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User:John S. de Banzie/Sandbox 2

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==Carboxypeptidase A with Substrate==
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==Zinc Finger==
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<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'>
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<StructureSection load='1mey' size='400' side='right' caption='Leucine Zipper, [[1mey]]' scene='59/590622/1meyspacefill/1'>
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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.
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This zinc finger protein has one subunit. <scene name='59/590622/1meyspacefillunits/1'>Three zinc finger motifs</scene> fit into a major groove in the DNA. Each consists of an <scene name='59/590622/1meycartoon/1'>alpha helix, two short segments of beta pleated sheet, and a zinc ion (violet)</scene>.
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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<ref name="quiocho">Quiocho, F. A. and W. N. Lipscomb (1971). "Carboxypeptidase A: a protein and an enzyme." Adv Protein Chem 25: 1-78.</ref>.
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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>.
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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>.
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<scene name='59/590622/3cpacatalysis/1'>Catalysis</scene><ref name="quiocho"/> 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.
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(X-ray crystallography with intact substrate was possible because Gly-Tyr is hydrolyzed very slowly and because X-ray crystallography was carried out at -9° C.)
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</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Current revision

Zinc Finger

Leucine Zipper, 1mey

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References

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John S. de Banzie

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