Carboxypeptidase A: Difference between revisions

In the same way that the S1' subsite is involved in anchoring the polypeptide substrate in place, the <scene name='69/694222/3cpas1subsitespacefill/3'>S1 subsite</scene> (spacefill view, subsite in magenta) contains several residues that help hold the substrate in the active site, but the S1 subsite also contains the residues that are involved in the catalytic chemical mechanism.  In general, the residues of the <scene name='69/694222/3cpas1subsitemeshfill/2'>S1 subsite</scene> (pseudo-mesh view, subsite in magenta) have polar or charged side chains that either allow for hydrogen bonding to stabilize negatively charged intermediates of the hydrolysis reaction or position particular atoms appropriately to allow for chemistry to occur.  Three residues (<scene name='69/694222/3cpas1subsiteresidues1/3'>Asn144, Arg145, and Tyr248</scene>) aid in the recognition of the C-terminal residue of a polypeptide substrate.<ref name="CPA1" />  The Asn144 and Tyr248 residues each engage in [http://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [http://en.wikipedia.org/wiki/Intermolecular_force ion-dipole interactions] with the carboxyl group at the C-terminus, while Arg145 provides additional stability by participating in [http://www.masterorganicchemistry.com/2010/10/01/how-intermolecular-forces-affect-boiling-points/ ion-ion interactions] with the carboxyl group (see Figure 3 in the section titled "Mechanism of Action").  <scene name='69/694222/3cpas1subsiteresidues2/2'>Arg71</scene> helps stabilize the substrate in the active site by engaging in ion-dipole interactions with the carbonyl oxygen of the penultimate substrate residue (Figure 3).  Three residues (<scene name='69/694222/3cpas1subsitezn/3'>His196, Glu72, and His69</scene>) are liganded to a catalytic Zn²⁺ ion that is complexed to a water molecule positioned one bond distance away from the C-terminal peptide bond carbonyl carbon (Figure 3).  This gives the Zn²⁺ ion a tetrahedral binding configuration.<ref name="CPA2" />  <scene name='69/694222/3cpas1subsiteglu270/3'>Glu270</scene> deprotonates this water molecule and acts as a base catalyst in the hydrolysis mechanism (Figure 3).  <scene name='69/694222/3cpas1subsitearg127/3'>Arg127</scene> and the positively charged Zn²⁺ ion help stabilize the negatively charged intermediate generated in the [http://www.masterorganicchemistry.com/tips/addition-elimination/ addition-elimination] step of the hydrolysis reaction (Figure 3).<ref name="CPA2" />