Goodsell Sandbox

Ribonuclease A Active Site Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A bound to short DNA strand composed of four thymidines. Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. are shown that are important for catalysis. The 3' carbon is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves cytidine and uridine best--the reason for this may be seen in a spacefilling representation. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.