Goodsell Sandbox: Difference between revisions

Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the , the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by , and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the . Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of . Discrimination between ATP and GTP is achieved through a close steric contact between the . Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids.

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

David S. Goodsell

@@ Line 1: / Line 1: @@
-{{STRUCTURE_1rta |  PDB=1rta  |  SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1  }}
+{{STRUCTURE_2q66 |  PDB=2q66  |  SCENE=Goodsell_Sandbox/PAP_summary/1  }}
-Ribonuclease A Active Site
+ATP Recognition
-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 RNA strands best next to cytidine and uridine nucleotides--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.
+Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_C2/2'>adenine C2 and THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids.

Goodsell Sandbox: Difference between revisions

Revision as of 01:30, 12 September 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Search