User:John S. de Banzie/Sandbox 2

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==Carboxypeptidase A with Substrate==
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==RNA Stem and Loop Structure==
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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='2qh2' size='400' side='right' caption='RNA hairpin loop from human telomerase RNA, [[2qh2]]' scene='59/590622/2qh2stick/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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Intramolecular hydrogen bonding in RNA molecules results in the formation of stem and loop (also known as hairpin loop) structures.
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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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Note that the stem portion is a double stranded <scene name='59/590622/2qh2stickends/1'>antiparallel</scene> right-handed helix with both <scene name='59/590622/2qh2spacefill/1'>major and minor grooves</scene>. Note also that the structure is not the same as that of DNA.
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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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Note the <scene name='59/590622/2qh2bases/1'>complementary base pairing</scene> in the stem (A: red, C: green, G: orange, T: blue) and the unpaired bases in the loop.
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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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(The stem and loop structure shown is part of the RNA in human telomerase. Telomerase protects chromosomes by restoring DNA that is lost from the ends during DNA replication. The RNA is used as a template and the enzyme is thus an internally templated RNA-dependant DNA polymerase.)
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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/>

Revision as of 15:50, 13 June 2014

RNA Stem and Loop Structure

RNA hairpin loop from human telomerase RNA, 2qh2

Drag the structure with the mouse to rotate

References

Proteopedia Page Contributors and Editors (what is this?)

John S. de Banzie

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