Carboxypeptidase A: Difference between revisions

The S1' subsite contains multiple hydrophobic residues that interact by [http://en.wikipedia.org/wiki/Van_der_Waals_force van der Walls forces] with C-terminal hydrophobic side chains of polypeptide substrates.  For this reason, the S1' subsite is referred to as the hydrophobic binding pocket.  It should be of note that the S1' subsite, despite being named as a hydrophobic pocket, is not another pocket in addition to the deep pocket active site.  Rather, it is simply a particular region of the deep pocket.  Specifically, the hydrophobic pocket includes the residues Ile243, Ile247, Ala250, Gly252, Gly253, Ser254, and Ile255.<ref name="CPA1" />  The hydrophobic nature of the S1' subsite assists in establishing some degree of [http://en.wikipedia.org/wiki/Chemical_specificity#Enzyme_specificity specificity] for CPA.  Because the hydrophobic pocket anchors the polypeptide substrate in the active site, the larger and more hydrophobic the side chain of the C-terminal substrate residue, the stronger the van der Walls interactions between the subsite and the substrate.  Therefore, the stability of substrate binding is increased when residues like phenylalanine are present at the C-terminus.  Essentially, the S1' subsite serves as a recognition site for the C-terminal side chain of the substrate.<ref name="CPA1" />