biochem 466homework7key - 466 Homework 7 due March 14, 2008...

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466 Homework 7 – due March 14, 2008 1. Retrieve 2gjw from the PDB. Follow the links to the paper in Science 2006 about the structure and mechanism of tRNA splicing endonculease (this one is from Archeaglobus fulgidus ). A) In Figure 1, the structure of the substrate in solution and bound to the enzyme is shown. What is the difference between the two? , and how is the bound form similar to the substrate in a DNA methylation reaction (cytosine-5 methyltransferase) and the cyclobutane dimer in a DNA photolyase reaction? The nucleotides surrounding the cleavage site in the endonuclease are flipped out of the substrate into the active site of the enzyme. This is similar to the cytosine that gets methylated and the cyclobutane dimer that is repaired. B) In Figure 2D, the three-dimensional character of the substrate is critically held together by two very important hydrogen bonds to the “non-bridging” oxygens of the 5’ phosphate of G16 (same as 3’ phosphate of A15 – only the P and the non-bridging oxygens are shown in ORANGE – the rest of G16 is not shown). Describe which atoms are involved in the two short H bonds (2.4 and 2.7 Ǻ ) to the non-bridging oxygens. The 2’O of C12 is hydrogen bonded to one of the non-bridging oxygens of the 5’phosphate of G16 (2.4
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biochem 466homework7key - 466 Homework 7 due March 14, 2008...

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