CHIME EXERCISE

 

 

1DUD: Deoxyuridine-5'-Nucleotide Hydrolase

(D-UTPase)

 

The structure to the right is dUTPase in a complex with a bound substrate analog, Deoxyuridine-5'-Diphosphate (dUDP).

 

(1)   Find the substrate in its binding site

(2)   Find C5 on the Uracil group. Is there enough room to attach a methyl group to C5?

(3)   Locate the ribose 2’ C. What protein group sterically prevents an –OH group from being attached to the 2’ C atom?

(4)   Find the H-bond donors and acceptors (to the uracil base) from the protein. What would be the effect on the H-bonding if the base was changed to cytosine?

1dud.pdb