Carboxypeptidase A: Difference between revisions
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# After aiding in the recognition of the substrate, <scene name='69/694222/3cpadeeppocket2/1'>Tyr248 "caps" the binding pocket</scene>. | # After aiding in the recognition of the substrate, <scene name='69/694222/3cpadeeppocket2/1'>Tyr248 "caps" the binding pocket</scene>. | ||
# The <scene name='69/694222/3cpas1subsitearg127/2'>catalytic Zn<sup>2+</sup> ion and Arg127 residue</scene> engage in ion-dipole interactions with the oxygen atom of the carbonyl group of the C-terminal peptide bond, further polarizing the carbon to oxygen double bond (see Figure 3). | # The <scene name='69/694222/3cpas1subsitearg127/2'>catalytic Zn<sup>2+</sup> ion and Arg127 residue</scene> engage in ion-dipole interactions with the oxygen atom of the carbonyl group of the C-terminal peptide bond, further polarizing the carbon to oxygen double bond (see Figure 3). | ||
# A water molecule, which has been [http://en.wikipedia.org/wiki/Deprotonation deprotonated] by <scene name='69/694222/3cpas1subsiteglu270/2'>Glu270</scene> ([http://bio.libretexts.org/Core/Biochemistry/Catalysis/METHODS_OF_CATALYSIS/General_Acid%2F%2FBase_Catalysis base catalyst]) and is being held in place one bond distance away from the partially positive carbon of the C-terminal carbonyl, acts as a [http://en.wikipedia.org/wiki/Nucleophile nucleophile] and attacks this carbon to generate a [http://goldbook.iupac.org/T06289.html tetrahedral intermediate] stabilized by both the Zn<sup>2+</sup> ion and surrounding positive charges of S1 subsite residues. | # A water molecule, which has been [http://en.wikipedia.org/wiki/Deprotonation deprotonated] by <scene name='69/694222/3cpas1subsiteglu270/2'>Glu270</scene> ([http://bio.libretexts.org/Core/Biochemistry/Catalysis/METHODS_OF_CATALYSIS/General_Acid%2F%2FBase_Catalysis base catalyst]) and is being held in place one bond distance away from the partially positive carbon of the C-terminal carbonyl, acts as a [http://en.wikipedia.org/wiki/Nucleophile nucleophile] and attacks this carbon to generate a [http://goldbook.iupac.org/T06289.html tetrahedral intermediate] stabilized by both the Zn<sup>2+</sup> ion and surrounding positive charges of S1 subsite residues. '''A water molecule was not crystallized in the active site of 3CPA. It has been displayed, however, in Figure 3 for reference.''' | ||
# The peptide bond is cleaved through an addition-elimination step. | # The peptide bond is cleaved through an addition-elimination step. | ||
# The Glu270 base catalyst is regenerated through a final [http://www.masterorganicchemistry.com/tips/proton-transfer/ proton transfer] with the nitrogen atom of the former C-terminal peptide bond. | # The Glu270 base catalyst is regenerated through a final [http://www.masterorganicchemistry.com/tips/proton-transfer/ proton transfer] with the nitrogen atom of the former C-terminal peptide bond. | ||