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User:John S. de Banzie/Sandbox 2
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==Carboxypeptidase A with Substrate== | ==Carboxypeptidase A with Substrate== | ||
<StructureSection load='3cpa' size='400' side='right' caption='Carboxypeptidase A with the dipeptide Gly-Tyr in the active site, [[3cpa]]' scene='59/590622/3cpaspacefill/2'> | <StructureSection load='3cpa' size='400' side='right' caption='Carboxypeptidase A with the dipeptide Gly-Tyr in the active site, [[3cpa]]' scene='59/590622/3cpaspacefill/2'> | ||
| - | Carboxypeptidase A catalyses the release of the C-terminal amino acid from a polypeptide chain. The initial image shows carboxypeptidase with a dipeptide (green) in the active site. | + | Carboxypeptidase A catalyses the release of the C-terminal amino acid from a polypeptide chain. The initial image shows carboxypeptidase with a dipeptide (green) in the active site. Natural substrates would usually be longer. |
The enzyme has <scene name='59/590622/3cpacartoon/1'>mixed secondary structure</scene>. A zinc ion (violet) is present. The ion is involved in binding and catalysis. | The enzyme has <scene name='59/590622/3cpacartoon/1'>mixed secondary structure</scene>. A zinc ion (violet) is present. The ion is involved in binding and catalysis. | ||
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Substrate binding involves three interactions between the substrate and the active site. | Substrate binding involves three interactions between the substrate and the active site. | ||
| - | 1. <scene name='59/590622/3cpabindone/1'>Between the carbonyl group of the penultimate residue in the substrate and the zinc ion and an arginyl residue in the enzyme</scene>. | + | 1. <scene name='59/590622/3cpabindone/1'>Between the carbonyl group of the penultimate residue in the substrate (in this case, Gly) and the zinc ion and an arginyl residue in the enzyme</scene>. |
2. <scene name='59/590622/3cpabindtwo/1'>Between the C-terminal carboxyl group and asparaginyl, arginyl, and tyrosyl residues in the enzyme</scene>. | 2. <scene name='59/590622/3cpabindtwo/1'>Between the C-terminal carboxyl group and asparaginyl, arginyl, and tyrosyl residues in the enzyme</scene>. | ||
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3. <scene name='59/590622/3cpabindthree/1'>Between the C-terminal R group and a hydrophobic pocket in the enzyme</scene>. | 3. <scene name='59/590622/3cpabindthree/1'>Between the C-terminal R group and a hydrophobic pocket in the enzyme</scene>. | ||
| - | + | <scene name='59/590622/3cpacatalysis/1'>Catalysis</scene> involves electron withdrawal from the carbonyl of the penultimate residue (in this case, Gly) by the zinc ion and an arginyl residue, and acid-base catalysis by a glutamyl residue of a nucleophilic attack on that same group. | |
(The substrate remained intact because Gly-Tyr is hydrolyzed very slowly and because X-ray crystallography was carried out at -9° C.) | (The substrate remained intact because Gly-Tyr is hydrolyzed very slowly and because X-ray crystallography was carried out at -9° C.) | ||
Revision as of 14:21, 13 June 2014
Carboxypeptidase A with Substrate
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