You discover that the protease cleaves polypeptides ONLY after lysine residues.
ID: 90826 • Letter: Y
Question
You discover that the protease cleaves polypeptides ONLY after lysine residues. What are the most likely physical characteristics of the protease specificity pocket?
A pocket that can accommodate a large side chain and that is lined with groups that are capable of acting as donors in hydrogen bonds.
A pocket that is designed to fit a small side chain and is lined with groups that will be negatively charged at physiological pH.
A pocket that can accommodate a large side chain and that is lined with groups that will be negatively charged at physiological pH.
A pocket that is capable of forming additional hydrogen bonds to stabilize the transition state of the proteolytic cleavage reaction.
a.A pocket that can accommodate a large side chain and that is lined with groups that are capable of acting as donors in hydrogen bonds.
b.A pocket that is designed to fit a small side chain and is lined with groups that will be negatively charged at physiological pH.
c.A pocket that can accommodate a large side chain and that is lined with groups that will be negatively charged at physiological pH.
d.A pocket that is capable of forming additional hydrogen bonds to stabilize the transition state of the proteolytic cleavage reaction.
Explanation / Answer
1. ANS: D. A pocket that is capable of forming additional hydrogen bonds to stabilize the transition state of the proteolytic cleavage reaction.
Explanation:
Additional hydrogen bonds formed by protease specificity pocket can stabilize the transition state of the proteolytic cleavage reaction.
Ex: A pair of electrons on the histidine nitrogen has the ability to accept the hydrogen from the serine -OH group, thus coordinating the attack of the peptide bond.
The serine -OH attacks the carbonyl carbon, and the nitrogen of the histidine accepts the hydrogen from the -OH of the [serine] and a pair of electrons from the double bond of the carbonyl oxygen moves to the oxygen. As a result, a tetrahedral intermediate is generated.
Protease specificity pocket are found ubiquitously in both eukaryotes and prokaryotes.
Protease specificity pocket can contain negative and positive charge its completely depends on amino acid residues.
Ex: Trypsin-like proteases cleave peptide bonds following a positively charged amino acid (lysine or arginine). This specificity is driven by the residue which lies at the base of the enzyme's S1 pocket (generally a negatively charged).
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