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Journal article details: Structure and Mechanism of the Amphibolic Enzyme D-Ribulose-5-phosphate 3-Epimerase from Potato Chloroplasts Jurgen Kopp, Stanislav Kopriva, Karl-Heinz Suss and Georg E. Schulz

Your assignment is to read the paper, discuss it thoroughly with your fellow students if you wish, and then submit a written assignment (individually) that answers the following questions: 1. What was the main objective of the study? Was there any known structure of epimerase that had indicated the use of direct de- and re-protonation mechanism?

2. Briefly describe the mechanism that is supported by the 3-D structure of this epimerase. 3. For the forward reaction, which amino acid residue is proposed to deprotonate the substrate? Which atom does it abstract a proton from the substrate? Which amino acid residue is proposed to re-protonate the intermediate? Which atom does it re-protonate? 4. Which part of the substrate turns into an oxyanion in the transition state? What does the structure suggest as the stabilizing environment of the oxyanion? 5. Among the acidic and basic amino acid residues depicted in figure 9, which ones are invariable in the aligned homologous sequences? 6. Would the epimerase work if the substrate were deprotonated and re-protonated by the same amino acid residue? Give your reason. Assignments should conform to the following style: Maximum 2 pages in length; Times New Roman font size 12; 1.5 spacing; 2 cm margins

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