Goodsell Sandbox: Difference between revisions
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Ribonuclease A Active Site | 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 (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> 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 <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space. | 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 (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon on the DNA 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 <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space. | ||
Revision as of 20:25, 19 August 2008
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 (in blue) bound to short DNA strand composed of four thymidines (in pink). 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 on the DNA 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 . Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.