most common nucleophile - it is negatively charged, small, and the negative charge is localized on the oxygen. This makes it a fantastic nucleophile.

The proposed mechanism in the passage is that the double-zincs at the catalytic center of hAcyl generate hydroxides that are then used to break terminal peptide bonds. You can already predict that this should result in nucleophilic attack at the carbonyl carbon, and replacement of the peptide bond with a terminal carboxyl group on the remaining peptide/protein, and with a terminal amine on the now monomeric aminoacid that was cleaved off.

Here is exactly the mechanism the passage is describing: https://upload.wikimedia.org/wikipedia/ ... maller.png
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