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 an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed 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 ATP. 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 of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>buried water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_c2/3'>adenine C2 (in white) and the sidechains of THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids.